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Poult Sci 2007. 86:453-459
© 2007 Poultry Science Association
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GENETICS

Description of a Synteny on the Chicken Chromosome Zp23-22

C. Y. Wang and F. C. Leung1

Department of Zoology, The University of Hong Kong, Hong Kong, China

1 Corresponding author: fcleung{at}hkucc.hku.hk


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Comparative genomics offers a powerful opportunity to identify the considerable synteny and thereby gain an understanding of how the genome has been remodeled during evolution. Using the chicken prolactin receptor (cPRLR) and growth hormone receptor (cGHR) genes as seed orthologs, 13 genes were mapped on the chicken chromosome Z and the synteny compared with those in other vertebrates including human, chimpanzee, rat, mouse, and zebrafish. Strikingly, highly conserved syntenies were noticed among the 4 mammalian species and chicken. However, changes in arrangement and orientation of genes within the conserved region were found among these species, indicating that intrachromosomal inversions had occurred more frequently than interchromosomal translocations since the divergence of birds and mammals. Although zebrafish PRLR and GHR were localized on 2 distinct linkage groups (LG21 and LG8), 2 syntenies on LG21 and LG5 were consistently observed in all species examined. The current result suggested that the 2 syntenies were extremely conserved during vertebrate genome evolution, and most large gene syntenies including the PRLR-GHR region were formed after teleosts.

Key Words: synteny • prolactin receptor • growth hormone receptor • chicken • chromosome Z


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Synteny refers to the linkage of 2 or more genes on the same chromosome of more than 1 species. It provides a concept for many conventional and convenient approaches useful in comparative genomics studies. Many conserved syntenic regions had been identified between birds and mammals (Burt et al., 1995, 1999; Groenen et al., 1999, 2000; Nanda et al., 2002). Detecting these syntenies in model organisms is a threshold to reunifying the ancestral synteny before the species diverged. For the chicken chromosome Z, previous studies demonstrated that major conserved syntenies were located on human chromosomes 9 and 5, and minor syntenies on human chromosomes 18 and 8 (Nanda et al., 1999, 2000, 2002; Schmid et al., 2000), implying the occurrence of strong interchromosomal rearrangements after the separation between birds and mammals. In local chromosomal regions, studies on synteny, in particular the gene order inside, will facilitate the understanding of intrachromosomal shuffling. However, due to low resolution of genomic maps in previously published reports, subtle internal rearrangements within the conserved syntenic regions have not been described. The current high-resolution genomic maps with confirmatively correct annotations provide a base to demonstrate the inter- and intrachromosomal rearrangements in detail, thus providing an opportunity for a detailed synteny characterization. Studying these molecular rearrangements is one of the approaches to understand biological evolution at the chromosome level. Using high-resolution human and mouse genomes, many conservative syntenic regions were later found to be interrupted by insertions, inversions, transpositions, deletions, translocations, and other sorts of rearrangements (Carver and Stubbs, 1997; Pevzner and Tesler, 2003).

Prolactin receptor (PRLR) and growth hormone receptor (GHR) belong to the growth hormone-prolactin cytokine receptor superfamily. Chicken PRLR and GHR genes were mapped onto the chicken chromosome Zp23-22 (Tanaka et al., 1992; Cheng et al., 1995). The linkage of PRLR and GHR genes was also found in human chromosome 5p14-13 (Barton et al., 1989; Arden et al., 1990), mouse chromosome 15 (Barton et al., 1989; Nanda et al., 1999), and rat chromosome 2 (Barker et al., 1992). In the current study, a conserved syntenic region was described that includes up to 13 genes in the human and chicken genomes. These genes are located on the human chromosome 5p14-q13 (HSA5) and chicken chromosome Z (GGAZ). A comparative analysis was done in their homologous chromosomes in the mouse, rat, and chimpanzee. In addition, the comparison was extended to zebrafish to test whether the GHR-PRLR syntenic region in chicken and mammals was formed before the evolutionary divergence between teleosts and tetrapods about 450 million yr ago (Kumar and Hedges, 1998).


