ArticleGenome biology and evolution2021
A Transcriptomic Pipeline Adapted for Genomic Sequence Discovery of Germline-Restricted Sequence in Zebra Finch, Taeniopygia guttata.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed, 14 citations in OpenAlex.
- Article
- Germline organoids develop in vitro from embryonic Taeniopygia guttata (zebra finch) cultures.Scientific reports · 2026Article
- Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species.bioRxiv : the preprint server for biology · 2025Article
- Rapid gene content turnover on the germline-restricted chromosome in songbirds.Nature communications · 2023Article
- Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.Molecular biology and evolution · 2023Article
- An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.Cell reports · 2023Article
- Mendelian nightmares: the germline-restricted chromosome of songbirds.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Songbirds have an unusual genomic element which is only found in their germline cells, known as the germline-restricted chromosome (GRC). Because germ cells contain both GRC and non-GRC (or A-chromosome) sequences, confidently identifying the GRC-derived elements from genome assemblies has proven difficult. Here, we introduce a new application of a transcriptomic method for GRC sequence identification. By adapting the Stringtie/Ballgown pipeline to use somatic and germline DNA reads, we find that the ratio of fragments per kilobase per million mapped reads can be used to confidently assign contigs to the GRC. Using this comparative coverage analysis, we successfully identify 733 contigs as high confidence GRC sequences (720 newly identified in this study) and 51 contigs which were validated using quantitative polymerase chain reaction. We also identified two new GRC genes, one hypothetical protein and one gene encoding an RNase H-like domain, and placed 16 previously identified but unplaced genes onto their host contigs. With the current focus on sequencing GRCs from different songbirds, our work adds to the genomic toolkit to identify GRC elements, and we provide a detailed protocol and GitHub repository at https://github.com/brachtlab/Comparative_Coverage_Analysis (last accessed May 12, 2021).
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