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基因组德尔塔：无需重复序列文库检测近期转座元件入侵

GenomeDelta: detecting recent transposable element invasions without repeat library.

作者信息

Pianezza Riccardo, Haider Anna, Kofler Robert

机构信息

Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.

Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria.

出版信息

Genome Biol. 2024 Dec 18;25(1):315. doi: 10.1186/s13059-024-03459-5.

DOI:10.1186/s13059-024-03459-5
PMID:39696539
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11656972/
Abstract

We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assemblies with short-read data to detect sequences absent from the short reads. It is applicable to both model and non-model organisms and can identify recent TE invasions, spatially heterogeneous sequences, viral insertions, and hotizontal gene transfers. GenomeDelta was validated with simulated and real data and used to discover three recent TE invasions in Drosophila melanogaster and a novel TE with geographic variation in Zymoseptoria tritici.

摘要

我们展示了GenomeDelta，这是一种用于识别样本特异性序列（如近期转座元件（TE）入侵）的新型工具，无需重复序列库。GenomeDelta将高质量组装序列与短读长数据进行比较，以检测短读长中不存在的序列。它适用于模式生物和非模式生物，可识别近期的TE入侵、空间异质序列、病毒插入和水平基因转移。GenomeDelta通过模拟数据和真实数据进行了验证，并用于发现黑腹果蝇中近期的三次TE入侵以及小麦黄斑叶枯病菌中一种具有地理变异的新型TE。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/37ad2c16dea6/13059_2024_3459_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/8a854543ffa0/13059_2024_3459_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/3115c3988ac9/13059_2024_3459_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/37ad2c16dea6/13059_2024_3459_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/8a854543ffa0/13059_2024_3459_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/3115c3988ac9/13059_2024_3459_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/58cd/11656972/37ad2c16dea6/13059_2024_3459_Fig3_HTML.jpg

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本文引用的文献

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Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s.Spoink，一种长末端重复序列转座子，于 20 世纪 90 年代入侵了 D. melanogaster 种群。
PLoS Genet. 2024 Mar 26;20(3):e1011201. doi: 10.1371/journal.pgen.1011201. eCollection 2024 Mar.
3
Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences.
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Mol Biol Evol. 2023 Nov 3;40(11). doi: 10.1093/molbev/msad243.
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Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution.来自历史上的黑腹果蝇标本的基因组揭示了超过 200 年的进化过程中适应性和人口变化。
PLoS Biol. 2023 Oct 12;21(10):e3002333. doi: 10.1371/journal.pbio.3002333. eCollection 2023 Oct.
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Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species.快速进化的多样性在 simulans 类群的果蝇种中 flamenco 基因座。
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