Document Detail

Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history.
Jump to Full Text
MedLine Citation:
PMID:  23145839     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The genes involved in host defences are known to undergo rapid evolution. Therefore, it is often difficult to assign orthologs in multigene families among various vertebrate species. Chemokines are a large family of small cytokines that orchestrate cell migration in health and disease. Herein, we have surveyed the genomes of 18 representative vertebrate species for chemokine genes and identified a total of 553 genes. We have determined their orthologous relationships and classified them in accordance with the current systematic chemokine nomenclature system. Our study reveals an interesting evolutionary history that gave origin and diversification to the vertebrate chemokine superfamily.
Authors:
Hisayuki Nomiyama; Naoki Osada; Osamu Yoshie
Related Documents :
23632419 - Cluster analysis reveals differential transcript profiles associated with resistance tr...
24267539 - Different stress responsive strategies to drought and heat in two durum wheat cultivars...
23285129 - Rsma regulates biofilm formation in xanthomonas campestris through a regulatory network...
23185409 - One out of four: hspl but no other small heat shock protein of agrobacterium tumefacien...
8001909 - Distribution of the 9-bp mitochondrial dna region v deletion among north american indians.
23087369 - Vea regulates conidiation, gliotoxin production, and protease activity in the opportuni...
12927969 - Archaefructus--angiosperm precursor or specialized early angiosperm?
23163799 - Gene therapy for noninfectious uveitis.
15326279 - Use of the fluorescent timer dsred-e5 as reporter to monitor dynamics of gene activity ...
Publication Detail:
Type:  Journal Article; Review     Date:  2012-11-12
Journal Detail:
Title:  Genes to cells : devoted to molecular & cellular mechanisms     Volume:  18     ISSN:  1365-2443     ISO Abbreviation:  Genes Cells     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-02     Completed Date:  2013-06-11     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  9607379     Medline TA:  Genes Cells     Country:  England    
Other Details:
Languages:  eng     Pagination:  1-16     Citation Subset:  IM    
Copyright Information:
© 2012 The Authors Genes to Cells © 2012 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd.
Affiliation:
Department of Molecular Enzymology, Kumamoto University Graduate School of Medical Sciences, Honjo, Kumamoto, 860-8556, Japan. nomiyama@gpo.kumamoto-u.ac.jp
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Animals
Chemokines / classification*,  genetics,  metabolism
Evolution, Molecular*
Genome, Human
Humans
Multigene Family
Phylogeny
Receptors, Chemokine / genetics,  metabolism
Synteny*
Chemical
Reg. No./Substance:
0/Chemokines; 0/Receptors, Chemokine
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

Full Text
Journal Information
Journal ID (nlm-ta): Genes Cells
Journal ID (iso-abbrev): Genes Cells
Journal ID (publisher-id): gtc
ISSN: 1356-9597
ISSN: 1365-2443
Publisher: Blackwell Publishing Ltd
Article Information
Download PDF
Genes to Cells © 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd
open-access:
Received Day: 07 Month: 7 Year: 2012
Accepted Day: 22 Month: 8 Year: 2012
Print publication date: Month: 1 Year: 2013
Electronic publication date: Day: 12 Month: 11 Year: 2012
Volume: 18 Issue: 1
First Page: 1 Last Page: 16
PubMed Id: 23145839
ID: 3568907
DOI: 10.1111/gtc.12013

Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history
Hisayuki Nomiyama1*
Naoki Osada2
Osamu Yoshie3
1Department of Molecular Enzymology, Kumamoto University Graduate School of Medical SciencesHonjo, Kumamoto, 860-8556, Japan
2Division of Evolutionary Genetics, Department of Population Genetics, National Institute of GeneticsMishima, Shizuoka, 411-8540, Japan
3Department of Microbiology, Kinki University Faculty of MedicineOsaka-Sayama, Osaka, 589-8511, Japan
Correspondence: *Correspondence: nomiyama@gpo.kumamoto-u.ac.jp
Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://wileyonlinelibrary.com/onlineopen#OnlineOpen_Terms.
Communicated by: Mitsuhiro Yanagida

Introduction

As the number of the genomes that have been sequenced or are in the process of being sequenced increases, it becomes possible to assign orthologous genes between species and this way follow the evolutionary path of a particular gene family. Orthologous genes are descendants of a single gene in the last common ancestor of two species, and this knowledge is critical for understanding their functions in each species. This is particularly important in multigene families where the orthologous relationships are often obscure. Their diversity results from recurrent gene duplications in a given lineage during evolution. Following duplication, one of the “progeny” genes often becomes a pseudogene (Nei & Rooney 2005). Alternatively, one copy acquires a new function, or each copy adopts a portion of the functional role of the parental gene. Thus, the descendent genes in two species may differ substantially in their sequences and copy numbers, further complicating the determination of their orthologous relationships. In some cases, another cause of diversification is whole-genome duplication (WGD). Two rounds of WGD are assumed to have occurred at the base of vertebrate evolution before the divergence of jawless and jawed vertebrates (Dehal & Boore 2005; Kasahara 2007). As a result of such duplications, vertebrate genomes contain closely linked sets of paralogs on more than two, and occasionally four, chromosomes (Dehal & Boore 2005); for example, there are four homeobox (HOX) gene clusters in the human genome. However, among vertebrates, the retained genes vary within each cluster and within each species (Hoegg & Meyer 2005). Furthermore, teleost fish, which account for over half of all known vertebrate species, experienced a teleost-specific third round of WGD before their divergence (Jaillon et al. 2004; Meyer & Van de Peer 2005). Thus, teleosts have duplicates of many genes that are present only as single copies in other vertebrate species. Finally, the selective pressures imposed by pathogens may be another potential cause of diversity, and they specially shape the repertoire of host defence proteins. For example, a number of viruses encode viral mimics of host defence proteins to subvert the immune system (Murphy 1993). To counteract this “molecular mimicry” by pathogens, the diversity of host defence proteins may be markedly enhanced, making it more difficult to determine orthologous relationships within gene families.

