Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.
Bottom Line: The obtained Y chromosome sequences contain protein-coding sequences, single nucleotide polymorphisms, microsatellites, and transposable elements that are useful for evolutionary studies.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.Thus, the identification of Y-linked scaffold sequences from unordered genome sequences yields valuable data to infer phylogenomic and population-genomic patterns in bears.
Affiliation: Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany International Graduate School of Science and Engineering (IGSSE), Technische UniversitÃ¤t MÃ¼nchen, Garching, Germany.Show MeSH
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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.â€”
Affiliation: Senckenberg Biodiversity and Climate Research Centre Frankfurt, Frankfurt am Main, Germany International Graduate School of Science and Engineering (IGSSE), Technische UniversitÃ¤t MÃ¼nchen, Garching, Germany.