ArticleGenome research2016
A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed, 107 citations in OpenAlex.
- Pervasive Positive Selection on X-linked Ampliconic Genes in Primates.Genome biology and evolution · 2026Article
- Genetic diversity of the Y-chromosome in domestic animals: from evolutionary insights to functional implications.Molecular biology reports · 2025Review
- Sex Chromosome Evolution: Hallmarks and Question Marks.Molecular biology and evolution · 2024Review
- Divergent evolution of male-determining loci on proto-Y chromosomes of the housefly.Nature communications · 2024Article
- Article
- Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2024Article
- T2T-YAO: A Telomere-to-telomere Assembled Diploid Reference Genome for Han Chinese.Genomics, proteomics & bioinformatics · 2023Article
- Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.Genome biology and evolution · 2023Article
- Eighty million years of rapid evolution of the primate Y chromosome.Nature ecology & evolution · 2023Article
- Y chromosome sequence and epigenomic reconstruction across human populations.Communications biology · 2023Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups.G3 (Bethesda, Md.) · 2022Article
- Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing.Zoological research · 2022Article
- 3D chromatin remodelling in the germ line modulates genome evolutionary plasticity.Nature communications · 2022Article
- Identification of sex chromosome and sex-determining gene of southern catfish (Proceedings. Biological sciences · 2022Article
- Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.Molecular biology and evolution · 2021Article
- New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion.Human molecular genetics · 2021Article
- Co-opting regulation bypass repair as a gene-correction strategy for monogenic diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2021Article
- 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
5 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.
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