Chemokines are a large family of small cytokines (Fig. 1). They were originally described as pro-inflammatory cytokines; however, recent studies indicate that their biological activities reach beyond that category: chemokines also play critical roles in development (Raz & Mahabaleshwar 2009) and homeostasis (Mantovani 1999; Zlotnik & Yoshie 2000; Moser et al. 2004; Zlotnik et al. 2011; Zlotnik & Yoshie 2012). In the human genome, there are 44 or more chemokine genes, which are a result of some copy number variations (Colobran et al. 2010; Nomiyama et al. 2010). Chemokine receptors belong to the family of seven-transmembrane G protein-coupled receptors (Murphy et al. 2000), and thus far, chemokines and chemokine receptors have only been described in vertebrates (DeVries et al. 2006; Bajoghli et al. 2009; Nomiyama et al. 2011). Interestingly, however, chemokine and chemokine receptor homologues are also found in some viral genomes (Lalani et al. 2000), suggesting that some chemokines and chemokine receptors genes have been “hijacked” by viruses to increase their pathogenicity. In our previous study, we surveyed the genome databases of 10 mammalian species for chemokine genes, which revealed their rapid evolution and generation of many lineage-specific chemokines (Nomiyama et al. 2010). We carefully determined the orthologous relationships of the chemokine genes among different species and pointed out some errors in the mouse chemokine terminology (Nomiyama et al. 2010). Such nomenclature errors may cause considerable confusion in extrapolation of mouse experimental results to humans. In an effort to better understand the evolution of chemokine genes, we have now extended our analysis to a wider group of vertebrate genomes, including some nonmammalian vertebrate species. We have identified a total of 553 vertebrate chemokines and determined their orthologous relationships through synteny conservation and evolutionary history analyses; this has allowed us to classify them into 63 orthologous groups. Previously, we surveyed the genomes of 16 vertebrate species for chemokine receptor genes and determined their orthologous relationships from phylogenetic and comparative genomic analyses (Nomiyama et al. 2011). Compared with chemokine genes, however, chemokine receptor genes were found to be relatively well conserved across vertebrate species. Here, to reflect the recent achievements of palaeogenomics in chemokine receptor classification, we have resurveyed the wider vertebrate genome databases for chemokine receptor genes. We have identified 364 chemokine receptor genes, determined their orthologous relationships through the same synteny conservation and evolutionary history analyses. We have classified them into 25 orthologous groups. Our present systematic classifications of vertebrate chemokines and chemokine receptors support the current chemokine and chemokine receptor nomenclature systems and are applicable to other species not included in this study.


Identification of chemokine and chemokine receptor genes

We searched for chemokine and chemokine receptor genes in vertebrate and invertebrate chordate genomes and replaced or added some organisms to our previous surveys (Nomiyama et al. 2010) so that the selected species cover a wider range of vertebrates. The sequences of most of the genomes are still incomplete. Data on the genomes of the elephant shark (cartilaginous fish) and sea lamprey (agnathan) are especially fragmented. However, we have included these genomes because they occupy key positions in the vertebrate evolution. In total, we have identified 553 chemokine genes and 364 chemokine receptor genes from 18 vertebrate species by BLAST searches of genome databases of these species in Ensembl (http://www.ensembl.org) (Fig. 2 and Fig. S1 in Supporting Information). Interestingly, we could not identify any chemokine genes in the genomes of invertebrate chordates such as lancelets (amphioxus) or sea squirts (ascidians).

There are large differences in gene numbers between mammals, birds, and teleosts. Although the genome assemblies are incomplete in most species surveyed, they reflect the lineage-specific expansion and contraction of the chemokine system. In general, mammals (represented by monotremes, marsupials, and placental mammals) and teleost fish have more chemokine and chemokine receptor genes than birds, whose immune gene families are generally much simpler than those of mammals (Dalloul et al. 2010). The major reason for the abundance of chemokine genes in mammals is attributable to the presence of large gene clusters (DeVries et al. 2006; Colobran et al. 2007; Nomiyama et al. 2010), whereas birds and teleosts have no such clusters in the corresponding chromosomal regions (Fig. S2 in Supporting Information). The chemokine receptor genes also tend to be clustered in mammals (DeVries et al. 2006; Nomiyama et al. 2011), although most of these genes arose before the emergence of birds. However, in teleosts, small-scale gene duplications and teleost-specific WGD have led to large increases in both chemokines and chemokine receptors (DeVries et al. 2006; Peatman & Liu 2007; Nomiyama et al. 2008) (Fig. S3 in Supporting Information).


Conserved synteny analysis

Phylogenetic analysis is widely used to determine orthologs in multiple genomes. However, this method is insufficient for determining the orthologous relationships of many chemokine genes, because the phylogenetic trees of vertebrate chemokines exhibit many collapsed or poorly supported nodes (Fig. S4 in Supporting Information). This is due in part to the short alignment of chemokine domains used for tree construction and also to gene duplications followed by gene losses or rapid lineage-specific gene expansions. In addition, most genomes are still incomplete, and the orthology assignments can be wrong. To overcome these problems, we also used micro- and macro-conserved synteny analyses. Although the linear order of a genome segment containing a set of genes may have been shuffled considerably during evolution, we are still able to trace conserved synteny even between relatively divergent vertebrate species (Nakatani et al. 2007; Catchen et al. 2011). Thus, conserved synteny analysis represents a powerful tool for establishing gene orthology between species.

First, we applied conserved synteny analysis to teleost genes, which had expanded by teleost-specific WGD. One such analysis is shown in Fig. 3. CCL25 is known to play an important role in T-cell differentiation in the thymus and mucosal immunity in the small intestine in human and mouse (Vicari et al. 1997; Wurbel et al. 2007), but its orthologs have not yet been characterized in teleosts. By using the Ensembl genome data (http://www.ensembl.org), we prepared microsynteny maps covering the genomic regions containing CCL25 from zebrafish, medaka, Tetraodon, and human (Fig. 3A). The maps reveal that each teleost fish contains two orthologs of human CCL25 located on different chromosomes. The conserved synteny dot plots drawn using Synteny Database (Catchen et al. 2009) (http://teleost.cs.uoregon.edu/synteny_db/), which is specifically designed to identify conserved synteny using Ensembl data, show that a large region of human chromosome 19 (Hsa19) surrounding CCL25 shares a well-recognizable synteny with the CCL25 regions on two chromosomes of each teleost (Fig. 3B), providing solid evidence for conserved synteny. Recently, ancestral vertebrate genomes have been reconstructed through identification of conserved vertebrate linkage (CVL) blocks in genomes (Kasahara et al. 2007; Nakatani et al. 2007). CVL blocks are groups of genes located on a single chromosome even after the two rounds of WGD and are similar to the conserved synteny mentioned earlier or the “doubly conserved synteny” (Jaillon et al. 2004; Kasahara et al. 2007) used for teleosts that experienced the teleost-specific third WGD. Correspondence of the orthologous chromosomes among teleosts can be determined by locating a gene of interest in a specific CVL block. Because ancestral chromosomes are represented by various combinations of CVL blocks, this method also allows us to deduce the evolutionary history of vertebrate genes and has been used successfully for orthology assignments of several genes (Laisney et al. 2010; Braasch & Postlethwait 2011). Using this method, we can conclude that the two regions containing fish CCL25 genes originated from a copy on a preduplication chromosome (protochromosome) “m” of the common teleost ancestor living before the teleost-specific WGD (Fig. 3B). Furthermore, the analysis shows that the CCL25 regions of medaka chromosome 17 (Ola17), zebrafish chromosome 2 (Dre2), and Tetraodon chromosome 15 (Tni15) are derived from the same protochromosome “m”. Therefore, we refer to the CCL25 genes on these chromosomes as CCL25a. Consequently, the CCL25 genes on medaka chromosome 4 (Ola4), zebrafish chromosome 11 (Dre11), and Tetraodon chromosome 1 (Tni1) are referred to as CCL25b. Zebrafish chromosome 22 (Dre22) also contains a region derived from the teleost protochromosome “m” after the teleost-specific WGD and subsequent chromosomal fusion and fission, but this region has apparently lost its CCL25 gene copy.