   MATERIALS AND METHODS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
RESULTS
 DISCUSSION
 REFERENCES
 
In a current study, the PRLR and GHR genes were used as key seed orthologs to define the gene synteny in this genomic region because of their similar and unique locations in homologous chicken and human chromosomes (Nanda et al., 2000). The identification of syntenic genes among different species is generally based on sequence similarity. In addition, the identification of syntenic genes depends heavily on the completeness and quality of gene annotations. The human, mouse, and rat genomes in the National Center for Biotechnology Information (NCBI) and chicken, chimpanzee, and zebrafish genomes in Ensembl (www.ensembl.org), as well as their associated annotation, were used, to demonstrate the method of ortholog detection. The putative genes and transcripts were then individually reviewed. To implement this method, based on the chicken release sequence data from Ensembl (Release 28, Feb. 2005), chicken candidate genes located around the PRLR and GHR regions were first identified as seed orthologous genes if they satisfied the following 3 criteria: 1) they have human counterparts; 2) they have single locus sites on the chicken chromosome Zp23-22; and 3) they have consistent order in the chicken and human genomes. Orthologous genes were generated by the following processes. First, the sequences of chicken candidate genes were used to run basic local alignment search tool (BLAST) for identifying the chromosomal position on the reference genome (chicken) in Ensembl. The BLAST results were evaluated by the E-value threshold. This initial step of matches was filtered to eliminate repeat sequences. By comparing E-values, the match between query and subject sequences, of at least 50 bp and sharing at least 80% identity, was retained. Second, the retained chicken genes acted as the seed to locate the orthologous genes in the human genome. The orthologous human genes were selected if they satisfied the 3 criteria described previously in the seed orthologous genes. Orthologous genes were sorted by their chromosome positions to identify the syntenic regions in chicken and human genomes. Using chicken and human cDNA sequences as query, the rat and mouse orthologous genes were identified from NCBI and chimpanzee and zebrafish orthologous genes from Ensembl through the same processes described in chicken and human.


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
DISCUSSION
 REFERENCES
 
A total of 13 orthologous chicken genes were identified; KIAA0303 protein (KIAA0303), centromere protein H (CENPH), Thrombospondin (THBS4), nicotinamide nucleiotide transhydorgenase (NNT), fibroblast growth factor 10 (FGF10), ISL1 transcription factor (ISL1), alpha integrin (ITGA1), Follistatin (FST), NADH dehydrogenase Fe-S protein (Ndufs4), glial cell line-derived neurotrophic factor (GDNF), and leukemia inhibitory factor receptor (LIFR) were identified and mapped. All of these genes were linked together in the chicken GGAZ, and their order in the chicken GGAZ served as a reference for the other species. Such a large gene synteny was identified for the first time in the chicken, and its corresponding syntenic regions were also characterized in the human genomic region HSA5p14-q13, rat genomic region 2q16-12, chimpanzee chromosome 5, mouse chromosomes 15 and 13, and 4 zebrafish linkage groups (LG5, LG8, LG10, and LG21). Tables 1Go and 2Go briefly summarize the results of chicken orthologs loci in human, chimpanzee, rat, mouse, and zebrafish with their corresponding NCBI or Ensembl gene accession numbers examined in the current study.


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  		Table 1. The summary of orthologous loci in the chicken, human, chimpanzee, rat, mouse, and zebrafish genomes
 

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  		Table 2. Gene accession numbers in GenBank and Ensembl
 
Comparative Mapping of the PRLR-GHR Syntenic Region of GGAZ on the Mammalian Chromosomes

With the limitation of the expressed sequence tag database and genome sequence collections, chicken PRLR-GHR syntenic regions holding more or less orthologous genes were found in the mouse, rat, and chimpanzee genomes. The KIAA0303 gene was not found in the mouse; the Ndufs4 and CENPH genes were not detected in rat; and 12 orthologous genes were identified in the chimpanzee chromosome 5. Figure 1Go is a graphical representation of the conserved syntenic regions of the human HSA5p14-q13, rat genomic region 2q16-12, chimpanzee chromosome 5, mouse chromosomes 15 (4.6 cM) and 13 (51.0 to 64.0 cM), and chicken GGAZ. The syntenic regions were further divided into 3 subunits in terms of internal reversed gene order. The KIAA0303, CENPH, and THBS4 genes were in subunit 1; and GHR, NNT, FGF10, ISL1, ITGA1, Ndufs4, and FST genes in subunit 2; and the PRLR, GDNF, and LIFR genes in subunit 3. The gene order was consistent in 3 subunits between chicken and the other 4 species.


Figure 1
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  		Figure 1. A graphical representation of the conserved syntenic regions of human HSA5p14-q13, chimpanzee chromosome 5, rat chromosome 2q16-12, mouse chromosomes 13 (51.0 to 64.0 cm) and 15 (4.6 cm), and chicken GGAZ. Dotted lines indicate that the conserved syntenic region is divided into 3 subunits in terms of internal reversed gene order.

