Comparative analysis of Aegilops speltoides and wheat repetitive elements and development of S genome-specific FISH painting.

IF 2.3 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Genome Pub Date : 2025-01-01 DOI:10.1139/gen-2024-0090
Tatiana V Danilova, Alina R Akhunova, Xiwen Cai
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引用次数: 0

Abstract

Aegilops speltoides (2n = 2x = 14, genome SS) is a wild relative of wheat and a donor of useful traits for wheat improvement. Several whole-genome studies compared genic regions of Aegilops from the Sitopsis section and wheat and found that Ae. speltoides is most closely related to the wheat B subgenome but is not its direct progenitor. The results showed that a B subgenome ancestor diverged from Ae. speltoides more than 4 MYA and either has not yet been discovered, or is extinct. To further explore the evolutionary relationship between wheat and Ae. speltoides and develop Ae. speltoides chromosome paints, we performed comparative analysis of repetitive fractions of the S genome and three subgenomes of hexaploid wheat. The low-coverage sequence data were analyzed with RepeatExplorer pipeline to annotate repeats and estimate their content. The LTR-retrotransposons comprised about 80% of repeats in Ae. speltoides and wheat datasets and about two-third of them were LTR/Ty3-Gypsy. Ae. speltoides had 1.5 times more LTR/Ty-Copia repeats and 1.5 times less DNA transposons than wheat subgenomes. Several S genome-specific dispersed repeats were found and annotated. Their sequences were used to develop S genome-specific paints for detecting Ae. speltoides chromatin in the wheat background using fluorescent in situ hybridization.

峨眉与小麦重复元件的比较分析及S基因组特异性FISH图谱的建立。
speltoides (2n=2x=14,基因组SS)是小麦的野生近缘种质,是小麦改良有用性状的供体。几项全基因组研究比较了来自Sitopsis切片和小麦的Aegilops基因区域,发现Ae。speltoides与小麦B亚基因组关系最密切,但不是其直接祖先。结果表明,B亚基因组的祖先是从伊蚊中分化出来的。speltoides的存在时间超过4000万年,要么尚未被发现,要么已经灭绝。为进一步探讨小麦与伊蚊的进化关系。蛭形和发育Ae。本文对小麦六倍体S基因组和3个亚基因组的重复部分进行了比较分析。利用RepeatExplorer管道对低覆盖率序列数据进行分析,对重复序列进行标注并估计其内容。ltr -逆转录转座子约占Ae中重复序列的80%。其中约三分之二为LTR/Ty3-Gypsy。Ae。与小麦亚基因组相比,speltoides的LTR/Ty-Copia重复数多1.5倍,DNA转座子数少1.5倍。发现了几个S基因组特异性的分散重复序列并进行了注释。他们的序列被用来开发S基因组特异性涂料用于检测Ae。利用荧光原位杂交技术研究小麦背景下的Speltoides染色质。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome
Genome 生物-生物工程与应用微生物
CiteScore
5.30
自引率
3.20%
发文量
42
审稿时长
6-12 weeks
期刊介绍: Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.
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