From similar analyses, we have determined the orthologous relationships of other chemokine genes duplicated by the teleost-specific WGD in the three teleosts (Figs. S3 and S5 in Supporting Information). These assignments may be useful for investigating biological functions, because the functions of co-orthologous genes may have diverged substantially since the teleost-specific WGD, which occurred approximately 350 million years ago (Mya). In zebrafish, for example, the chemokine receptor CXCR4b regulates migration of various cell types, including primordial germ cells (David et al. 2002; Doitsidou et al. 2002; Knaut et al. 2003), whereas CXCR4a has been shown to mediate endodermal migration (Nair & Schilling 2008). The original CXCR4 in the teleost ancestor may have had both functions, which may have been separated in the two co-orthologous genes in teleosts.


Evolutionary history analysis

We next applied the method of evolutionary history analysis to chemokine and chemokine receptor genes to track them back to a protochromosome of a common ancestor of teleosts and amniotes. For this purpose, we used chemokines and chemokine receptors common to teleosts and amniotes, most of which have homeostatic functions. Some chemokines present in only one lineage may have been lost in the other lineage during evolution. We omitted such chemokines from the analysis because they may not have existed at all in the common ancestor of teleosts and amniotes.

We again use CCL25 as an example. Fig. 4 shows a deduced evolutionary history of the CCL25 gene. As mentioned earlier, teleosts contain two CCL25 genes (CCL25a and CCL25b), each on a different chromosome. The regions containing these two genes are derived from the protochromosome “m” of the teleost ancestor (Kasahara et al. 2007; Nakatani et al. 2007). Given that amniotes have a single CCL25 gene (except birds, where CCL25 has not been identified), the ancestor of bony vertebrates (including teleosts and amniotes) must have had only a single CCL25 gene. According to the reconstructed protochromosomes, the CCL25 ancestral gene is located on protochromosome “A1” of the six protochromosomes of the ancestral gnathostome (jawed vertebrate), the common ancestor of both bony vertebrates and cartilaginous fish. This assumption is strengthened by the existence of a single CCL25 gene in the elephant shark, a cartilaginous fish that diverged from bony vertebrates shortly after the second round of WGD and thus did not undergo the teleost-specific WGD. The reconstruction also shows that protochromosome “A1” was in turn derived from the vertebrate protochromo-some “A”. However, the presence of a CCL25 gene on the very first vertebrate protochromosome “A” is only hypothetical. If indeed the gene existed on protochromosome “A”, then the CCL25 ancestral genes on the other five gnathostome protochromosomes (known as ohnologs (Wolfe 2000)) must have “gone missing”. The ancestral gene of the fish-specific CCL44, which is closely linked to CCL25b but exhibits low similarity to CCL25, may also have been on the teleost protochromosome “m”; but, whether the gnathostome or bony vertebrate protochromosome had CCL44 is unknown because amniotes do not have this gene. Similarly, we reconstructed the evolutionary history of eight other chemokine genes and 12 chemokine receptor genes that are shared by teleosts and amniotes (Fig. S6 in Supporting Information).


Nomenclature

As mentioned earlier, we use “a” and “b” to distinguish duplicates such as CCL25a and CCL25b on the teleost chromosomes originating from the same protochromosome. We add a further suffix “a” or “b” to designate the locally duplicated copies of the co-orthologs; for example, the three tandem CXCL8 genes on zebrafish chromosome 7 (Dre7) are thus designated CXCL8ba, CXCL8bb, and CXCL8bc. According to the zebrafish nomenclature guidelines at the Zebrafish Model Organism Database (ZFIN), these genes should be designated as CXCL8b.1, CXCL8b.2, and CXCL8b.3, respectively. However, this rule can be applicable only to transcribed genes, and one or two of such co-orthologous genes may still be a pseudogene or the result of sequence editing errors. Therefore, we have not followed this rule here.

The nomenclature of chemokine and chemokine receptor genes of the organisms other than teleosts is basically identical to that in our previous reports (Nomiyama et al. 2010, 2011). In Table S1 in Supporting Information, we list the names of the chemokines and chemokine receptors used in previous reports together with those proposed in this article. We should point out that the gene names used by other researchers based exclusively on BLAST searches or percent similarities often differ from the names we propose here, particularly in species other than mammals.


Classifying the vertebrate chemokines and chemokine receptors

There are closely related sets of chemokines that are apparently the products of recent duplications and thus are very similar to one another. Most of these are species- or lineage-specific chemokines that are tandemly organized in the genomes. In addition, teleost chemokines that were duplicated by teleost-specific WGD are also highly similar to one another. Such chemokines, which are likely to bind the same or closely related receptor(s), can be grouped together. We thus classify the vertebrate chemokines into 63 groups in accordance with the current human chemokine nomenclature system and used “G” to indicate each group (Table 1, and Tables S2 and S3 in Supporting Information). Similarly, we classify the vertebrate chemokine receptors into 25 groups (Nomiyama et al. 2011), again using “G” to indicate each group (Table 2). For example, the set of chemokines CXCL1, CXCL2, and CXCL3 are grouped to CXCL1/2/3G because they are quite similar to each other, and we cannot distinguish between these genes in species other than human. Likewise, three sets of chemokine receptors, CXCR1 and CXCR2, CCR1 and CCR3, and CCR2 and CCR5, are similar enough to be grouped into CXCR1/2G, CCR1/3G, and CCR2/5G, respectively.


Gene clusters and binding promiscuity

A prominent feature of the chemokine system is its high degree of promiscuity that allows a single receptor to bind several chemokines and a single chemokine to bind several receptors (Mantovani 1999). It is likely that this ligand–receptor promiscuity, together with redundancy in their actions makes this a highly robust biological system. Among the chemokines, the inflammatory and related plasma/platelet chemokines are the most promiscuous (Fig. 1). Their genes reside within the two major clusters in the genomes of mammals (Fig. S2 in Supporting Information), and consequently, most of them have been generated relatively recently in mammalian evolution (Nomiyama et al. 2010). Correspondingly, most of their receptors (CCR1, 2, 3, and 5 and CXCR1 and 2) also form gene clusters (Nomiyama et al. 2011) (Fig. S2 in Supporting Information). Although human CXCR3 is not located in these clusters, it may have been within the cluster of the amniote ancestor where CCR1, 2, 3, and 5 existed (see Fig. S6 in Supporting Information). As mentioned previously, CCR1 and CCR3 are closely related and so are CCR2 and CCR5. They are found only in the lineages leading to mammals and birds. Mammals have all four genes, whereas birds have only two genes, which we tentatively refer to here as bird CCR2 and CCR5. Thus, gene duplications occurred in the mammalian lineage. Their recent duplications coupled with sequence homogenization by gene conversion (Shields 2000; Vazquez-Salat et al. 2007) could account for their high promiscuity. In contrast, the origins of CXCR1, CXCR2, and CXCR3 are much older than the four CCRs (Table 2), dating back to a teleost ancestor or even to a gnathostome ancestor (Fig. S6 in Supporting Information). Nevertheless, except for CXCL8, their ligands have been duplicated recently. Thus, each of them has multiple specific ligands. The exceptions are CXCL6 and CXCL8, which are shared by CXCR1 and CXCR2. CXCR1 and CXCR2 may have been generated by gene duplication early in the amniote lineage (Fig. S6 in Supporting Information) and may have been homogenized by gene conversion (Shields 2000). It therefore seems logical that they share some of their ligands.


