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Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

Bidon T, Schreck N, Hailer F, Nilsson MA, Janke A - Genome Biol Evol (2015)

Bottom Line: A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes.Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears.Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.

View Article: PubMed Central - PubMed

Affiliation: Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany International Graduate School of Science and Engineering (IGSSE), Technische Universität München, Garching, Germany.

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Identified scaffolds in the polar bear assembly. (A) Scaffolds identified by the similarity search, the AD-ratio, and by both approaches (overlap). Scaffolds ≥10 kb are shown by their ID numbers. Details for 92 additionally Y-linked scaffolds (<10 kb, combined length: ∼170 kb) are listed in supplementary table S2, Supplementary Material online. Some scaffolds identified by the similarity search showed AD-ratio characteristic of autosomal linkage (red) or X-linkage (blue). Scaffolds with an asterisk (*) have been verified in vitro to be male-specific. Two asterisks indicate scaffolds that show PCR amplification in both sexes. No reads mapped with sufficient mapping quality to scaffold 4889, so its AD-ratio could not be calculated, and scaffold 6612 was shorter than 1 kb. (B) AD-ratios of X-linked (blue), autosomal (red), and Y-linked (green) scaffolds.
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evv103-F1: Identified scaffolds in the polar bear assembly. (A) Scaffolds identified by the similarity search, the AD-ratio, and by both approaches (overlap). Scaffolds ≥10 kb are shown by their ID numbers. Details for 92 additionally Y-linked scaffolds (<10 kb, combined length: ∼170 kb) are listed in supplementary table S2, Supplementary Material online. Some scaffolds identified by the similarity search showed AD-ratio characteristic of autosomal linkage (red) or X-linkage (blue). Scaffolds with an asterisk (*) have been verified in vitro to be male-specific. Two asterisks indicate scaffolds that show PCR amplification in both sexes. No reads mapped with sufficient mapping quality to scaffold 4889, so its AD-ratio could not be calculated, and scaffold 6612 was shorter than 1 kb. (B) AD-ratios of X-linked (blue), autosomal (red), and Y-linked (green) scaffolds.

Mentions: The first approach identified scaffolds in the polar bear assembly that showed similarity to known Y-linked gene sequences from four different mammals (human, mouse, chimpanzee, and dog). Exons from 18 of 32 Y-linked candidate genes that were blasted against the polar bear assembly identified polar bear scaffold sequences above a threshold of 80% identity (table 1 and supplementary table S1, Supplementary Material online). The hits were distributed across 23 scaffolds, ranging from 0.7 to 26,707 kb in size (table 1 and fig. 1). The full sequence length of scaffold 3836 (1,069 bp) had an identical sequence stretch on scaffold 318 (237 kb), with no nucleotide mismatches. Thus, we do not report scaffold 3836 as a distinct scaffold, although it is a separate entry in the current polar bear assembly.Fig. 1.—


Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.

Bidon T, Schreck N, Hailer F, Nilsson MA, Janke A - Genome Biol Evol (2015)

Identified scaffolds in the polar bear assembly. (A) Scaffolds identified by the similarity search, the AD-ratio, and by both approaches (overlap). Scaffolds ≥10 kb are shown by their ID numbers. Details for 92 additionally Y-linked scaffolds (<10 kb, combined length: ∼170 kb) are listed in supplementary table S2, Supplementary Material online. Some scaffolds identified by the similarity search showed AD-ratio characteristic of autosomal linkage (red) or X-linkage (blue). Scaffolds with an asterisk (*) have been verified in vitro to be male-specific. Two asterisks indicate scaffolds that show PCR amplification in both sexes. No reads mapped with sufficient mapping quality to scaffold 4889, so its AD-ratio could not be calculated, and scaffold 6612 was shorter than 1 kb. (B) AD-ratios of X-linked (blue), autosomal (red), and Y-linked (green) scaffolds.
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Related In: Results  -  Collection

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evv103-F1: Identified scaffolds in the polar bear assembly. (A) Scaffolds identified by the similarity search, the AD-ratio, and by both approaches (overlap). Scaffolds ≥10 kb are shown by their ID numbers. Details for 92 additionally Y-linked scaffolds (<10 kb, combined length: ∼170 kb) are listed in supplementary table S2, Supplementary Material online. Some scaffolds identified by the similarity search showed AD-ratio characteristic of autosomal linkage (red) or X-linkage (blue). Scaffolds with an asterisk (*) have been verified in vitro to be male-specific. Two asterisks indicate scaffolds that show PCR amplification in both sexes. No reads mapped with sufficient mapping quality to scaffold 4889, so its AD-ratio could not be calculated, and scaffold 6612 was shorter than 1 kb. (B) AD-ratios of X-linked (blue), autosomal (red), and Y-linked (green) scaffolds.
Mentions: The first approach identified scaffolds in the polar bear assembly that showed similarity to known Y-linked gene sequences from four different mammals (human, mouse, chimpanzee, and dog). Exons from 18 of 32 Y-linked candidate genes that were blasted against the polar bear assembly identified polar bear scaffold sequences above a threshold of 80% identity (table 1 and supplementary table S1, Supplementary Material online). The hits were distributed across 23 scaffolds, ranging from 0.7 to 26,707 kb in size (table 1 and fig. 1). The full sequence length of scaffold 3836 (1,069 bp) had an identical sequence stretch on scaffold 318 (237 kb), with no nucleotide mismatches. Thus, we do not report scaffold 3836 as a distinct scaffold, although it is a separate entry in the current polar bear assembly.Fig. 1.—

Bottom Line: A high-resolution phylogeny of the polar bear patriline shows two highly divergent Y chromosome lineages, obtained from analysis of the identified Y scaffolds in 12 previously published male polar bear genomes.Moreover, we find evidence of gene conversion among ZFX and ZFY sequences in the giant panda lineage and in the ancestor of ursine and tremarctine bears.Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.

View Article: PubMed Central - PubMed

Affiliation: Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany International Graduate School of Science and Engineering (IGSSE), Technische Universität München, Garching, Germany.

Show MeSH