ArticleGenome biology and evolution2015
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 44 citations in OpenAlex.
- Diverging transposon activity among polar bear sub-populations inhabiting different climate zones.Mobile DNA · 2025Article
- Linking Measures of Inbreeding and Genetic Load to Demographic Histories Across Three Species of Bears.Evolutionary applications · 2025Article
- Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas.Immunogenetics · 2024Article
- Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha.G3 (Bethesda, Md.) · 2024Article
- A Beary Good Genome: Haplotype-Resolved, Chromosome-Level Assembly of the Brown Bear (Ursus arctos).Genome biology and evolution · 2022Article
- A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication.Science China. Life sciences · 2021Article
- The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat.Ecology and evolution · 2021Article
- Article
- Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals.Genome biology and evolution · 2020Article
- Review
- Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction.BMC genomics · 2020Article
- Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing.Scientific reports · 2020Article
- Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas.Science advances · 2020Article
- The firstGigaByte (Hong Kong, China) · 2020Article
- The Red Fox Y-Chromosome in Comparative Context.Genes · 2019Article
- The evolutionary history of grey wolf Y chromosomes.Molecular ecology · 2019Article
- The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.Current biology : CB · 2018Article
- New WGS data and annotation of the heterosomalData in brief · 2018Article
- Deep Sequencing of Fosmid Clones Indicates Gene Conversion in the Male-Specific Region of the Giant Panda Y Chromosome.Genome biology and evolution · 2018Article
- Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial.Molecular biology and evolution · 2018Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The male-inherited Y chromosome is the major haploid fraction of the mammalian genome, rendering Y-linked sequences an indispensable resource for evolutionary research. However, despite recent large-scale genome sequencing approaches, only a handful of Y chromosome sequences have been characterized to date, mainly in model organisms. Using polar bear (Ursus maritimus) genomes, we compare two different in silico approaches to identify Y-linked sequences: 1) Similarity to known Y-linked genes and 2) difference in the average read depth of autosomal versus sex chromosomal scaffolds. Specifically, we mapped available genomic sequencing short reads from a male and a female polar bear against the reference genome and identify 112 Y-chromosomal scaffolds with a combined length of 1.9 Mb. We verified the in silico findings for the longer polar bear scaffolds by male-specific in vitro amplification, demonstrating the reliability of the average read depth approach. 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. 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.
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