Functional nonredundancy of the chemokine system

In addition to the binding promiscuity of the chemokine system, the presence of multiple chemokine receptors on a single cell type also causes biologic redundancy, where a single cell responds to many chemokines and, conversely, one chemokine might act on different cell types. After gene duplication, one of the duplicated copies can acquire new roles or functions based on changes in the regulatory regions or coding regions of the gene. When the duplicated copy has different temporal or spatial regulation of gene expression from the other copy, more refined and robust regulation of cell recruitment might be possible. Fig. S7A in Supporting Information illustrates cell recruitment by multiple chemokine, where cells expressing two promiscuous receptors generated by recent gene duplication. In this case, the cells are guided by chemokines, which may bind one or both of the receptors on the cells, expressed at somewhere along the way between the start and final destination. Because the distance between the location of the cells and the site where each chemokine is secreted is short, the gradient of each chemokine can be very steep and the cells can move quickly between the sites. This is in contrast to the case where the cells express only one type of nonpromiscuous receptors. The long distance between the start and final destination makes the chemokine gradient small, making the cells to take time to reach the final destination (Fig. S7B in Supporting Information). Therefore, the former strategy is suitable for coping with acute situations, whereas the latter may be adequate in homeostasis. One example for the former case can be seen in the roles of chemokine receptors CCR2 and CCR5 in West Nile virus (WNV) infection. As described previously, CCR2 and CCR5 have been generated by duplication relatively recently in vertebrate evolution and share some ligands. Infection with WNV causes severe meningitis and encephalitis in a subset of susceptible humans. WNV encephalitis is characterized by infiltration of leukocytes, including monocytes and T cells in the central nervous system (CNS). Although both CCR2 and CCR5 have been shown to control leukocyte recruitment during infection, CCR2 is required for the release of monocytes from bone marrow to blood, while CCR5 is likely involved in the migration of monocytes from circulation to CNS (Lim et al. 2006, 2011). Thus, these promiscuous receptors have in fact nonredundant functions in vivo, and similar nonredundant and highly cooperative functions are also likely to be played by the promiscuous chemokines.


Search for missing binding partners

The groups of chemokines and chemokine receptors in our classification may provide a valuable source to search for missing binding partners (Tables 1 and 2, and Table S2 in Supporting Information). Based on the ligand–receptor relationships in human (Fig. 1), which are usually applicable to other animals, some ligands and receptors appear to be missing in some species. This may be due to incomplete genome sequencing in these species. Alternatively, the binding partners in such species may be different from those in humans. One example is CCR9, the receptor for CCL25 in humans. The CCR9 gene has been identified in all surveyed vertebrate species except for sea lamprey. However, the CCL25 gene is not found in bird genomes (Table S2 in Supporting Information) and CCL25 expressed sequence tags (ESTs) have not been identified in birds so far. Therefore, bird CCR9 may have a different ligand(s) than CCL25. Novel bird chemokines in the CCL30, 31 or 41 groups may include the bird CCR9 ligand(s). Another example is fish XCR1. Its ligand, XCL1, is missing in fish. Again, the groups CCL32, 33, 34, 35, 36, 40, or 44, most of which have been identified only in fish (Table S2 in Supporting Information), may contain the ligand(s) for fish XCR1. Because XC chemokines are more homologous to CC chemokines than to other classes of chemokines, it is not surprising that a CC chemokine(s) binds XCR1 in fish. In fact, a CC chemokine, vCCL3, encoded by Kaposi sarcoma-associated herpes virus is a highly selective and potent agonist of human XCR1 (Luttichau et al. 2007). Thus, a close comparison of the ligand and receptor groups could be informative for locating missing binding partners. Increasing the number of surveyed genomes will further narrow the binding partner candidates.


Vertebrate ancestral chemokine and chemokine receptor genes

The candidates for ancestral chemokine genes are located on two to four vertebrate protochromosomes, of which the total number is assumed to be 10 to 13 (Fig. 5). There are five CXC genes (CXCL8, 11, 12, 13, and 14) on protochromosome “C” and two CC genes, CCL25 and CCL20, on protochromosomes “A” and “F”, respectively. We could not specify the protochromosome(s) that have the ancestral CCL27 and CCL19 genes. As for the chemokine receptors, 10 genes (CXCR1, 3, 3L, 4, and 7; CCR7, 9, and 10; XCR1 and CCRL1) mapped to protochromosome “E”), whereas CCR6 and CXCR5 localized to protochromosomes “B” and “J”, respectively. Obviously, most of the receptors on the protochromosomes have their ligands on protochromosomes, supporting their ancient evolutionary origin and ligand–receptor coevolution (Zlotnik et al. 2006) (Fig. 5). However, it is not certain whether all these genes actually existed in the vertebrate ancestor. Among these genes, only two chemokines (CXCL8 and CXCL12) and two chemokine receptors (CXCR4 and CXCR7) have been identified in the agnathan sea lamprey, the oldest extant vertebrate species. Therefore, even after considering the incompleteness of the genome data, it seems likely that only one or a few chemokine ligand–receptor pairs were originally present on the vertebrate protochromosome(s). If this were the case, the protochromosomes carrying the oldest ancestral genes may have been “C” (ligand) and “E” (receptor), where the genes may have expanded by repeated intrachromosomal gene duplications during evolution from the vertebrate ancestor to the gnathostome ancestor. If one of the binding partners does not map to protochromosome “C” or “E,” it may have undergone an interchromosomal translocation; for example, CCR9 (protochromosome “E”) and its sole ligand CCL25 (protochromosome “A”). However, CCL20 and CCR6, another specific pair, are located on protochromosomes “F” and “B,” respectively. Although both genes could have translocated from the protochromosomes “C” and “E,” respectively, another possibility is that there were originally two ligand–receptor pairs in the vertebrate ancestor, one pair on protochromosomes “C” and “E” and another pair on different protochromosomes. In that case, the ultimate original pair might be tracked to an invertebrate genome.


Origin of the chemokine system

Among the genes localized on vertebrate protochromosome “C,” CXCL8 and CXCL12 are both found in sea lamprey. Although the receptor for CXCL8 has not been identified in sea lamprey, the receptors for CXCL12 (CXCR4 and CXCR7) have been found. Given that CXCL8 (Oppenheim et al. 1991) and CXCL12 (Nagasawa et al. 1996; Raz & Mahabaleshwar 2009) are the prototype inflammatory and homeostatic chemokines, respectively, they may represent the primordial set of chemokines essential for the survival of vertebrate ancestors. Furthermore, most of the chemokine and chemokine receptor genes localized on vertebrate protochromosomes are present in elephant shark (a cartilaginous fish) and are therefore likely to have existed in the genome of the gnathostome ancestor.