 
A comparative map of the human HSA5q14-p13 and the chicken GGAZp showed, within the 3 subunits, the orthologs gene order was conserved, in spite of completely reverse gene order found in the human chromosome region (Figure 2Go). On the chicken-mouse comparative map (Figure 3Go), 12 chicken orthologous genes (excluding the KIAA0303 gene) were mapped on 2 mouse chromosomes 13 and 15, respectively. Subunit 1 was well preserved but in the reversed direction. Subunit 2 (excluding the GHR gene) was inversely located on mouse chromosome 13. Interestingly, the NNT, FGF10, ISI1, ITGA1, FST, and Ndufs4 loci of subunit 2 on mouse chromosome 13 were in the same order as in the chicken. The GHR gene in the chicken was split from subunit 2 and moved to the mouse chromosome 15 along with PRLR, GDNF, and LIFR genes.


Figure 2
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  		Figure 2. Comparative map of chicken GGAZ aligned with the homologous human chromosome 5 (HSA5). Thirteen human orthologous genes were mapped on the chicken GGAZ, including CENPH, GHR, FST, and PRLR previously reported (Nanda et al., 2000). Gene order within every subunit was conserved, with the exception of gene order within the PRLR-GHR syntenic region, which was not preserved between the chicken GGAZ and human HSA5.

 

Figure 3
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  		Figure 3. Chicken GGAZ–mouse genes synteny comparative map. Twelve chicken orthologous genes (excluding KIAA0303 gene) were mapped on the mouse chromosomes 13 and 15, respectively. Subunit 1 was well conserved in spite of the reversed direction. Subunit 2 (excluding GHR) was inversely located on mouse chromosome 13, subunit 1. The GHR in chicken was shown to be split off from subunit 2, along with PRLR, GDNF, and LIFR, and moved to the mouse chromosome 15.

 
Comparative Mapping of the GHR-PRLR Syntenic Region of GGAZ on Zebrafish Chromosomes

To investigate whether the conserved syntenic region was also conserved in fish, zebrafish genome was studied as an out-group for tracing the ancestral genome structure of avian and mammalian genomes. Figure 4Go shows that 10 chicken orthologous genes were identified in 4 zebrafish linkage groups (LG). Although the GHR and PRLR were located on distinct zebrafish linkage groups (LG8 and LG21), 2 syntenies (THBS4-FST-ISL1-Ndufs4-LIFR and THBS4-FGF10-NNT-PRLR) were identified on zebrafish LG5 and LG21, respectively. Only 2 genes, GHR and GDNF, were located on the LG8 and LG10. In addition, THBS4, GHR, and NNT were not single copy genes. These genes were located on more than 1 position of the zebrafish linkage groups. Zebrafish LG5 and LG21 are thus probably syntenic to chicken GGAZ.


Figure 4
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  		Figure 4. Conserved synteny with chicken GGAZ and the homologous zebrafish linkage groups (LG). The orthologous chicken genes are scattered into 4 zebrafish linkage groups; LG5, LG8, LG10, and LG21. One synteny THBS4-FGF10-NNT-PRLR was localized on the LG21. Another synteny FST-Ndufs4-ISL1-LIFR was mapped on the LG5. Genes GHR and GNDF were identified on the LG 8 and LG 10, respectively.

 

   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
REFERENCES
 
A large conserved synteny of 13 chicken orthologous genes has been identified in the chicken chromosome Z and 5 other species. Although 13 chicken orthologous genes were mapped in the PRLR-GHR syntenic region of human chromosome 5, and more or less orthologous genes in the other 4 species PRLR-GHR syntenic region, the gene order within 3 subunits was conserved in the species examined (excluding zebrafish). In the mouse, probably because of interchromosomal rearrangements, the conserved syntenic region was split and 2 chromosomal regions were found. Nanda et al. (2000) revealed that the homologous region between chicken GGAZ and human HSA9 was mapped into 7 different mouse chromosomes, providing another example for the special nature of gene syntenies in the mouse genome. Therefore, conserved syntenies are more frequently disrupted by interchromosomal rearrangements than by intrachromosomal rearrangements in mice. In contrast to human genome, the mouse genome is highly derived (Burt et al., 1999), probably because of generation time (Laird et al., 1969; Li et al., 1996) or body size (Martin and Palumbi, 1993; Bromham, 2002). Although the conserved syntenic region was interrupted, the gene order was intact within the 2 small syntenic regions. In view of the nearly identical synteny in human, chimpanzee, and rat, the interchromosomal rearrangements in the mouse are inferred to be recent events. As to the difference between the human and chimpanzee, what drives the completely reversed gene arrangement order remains a question. In summary, the extensive orthologous chromosomal regions were generally disrupted by intrachromosomal rearrangements, such as inversions and translocations. Hopefully, the rearrangement history of the chromosomes can be discerned after sufficiently detailed genomes for model organisms become available.

