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A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts.

Guyomard R, Boussaha M, Krieg F, Hervet C, Quillet E - BMC Genet. (2012)

Bottom Line: This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM.Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor.Finally, the persistence of large conserved syntenies across teleosts should facilitate the identification of candidate genes through comparative mapping, even if the occurrence of intra-chromosomal micro-rearrangement may hinder the accurate prediction their genomic location.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR1313, Animal Genetics and Integrative Biology, Domaine de Vilvert, 78350 Jouy-en-Josas, France. rene.guyomard@jouy.inra.fr

ABSTRACT

Background: Rainbow trout is an economically important fish and a suitable experimental organism in many fields of biology including genome evolution, owing to the occurrence of a salmonid specific whole-genome duplication (4th WGD). Rainbow trout is among some of the most studied teleosts and has benefited from substantial efforts to develop genomic resources (e.g., linkage maps. Here, we first generated a synthetic map by merging segregation data files derived from three independent linkage maps. Then, we used it to evaluate genome conservation between rainbow trout and three teleost models, medaka, stickleback and zebrafish and to further investigate the extent of the 4th WGD in trout genome.

Results: The INRA linkage map was updated by adding 211 new markers. After standardization of marker names, consistency of marker assignment to linkage groups and marker orders was checked across the three different data sets and only loci showing consistent location over all or almost all of the data sets were kept. This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM. Blastn searches against medaka, stickleback, and zebrafish genomic databases resulted in 778, 824 and 730 significant hits respectively while blastx searches yielded 505, 513 and 510 significant hits. Homology search results revealed that, for most rainbow trout chromosomes, large syntenic regions encompassing nearly whole chromosome arms have been conserved between rainbow trout and its closest models, medaka and stickleback. Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor. These syntenies consolidated the known homeologous affinities between rainbow trout chromosomes due to the 4th WGD and suggested new ones.

Conclusions: The synthetic map constructed herein further highlights the stability of the teleost genome over long evolutionary time scales. This map can be easily extended by incorporating new data sets and should help future rainbow trout whole genome sequence assembly. Finally, the persistence of large conserved syntenies across teleosts should facilitate the identification of candidate genes through comparative mapping, even if the occurrence of intra-chromosomal micro-rearrangement may hinder the accurate prediction their genomic location.

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Graphic representation of evolutionary relationships between rainbow trout chromosome arms and teleost ancestor proto-chromosomes. In lines 1 and 2 (top to bottom), rainbow trout chromosome arms are arranged in identified homeologous pairs. In line 3 (bottom), chromosome arm pairing is based on putative homeologies (see text). Teleost ancestor proto-chromosome names and colours are the same as in [12].
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Figure 3: Graphic representation of evolutionary relationships between rainbow trout chromosome arms and teleost ancestor proto-chromosomes. In lines 1 and 2 (top to bottom), rainbow trout chromosome arms are arranged in identified homeologous pairs. In line 3 (bottom), chromosome arm pairing is based on putative homeologies (see text). Teleost ancestor proto-chromosome names and colours are the same as in [12].

Mentions: Finally, since medaka has not undergone any major interchromosomal rearrangement after those occurred in the teleost ancestor, we used the chromosome affinities found between medaka and the reconstructed teleost ancestor genome [12] to recover the contribution of this teleost ancestor to the rainbow trout chromosome arms. Twenty chromosome arms, out of 52, were traced back to only one ancestral chromosome (Figure 3; Additional file 6, sheet 2; column H). In contrast, Omy7p(RT12), Omy18p(RT16) and Omy17q(RT29) were assemblages of 4 and 5 fragments of ancestor chromosomes (Figure 3; Additional file 6, sheet 2; column H)


A synthetic rainbow trout linkage map provides new insights into the salmonid whole genome duplication and the conservation of synteny among teleosts.

Guyomard R, Boussaha M, Krieg F, Hervet C, Quillet E - BMC Genet. (2012)

Graphic representation of evolutionary relationships between rainbow trout chromosome arms and teleost ancestor proto-chromosomes. In lines 1 and 2 (top to bottom), rainbow trout chromosome arms are arranged in identified homeologous pairs. In line 3 (bottom), chromosome arm pairing is based on putative homeologies (see text). Teleost ancestor proto-chromosome names and colours are the same as in [12].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368724&req=5

Figure 3: Graphic representation of evolutionary relationships between rainbow trout chromosome arms and teleost ancestor proto-chromosomes. In lines 1 and 2 (top to bottom), rainbow trout chromosome arms are arranged in identified homeologous pairs. In line 3 (bottom), chromosome arm pairing is based on putative homeologies (see text). Teleost ancestor proto-chromosome names and colours are the same as in [12].
Mentions: Finally, since medaka has not undergone any major interchromosomal rearrangement after those occurred in the teleost ancestor, we used the chromosome affinities found between medaka and the reconstructed teleost ancestor genome [12] to recover the contribution of this teleost ancestor to the rainbow trout chromosome arms. Twenty chromosome arms, out of 52, were traced back to only one ancestral chromosome (Figure 3; Additional file 6, sheet 2; column H). In contrast, Omy7p(RT12), Omy18p(RT16) and Omy17q(RT29) were assemblages of 4 and 5 fragments of ancestor chromosomes (Figure 3; Additional file 6, sheet 2; column H)

Bottom Line: This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM.Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor.Finally, the persistence of large conserved syntenies across teleosts should facilitate the identification of candidate genes through comparative mapping, even if the occurrence of intra-chromosomal micro-rearrangement may hinder the accurate prediction their genomic location.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR1313, Animal Genetics and Integrative Biology, Domaine de Vilvert, 78350 Jouy-en-Josas, France. rene.guyomard@jouy.inra.fr

ABSTRACT

Background: Rainbow trout is an economically important fish and a suitable experimental organism in many fields of biology including genome evolution, owing to the occurrence of a salmonid specific whole-genome duplication (4th WGD). Rainbow trout is among some of the most studied teleosts and has benefited from substantial efforts to develop genomic resources (e.g., linkage maps. Here, we first generated a synthetic map by merging segregation data files derived from three independent linkage maps. Then, we used it to evaluate genome conservation between rainbow trout and three teleost models, medaka, stickleback and zebrafish and to further investigate the extent of the 4th WGD in trout genome.

Results: The INRA linkage map was updated by adding 211 new markers. After standardization of marker names, consistency of marker assignment to linkage groups and marker orders was checked across the three different data sets and only loci showing consistent location over all or almost all of the data sets were kept. This resulted in a synthetic map consisting of 2226 markers and 29 linkage groups spanning over 3600 cM. Blastn searches against medaka, stickleback, and zebrafish genomic databases resulted in 778, 824 and 730 significant hits respectively while blastx searches yielded 505, 513 and 510 significant hits. Homology search results revealed that, for most rainbow trout chromosomes, large syntenic regions encompassing nearly whole chromosome arms have been conserved between rainbow trout and its closest models, medaka and stickleback. Large conserved syntenies were also found between the genomes of rainbow trout and the reconstructed teleost ancestor. These syntenies consolidated the known homeologous affinities between rainbow trout chromosomes due to the 4th WGD and suggested new ones.

Conclusions: The synthetic map constructed herein further highlights the stability of the teleost genome over long evolutionary time scales. This map can be easily extended by incorporating new data sets and should help future rainbow trout whole genome sequence assembly. Finally, the persistence of large conserved syntenies across teleosts should facilitate the identification of candidate genes through comparative mapping, even if the occurrence of intra-chromosomal micro-rearrangement may hinder the accurate prediction their genomic location.

Show MeSH
Related in: MedlinePlus