The host defence system is composed of two major branches: germ-line-encoded innate immunity and somatically modified adaptive immunity. The chemokines play essential roles in both innate and adaptive immunity (Yoshie et al. 2001; Luster 2002; Coelho et al. 2005). Although a complex innate immune system is found in every multicellular organism, the immunoglobulin-type adaptive immune system is thought to have emerged before the divergence of gnathostomes (Cooper & Alder 2006) (Fig. 2). The chemokine system also seems to have emerged at about the time when agnathans appeared. However, the sea lamprey has only a few chemokines: CXCL8 and CXCL12, the primordial combination of inflammatory and homeostatic chemokines mentioned earlier, and two other chemokines of unknown function. In contrast, the elephant shark seems to have already acquired the basic sets of chemokines and chemokine receptors that are common in extant vertebrates (Fig. 5). Thus, the basic set of chemokines for vertebrate species may have been established early in the gnathostome lineage, in parallel with the appearance of adaptive immunity.

Although the chemokines and chemokine receptors identified in sea lamprey and elephant shark provide a crucial guide for our argument, their sequenced genomes are still far from complete to enable retrieval of a complete set of genes encoded by these species. Furthermore, as we have previously observed in the Tetraodon and Fugu genomes (Nomiyama et al. 2008, 2011), some species may have lost a considerable number of chemokine and chemokine receptor genes during evolution. Therefore, we must wait until more genomes of agnathans, cartilaginous fish and sea squirts are sequenced to near completion to draw a more definitive conclusion concerning the origin and evolution of the ancestral chemokine and chemokine receptor genes.


Concluding remarks

Based on conserved synteny and evolutionary history, we have been able to deduce the orthologous relationships of vertebrate chemokine and chemokine receptor genes. We have classified the vertebrate chemokines and chemokine receptors into 63 and 25 groups, respectively. Our method has proved useful, even for such a large and rapidly evolving gene family such as the chemokine system. Our study has reconstructed the evolutionary history of the chemokine system to a substantial extent, providing a useful platform for understanding this rapidly diversifying multigene family. In particular, the deduced evolutionary history of the duplicated genes among teleosts will greatly facilitate their functional investigation. Our classifications based on the orthologous relationships will be useful for studying chemokines in each species and also for identifying missing binding partners. With an increasing amount of genome data becoming available for vertebrates and invertebrate chordates, it will be of great interest to elucidate the evolutionary histories of various multigene families using the strategy presented in this study.


We thank Drs Y. Nakatani of the University of Tokyo and A. Zlotnik of the University of California for their helpful comments and suggestions.