No matter as a branch-end or intermediate species, the chicken is a model to determine an ancestral synteny for mammals. Burt et al. (1999) demonstrated that the number of chromosomal rearrangements between chicken and human is lower, implying that the organization and structure of the chicken genome is closer to the human (Burt et al., 1999). Furthermore, Bourque et al. (2005) revealed that the number of interchromosomal rearrangements that occurred on the evolutionary path from human to chicken is slightly higher than that of interchromosomal rearrangements on the path from human to mouse and rat, implying that the chicken underwent an extremely low rate of interchromosomal rearrangements during the evolutionary path (Bourque et al., 2005). So the chicken, as a model, provides an available opportunity to reconstruct the architecture of the ancestral mammalian synteny. A comparative map of human HSA5p14-q13 and chicken GGAZp showed a translocation within a synteny that can be divided into several subunit syntenic regions. Recently, several analyses revealed a slower rearrangement rate in the chicken lineage (Hillier et al., 2004), suggesting that gene order of chicken syntenies is closer to ancestral status than that of mammalian syntenies. Thus, the present results indicated that at least 3 intrachromosomal rearrangements occurred in mammals during evolution, 2 translocations between subunit 1 and subunit 3, and an orientation inversion within subunit 3. Identification of more genes on GGAZp will allow the identification of more rearrangements. Moreover, the comparative map between chicken and mouse suggested the occurrence of at least 4 intrachromosomal rearrangements and 1 interchromosomal rearrangement. The order inversions of subunit 1, subunit 3, and subunit 2 (excluding GHR) and local inversion of GHR orientation were present in corresponding local regions. This synteny was divided by interchromosomal rearrangement, accounting for its being mapped on different chromosomes. These results supported a closer relationship between the human and chicken than between the human and mouse in terms of gene organization in chromosomes (Burt et al., 1999; Hillier et al., 2004). Taken together, the current study suggested that intrachromosomal rearrangement was more common than interchromosomal rearrangement, although the separated evolution routines between avian and mammals were suggested in a previous report (Hillier et al., 2004). The present comparisons between chicken and the 4 mammalian species indicated that chicken chromosome Z syntenic to human HSA5 p14-q13 might have been conserved for more than 300 million yr.

In addition, 10 chicken orthologous genes were identified in 4 zebrafish linkage groups, in agreement with previous comparative analyses (Groenen et al., 2000; Woods et al., 2000) and hereby suggesting that LG5 and LG21 in zebrafish are highly conserved in evolutionary history from zebrafish to human. Although the PRLR-GHR syntenic region of the chicken Z-orthologs was scattered in zebrafish linkage groups, most chicken Z-orthologs described in the current study were identified on the LG5 and LG21. These data support the hypothesis that LG5 and LG21 are highly conserved in evolutionary history from zebrafish to human and also suggest that syntenies on GGAZp may have originated from the teleosts.

The current study indicated that the syntenic regions between GGAZ and chromosomes of the other 5 species, all with segments of conserved gene order, underwent intrachromosomal rearrangements. Here, the present studies of the PRLR-GHR regional syntenies among 6 species revealed that 2 members of growth hormone-prolacin cytokine receptor superfamily, PRLR and GHR, and unrelated genes were linked together after teleosts. In local chromosome regions, variance in gene orders in syntenies are intriguing and worth further investigation.


   ACKNOWLEDGMENTS
 
The current study was partly funded and supported by Research Grant Council of the Hong Kong Government, HKU7345/03M, Faculty of Science Research Development Fund, and The University of Hong Kong Research Development Fund for Strategic Research Theme on Genomics, Proteomics and Bio-informatics 10206152-11222-21700-302-01. The authors are grateful to P. Y. Wang for revising the manuscript and giving helpful comments.

Received for publication March 15, 2006. Accepted for publication September 21, 2006.


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