References
Bajoghli B,Aghaallaei N,Hess I,Rode I,Netuschil N,Tay BH,Venkatesh B,Yu JK,Kaltenbach SL,Holland ND,Diekhoff D,Happe C,Schorpp M,Boehm T. Evolution of genetic networks underlying the emergence of thymopoiesis in vertebratesCellYear: 200913818619719559469
Braasch I,Postlethwait JH. The teleost agouti-related protein 2 gene is an ohnolog gone missing from the tetrapod genomeProc. Natl Acad. Sci. USAYear: 2011108E47E4821406593
Catchen JM,Braasch I,Postlethwait JH. Conserved synteny and the zebrafish genomeMethods Cell BiolYear: 201110425928521924168
Catchen JM,Conery JS,Postlethwait JH. Automated identification of conserved synteny after whole-genome duplicationGenome ResYear: 2009191497150519465509
Coelho AL,Hogaboam CM,Kunkel SL. Chemokines provide the sustained inflammatory bridge between innate and acquired immunityCytokine Growth Factor RevYear: 20051655356015967703
Colobran R,Pedrosa E,Carretero-Iglesia L,Juan M. Copy number variation in chemokine superfamily: the complex scene of CCL3L-CCL4L genes in health and diseaseClin. Exp. ImmunolYear: 2010162415220659124
Colobran R,Pujol-Borrell R,Armengol MP,Juan M. The chemokine network. I. How the genomic organization of chemokines contains clues for deciphering their functional complexityClin. Exp. ImmunolYear: 200714820821717437419
Cooper MD,Alder MN. The evolution of adaptive immune systemsCellYear: 200612481582216497590
Dalloul RA,Long JA,Zimin AV,et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysisPLoS BiolYear: 20108e100047520838655
David NB,Sapede D,Saint-Etienne L,Thisse C,Thisse B,Dambly-Chaudiere C,Rosa FM,Ghysen A. Molecular basis of cell migration in the fish lateral line: role of the chemokine receptor CXCR4 and of its ligand, SDF1Proc. Natl Acad. Sci. U S AYear: 200299162971630212444253
Dehal P,Boore JL. Two rounds of whole genome duplication in the ancestral vertebratePLoS BiolYear: 20053e31416128622
Delsuc F,Brinkmann H,Chourrout D,Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebratesNatureYear: 200643996596816495997
DeVries ME,Kelvin AA,Xu L,Ran L,Robinson J,Kelvin DJ. Defining the origins and evolution of the chemokine/chemokine receptor systemJ. ImmunolYear: 200617640141516365434
Doitsidou M,Reichman-Fried M,Stebler J,Koprunner M,Dorries J,Meyer D,Esguerra CV,Leung T,Raz E. Guidance of primordial germ cell migration by the chemokine SDF-1CellYear: 200211164765912464177
Graham GJ. D6 and the atypical chemokine receptor family: novel regulators of immune and inflammatory processesEur. J. ImmunolYear: 20093934235119130487
Hedges SB,Kumar S. Genomic clocks and evolutionary timescalesTrends GenetYear: 20031920020612683973
Hoegg S,Meyer A. Hox clusters as models for vertebrate genome evolutionTrends GenetYear: 20052142142415967537
Islam SA,Chang DS,Colvin RA,Byrne MH,McCully ML,Moser B,Lira SA,Charo IF,Luster AD. Mouse CCL8, a CCR8 agonist, promotes atopic dermatitis by recruiting IL-5+ T(H)2 cellsNat. ImmunolYear: 20111216717721217759
Jaillon O,Aury JM,Brunet F,et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotypeNatureYear: 200443194695715496914
Kasahara M. The 2R hypothesis: an updateCurr. Opin. ImmunolYear: 20071954755217707623
Kasahara M,Naruse K,Sasaki S,et al. The medaka draft genome and insights into vertebrate genome evolutionNatureYear: 200744771471917554307
Knaut H,Werz C,Geisler R,Nusslein-Volhard C. A zebrafish homologue of the chemokine receptor Cxcr4 is a germ-cell guidance receptorNatureYear: 200342127928212508118
Kuraku S,Meyer A,Kuratani S. Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after?Mol. Biol. EvolYear: 200926475918842688
Laisney JA,Braasch I,Walter RB,Meierjohann S,Schartl M. Lineage-specific co-evolution of the Egf receptor/ligand signaling systemBMC Evol. BiolYear: 2010102720105326
Lalani AS,Barrett JW,McFadden G. Modulating chemokines: more lessons from virusesImmunol. TodayYear: 20002110010610652469
Leick M,Catusse J,Follo M,Nibbs RJ,Hartmann TN,Veelken H,Burger M. CCL19 is a specific ligand of the constitutively recycling atypical human chemokine receptor CRAM-BImmunologyYear: 201012953654620002784
Lim JK,Glass WG,McDermott DH,Murphy PM. CCR5: no longer a “good for nothing” gene–chemokine control of West Nile virus infectionTrends ImmunolYear: 20062730831216753343
Lim JK,Obara CJ,Rivollier A,Pletnev AG,Kelsall BL,Murphy PM. Chemokine receptor Ccr2 is critical for monocyte accumulation and survival in West Nile virus encephalitisJ. ImmunolYear: 201118647147821131425
Luster AD. The role of chemokines in linking innate and adaptive immunityCurr. Opin. ImmunolYear: 20021412913511790543
Luttichau HR,Johnsen AH,Jurlander J,Rosenkilde MM,Schwartz TW. Kaposi sarcoma-associated herpes virus targets the lymphotactin receptor with both a broad spectrum antagonist vCCL2 and a highly selective and potent agonist vCCL3J. Biol. ChemYear: 2007282177941780517403668
Mantovani A. The chemokine system: redundancy for robust outputsImmunol. TodayYear: 19992025425710354549
Mantovani A,Bonecchi R,Locati M. Tuning inflammation and immunity by chemokine sequestration: decoys and moreNat. Rev. ImmunolYear: 2006690791817124512
Meyer A,Van de Peer Y. From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)BioEssaysYear: 20052793794516108068
Mortier A,Van Damme J,Proost P. Regulation of chemokine activity by posttranslational modificationPharmacol. TherYear: 200812019721718793669
Moser B,Wolf M,Walz A,Loetscher P. Chemokines: multiple levels of leukocyte migration controlTrends ImmunolYear: 200425758415102366
Murphy PM. Molecular mimicry and the generation of host defense protein diversityCellYear: 1993728238268458078
Murphy PM,Baggiolini M,Charo IF,Hebert CA,Horuk R,Matsushima K,Miller LH,Oppenheim JJ,Power CA. International union of pharmacology. XXII. Nomenclature for chemokine receptorsPharmacol. RevYear: 20005214517610699158
Nagasawa T,Hirota S,Tachibana K,Takakura N,Nishikawa S,Kitamura Y,Yoshida N,Kikutani H,Kishimoto T. Defects of B-cell lymphopoiesis and bone-marrow myelopoiesis in mice lacking the CXC chemokine PBSF/SDF-1NatureYear: 19963826356388757135
Nair S,Schilling TF. Chemokine signaling controls endodermal migration during zebrafish gastrulationScienceYear: 2008322899218719251
Nakatani Y,Takeda H,Kohara Y,Morishita S. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebratesGenome ResYear: 2007171254126517652425
Nakayama T,Watanabe Y,Oiso N,Higuchi T,Shigeta A,Mizuguchi N,Katou F,Hashimoto K,Kawada A,Yoshie O. Eotaxin-3/CC chemokine ligand 26 is a functional ligand for CX3CR1J. ImmunolYear: 20101856472647920974991
Naumann U,Cameroni E,Pruenster M,Mahabaleshwar H,Raz E,Zerwes HG,Rot A,Thelen M. CXCR7 functions as a scavenger for CXCL12 and CXCL11PLoS ONEYear: 20105e917520161793
Nei M,Rooney AP. Concerted and birth-and-death evolution of multigene familiesAnnu. Rev. GenetYear: 20053912115216285855
Nomiyama H,Egami K,Tanase S,Miura R,Hirakawa H,Kuhara S,Ogasawara J,Morishita S,Yoshie O,Kusuda J,Hashimoto K. Comparative DNA sequence analysis of mouse and human CC chemokine gene clustersJ. Interferon Cytokine ResYear: 200323374512639297
Nomiyama H,Hieshima K,Osada N,Kato-Unoki Y,Otsuka-Ono K,Takegawa S,Izawa T,Yoshizawa A,Kikuchi Y,Tanase S,Miura R,Kusuda J,Nakao M,Yoshie O. Extensive expansion and diversification of the chemokine gene family in zebrafish: identification of a novel chemokine subfamily CXBMC GenomicsYear: 2008922218482437
Nomiyama H,Osada N,Yoshie O. The evolution of mammalian chemokine genesCytokine Growth Factor RevYear: 20102125326220434943
Nomiyama H,Osada N,Yoshie O. A family tree of vertebrate chemokine receptors for a unified nomenclatureDev. Comp. ImmunolYear: 20113570571521295066
Oppenheim JJ,Zachariae CO,Mukaida N,Matsushima K. Properties of the novel proinflammatory supergene “intercrine” cytokine familyAnnu. Rev. ImmunolYear: 199196176481910690
Peatman E,Liu Z. Evolution of CC chemokines in teleost fish: a case study in gene duplication and implications for immune diversityImmunogeneticsYear: 20075961362317541578
Raz E,Mahabaleshwar H. Chemokine signaling in embryonic cell migration: a fisheye viewDevelopmentYear: 20091361223122919304885
Sarafi MN,Garcia-Zepeda EA,MacLean JA,Charo IF,Luster AD. Murine monocyte chemoattractant protein (MCP)-5: a novel CC chemokine that is a structural and functional homologue of human MCP-1J. Exp. MedYear: 1997185991098996246
Shields DC. Gene conversion among chemokine receptorsGeneYear: 200024623924510767545
Soto H,Wang W,Strieter RM,Copeland NG,Gilbert DJ,Jenkins NA,Hedrick J,Zlotnik A. The CC chemokine 6Ckine binds the CXC chemokine receptor CXCR3Proc. Natl Acad. Sci. USAYear: 199895820582109653165
Vazquez-Salat N,Yuhki N,Beck T,O'Brien SJ,Murphy WJ. Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerizationGenomicsYear: 20079021322417544254
Vicari AP,Figueroa DJ,Hedrick JA,Foster JS,Singh KP,Menon S,Copeland NG,Gilbert DJ,Jenkins NA,Bacon KB,Zlotnik A. TECK: a novel CC chemokine specifically expressed by thymic dendritic cells and potentially involved in T cell developmentImmunityYear: 199772913019285413
Wolfe K. Robustness–it's not where you think it isNat. GenetYear: 2000253410802639
Wurbel MA,Malissen M,Guy-Grand D,Malissen B,Campbell JJ. Impaired accumulation of antigen-specific CD8 lymphocytes in chemokine CCL25-deficient intestinal epithelium and lamina propriaJ. ImmunolYear: 20071787598760617548595
Yoshie O,Imai T,Nomiyama H. Chemokines in immunityAdv. ImmunolYear: 2001785711011432208
Zlotnik A,Burkhardt AM,Homey B. Homeostatic chemokine receptors and organ-specific metastasisNat. Rev. ImmunolYear: 20111159760621866172
Zlotnik A,Yoshie O. Chemokines: a new classification system and their role in immunityImmunityYear: 20001212112710714678
Zlotnik A,Yoshie O. The chemokine superfamily revisitedImmunityYear: 20123670571622633458
Zlotnik A,Yoshie O,Nomiyama H. The chemokine and chemokine receptor superfamilies and their molecular evolutionGenome BiolYear: 2006724317201934
Supporting Information/Supplementary Material

Additional Supporting Information may be found in the online version of this article at the publisher's web site:

Figure S1 Amino acid sequences of vertebrate chemokines and chemokine receptors.

Click here for additional data file (gtc0018-0001-SD1.doc)

Figure S2 Chemokine and chemokine receptor gene clusters.

Click here for additional data file (gtc0018-0001-SD12.png)

Click here for additional data file (gtc0018-0001-SD18.txt)

Figure S3 Conserved synteny around chemokine and chemokine receptor genes in vertebrates.

Click here for additional data file (gtc0018-0001-SD13.png)

Figure S4 Phylogenetic trees of vertebrate chemokines and chemokine receptors.

Click here for additional data file (gtc0018-0001-SD14.png)

Figure S5 Conserved synteny dot plots of chemokine and chemokine receptor genes.

Click here for additional data file (gtc0018-0001-SD15.png)

Figure S6 Proposed ancestry of vertebrate chemokine and chemokine receptor genes.

Click here for additional data file (gtc0018-0001-SD16.png)

Figure S7 Functional nonredundancy of the chemokine system.

Click here for additional data file (gtc0018-0001-SD17.png)

Click here for additional data file (gtc0018-0001-SD19.txt)

Table S1 Comparison of the chemokine genes identified in this study with those reported in other studies.

Click here for additional data file (gtc0018-0001-SD8.xls)

Table S2 Vertebrate chemokine and chemokine receptor gene groups.

Click here for additional data file (gtc0018-0001-SD9.xls)

Table S3 Members of the gene groups of vertebrate chemokines and chemokine receptors.

Click here for additional data file (gtc0018-0001-SD10.xls)

Table S4 CVL blocks and ancestral chromosomes containing chemokine and chemokine receptor genes.

Click here for additional data file (gtc0018-0001-SD11.xls)


Figures

[Figure ID: fig01]
Figure 1 

Chemokine ligand–receptor binding relationships. Five subfamilies of chemokines, CXC, CC, XC, CX3C, and CX, have been recognized on the basis of the arrangement of the two N-terminal residues of four conserved cysteines. One and three amino acids separate the first and second cysteines in the CXC and CX3C chemokines, respectively, whereas the two cysteines are adjacent to each other in the CC subfamily. The XC (or C) subfamily lacks the first and paired third cysteine residues. The fifth subfamily, CX, which has so far been identified only in zebrafish, lacks one of the two N-terminal cysteine residues but retains the third and fourth (Nomiyama et al. 2008). Chemokines can also be functionally classified into several groups, based on their mode of expression and function (Zlotnik & Yoshie 2000; Moser et al. 2004; Mantovani et al. 2006). These groups are shown in different colors. Both the common names and systematic nomenclature are shown in the figure. Recently, Islam et al. (2011) showed that mouse Ccl8 serves as an agonist for Ccr8 but not for Ccr2, whereas human CCL8 binds CCR2 but not CCR8. We previously proposed that the mouse ortholog of human CCL8 is Ccl12 rather than Ccl8 (Nomiyama et al. 2003). Thus, mouse Ccl8 is now likely to be a mouse-specific gene without a human counterpart. Consistent with this, mouse Ccl12 has been shown to bind Ccr2, as does human CCL8 (Sarafi et al. 1997). Therefore, the mouse genes require renaming. The other discrepancies between human and mouse chemokine gene names are described in our previous review (Nomiyama et al. 2010). All known chemokine receptors are seven-transmembrane G protein-coupled receptors. Chemokine receptors are classified according to their ability to bind a specific subclass of chemokines (CXCR, CCR, XCR, and CX3CR) (Murphy et al. 2000). However, mouse Cxcr3 and human CX3CR1 have been shown to bind ligands of a different subclass, mouse Ccl21 (Soto et al. 1998) and human CCL26 (Nakayama et al. 2010), respectively, in addition to their cognate ligands. The receptor(s) for the CX chemokines has not yet been identified. Thus far, 18 signaling chemokine receptors have been identified in the human genome. Besides these classic chemokine receptors, five atypical (nonsignaling) chemokine receptors have been identified (DARC, CCBP2, CCRL1, CCRL2, and CXCR7) (Graham 2009; Leick et al. 2010; Naumann et al. 2010). These atypical receptors bind chemokines but do not elicit standard chemotactic responses after ligand binding. Both DARC and CCBP2 primarily bind inflammatory chemokines of the CXC and CC subfamilies. The ligand specificity of the receptors shown here may change by post-translational modification of the ligands (Mortier et al. 2008).



[Figure ID: fig02]
Figure 2 

Number of chemokine and chemokine receptor genes identified in vertebrate genomes. We had previously identified chemokine genes from 10 mammalian genomes (Nomiyama et al. 2010). Here, we have omitted five genomes from the survey list but added two genomes to cover a wide range of mammals. In total, we searched seven mammalian genomes (human, mouse, cow, elephant, opossum, wallaby, and platypus) for the analyses. In addition, three birds (chicken, zebra finch, and duck), a reptile (anole lizard), an amphibian (Xenopus), four teleost fish (medaka, stickleback, zebrafish, and Tetraodon), a cartilaginous fish (elephant shark) and a jawless fish (sea lamprey) were included in the survey. Phylogenetic relationships of these organisms among chordates are shown. More detailed taxonomic classifications are shown in Fig. S1 in Supporting Information. The first split in vertebrates occurred between jawed and jawless vertebrates (gnathostomes and agnathans), followed by the divergence of jawed vertebrates into cartilaginous and bony fish (chondrichthyes and osteichthyes). Divergence times (Mya, million years ago) (Hedges & Kumar 2003) are not to scale. A hypothetical origin time for the adaptive immune system is indicated. The timings of the two successive rounds of WGD (1R and 2R) and the teleost-specific WGD (3R) are also shown. Although the timing of the 2R has long been in dispute, Kuraku et al. (2009) recently showed that both 1R and 2R occurred before the split between jawed and jawless vertebrates. Recent studies indicate that tunicates (previously known as urochordates) are the invertebrates most closely related to vertebrates (Delsuc et al. 2006). The amino acid sequences of the chemokines and their database accession numbers are shown in Fig. S1A in Supporting Information. The chemokine receptor sequences and their accession numbers (Nomiyama et al. 2011) have been updated and are shown in Fig. S1B in Supporting Information. Phylogenetic trees of vertebrate chemokines and chemokine receptors are shown in Fig. S4 in Supporting Information.



[Figure ID: fig03]
Figure 3 

Conserved synteny analysis of vertebrate chemokine CCL25. (A) Comparative maps of CCL25 gene regions. Fish-specific CCL44 genes are also shown. Arrows indicate transcriptional orientation. Comparative maps of other chemokine and chemokine receptor genes are shown in Fig. S3 in Supporting Information. (B) Conserved synteny dot plots. The plots were drawn using the Synteny Database (Catchen et al. 2009, 2011). In the plots, fish orthologs of genes on Hsa19 (0–20 Mb) are indicated as red crosses on fish chromosomes in the order found on the human chromosome (gene orders on fish chromosomes are different from those of humans). Correspondence of the chromosomes among teleosts containing the CCL25 genes was examined as follows. First, the CVL number was obtained using the human CCL25 gene locus (chromosome 19, 8.1 Mb) (Nakatani et al. 2007). Supplemental Fig. S2 in reference 20 shows that the human genes in this CVL block “88” are orthologous to the genes on medaka chromosomes 4 and 17, where the two medaka CCL25 genes are located. Next, protochromosome numbers of the teleost, gnathostome, and vertebrate ancestors (m, A1 and A, respectively) were identified from Supplemental Table S2 in reference 20. Using the teleost protochromosome number, the orthologous chromosomes of the three teleosts were then identified in the Supplemental information of reference 25. In case of teleost-specific genes, teleost protochromosome numbers and correspondence of the chromosomes in each teleost can be obtained by consulting the Supplemental information in reference 25. Dre2, Ola17, and Tni15, all containing CCL25a, were derived from one of the duplicated chromosomes of teleost protochromosome m. Dre11, Ola4, and Tni1, all containing CCL25b, were derived from another duplicated copy of the same protochromosome. Dre11 and Dre22 are the products of chromosome fission. Human and teleost chromosomes containing the CCL25 regions were all derived from gnathostome protochromosome A1 and also from vertebrate ancestral chromosome A (see also Fig. 4). Synteny dot plots of other chemokine and chemokine receptor genes and the CVL numbers are shown in Fig. S5 and Table S4 in Supporting Information, respectively.



[Figure ID: fig04]
Figure 4 

Proposed ancestry of vertebrate chemokine CCL25. Vertebrate protochromosome A, on which an ancestral CCL25 gene is assumed to reside, was duplicated by the 1R and 2R WGDs and also by a fission event between the 1R and 2R, resulting in six gnathostome protochromosomes (Nakatani et al. 2007). The CCL25 gene on gnathostome protochromosome A1 was transferred to teleost and amniote protochromosomes, whereas the genes on the other gnathostome protochromosomes were lost. Fish-specific CCL44 must have been generated by tandem duplication of the ancestral CCL25 gene on teleost protochromosome m. Two copies of the teleost CCL25 gene were maintained on duplicated chromosomes, and one of the CCL44 copies on one of the duplicated chromosomes may have been lost. Tetraodon CCL44 and bird CCL25 genes have not yet been identified. The evolutionary history of other chemokine and chemokine receptor genes are shown in Fig. S6 in Supporting Information. 3R indicates the teleost-specific WGD.



[Figure ID: fig05]
Figure 5 

Vertebrate ancestral genes for chemokines and chemokine receptors. The vertebrate and gnathostome protochromosomes on which chemokine and chemokine receptor genes were localized are shown. Among the genes contained by sea lamprey and elephant shark, only those that are shared by vertebrate or gnathostome ancestors are shown. Because the genome sequences of sea lamprey and elephant shark are still fragmented, it is not known whether the genes are linked on the same chromosomes. The lines that link the vertebrate chemokine ancestors with the chemokine receptor ancestors indicate the ligand–receptor relationships based on the human chemokine system. The receptor for CXCL14 and the ligand(s) for CXCR3L have not yet been identified. The ligand(s) for the ancestral XCR1 is unknown. The predicted locations of HOX gene clusters on the protochromosomes are also indicated. Colocalization of HOX clusters with chemokine receptor genes on vertebrate protochromosome E shows that some of the chemokine receptor genes accompanied HOX cluster duplication (DeVries et al. 2006). HOXD, HOXA, and HOXB on gnathostome protochromosomes E0, E1, and E2, respectively, were omitted for simplicity (see also Fig. S6 in Supporting Information). 1R and 2R indicate the two successive rounds of WGD.



Tables
[TableWrap ID: tbl1] Table 1 

Vertebrate CXC chemokine gene groups*


Cluster (human) Chemokine Group Human Mouse Cow Elephant Opossum Wallaby Platypus Chicken Zebra finch Duck Anole lizard X. tropicalis Medaka Stickleback Zebrafish Tetraodon§ Elephant shark Sea lamprey
C CXCL1/2/3G 3 3 3 1 2 2 2
C CXCL4/4LG 2 1 1 1
C CXCL5/6G 2 1 1 1
C CXCL7G 1 1 1 1
C CXCL8G 1 1 1 1 1 3 2 2 2 5 2 1 4 1 4 1
C CXCL9G 1 1 1 1 1
C CXCL10G 1 1 1 1 1 1 1 3
C CXCL11G 1 1 1 1 1 1 8
CXCL12G 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 1
C CXCL13G 1 1 1 1 3 2 3 2 2 1 1 1 1 1
CXCL14G 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
CXCL15G 1 1 2 1
CXCL16G 1 1 1 1 1
CXCL17G 1 1 1 1
CXCL18G 1 2 2 3 1
CXCL19G 1 1 1 1
CXCL20G 2 1 1 1
CXCL21G 1
CXCL22G 4
CXCL23G 1

Total†† >44 46 45 37 36 29 21 25 20 23 9 28 36 24 89 20 17 4

*Only CXC chemokine gene groups are shown. Other gene groups (CC, CX3C and XC chemokines) are shown in Table S1 in Supporting Information.

‘C’ indicates chemokine genes in the human major clusters (see also Fig. 3).

Genes identified in X. laevis are included.

§Genes identified in Takifugu rubripes are included.

X. tropicalis CXCL16 lacks the amino acid residue between the first and second conserved cysteine residues.

††Total gene numbers of each species include those of other gene groups (CC, CX3C and XC chemokines).


[TableWrap ID: tbl2] Table 2 

Vertebrate chemokine receptor gene groups


Cluster (human)* Chemokine Receptor Group Human Mouse Cow Elephant Opossum Wallaby Platypus Chicken Zebra finch Duck Anole lizard X. tropicalis Medaka Stickleback Zebrafish Tetraodon Elephant shark Sea lamprey
CXCR1/2G 2 2 2 2 2 2 1 1 2 1 3 3 2 3 2
CXCR3G 1 1 1 1 1 1 4 2 2 2
CXCR3LG 1 1 1 1 1 1
CXCR4G 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 1 1
CXCR5G 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
C CXCR6G 1 1 1 1 1 2 1 1 1 1
C CCR1/3G 2 3 3 2 2 1 2
C CCR2/5G 2 2 2 2 2 2 2 2 2 3
C CCR4G 1 1 1 1 1 1 1 1 1 1 1 1
CCR4LG 3 2 3 2
CCR6G 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1
CCR7G 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
C CCR8G 1 1 1 1 2 2 3 3 1
C CCR9G 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 1
CCR10G 1 1 1 1 1 1 1 1 1 1 1 1 1
CCR11G 2 4 3 1
CCR12G 1 2 4 3 2
CCR13G 2
C CX3CR1G 1 1 1 1 1 1 1 1 1 1
C XCR1G 1 1 1 1 1 1 1 1 1 1 4 2 6 2 3
CXCR7G 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 2
C CCBP2G 1 1 1 1 1 1 2 1
C CCRL1G 1 1 1 1 1 1 1 1 2 1 1 1 2 2 2 2
C CCRL2G 1 1 1 1 1 1
DARC-G 1 1 1 1 1 1

Total 23 24 24 20 23 9 17 16 18 18 20 16 31 29 33 24 14 5

*‘C’ indicates chemokine receptor genes in the human major cluster (see also Fig. 3).

Genes identified in X. laevis are included.

Genes identified in Takifugu rubripes are included.



Article Categories:
  • Reviews


Previous Document:  Babesia microti seroprevalence in Minnesota blood donors.
Next Document:  Characteristics of student preparedness for clinical learning: clinical educator perspectives using ...