Identification of a genome-specific repetitive element in the Gossypium D genome
Identification of a genome-specific repetitive element in the Gossypium D genome
复制标题
鉴定棉属 D 基因组中基因组特异性重复元件
DOI：
10.7717/peerj.8344
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发表时间：
2020-01-03
期刊：
影响因子：
2.7
通讯作者：
Liu，Fang
中科院分区：
文献类型：
--
作者：
Lu，Hejun;Cui，Xinglei;Liu，Fang
基因组特异性重复序列的活性是棉属A、D基因组间基因组变异的主要原因。通过对两个基因组的比较分析，我们发现了一个在二倍体雷蒙棉（Gossypium raimondii，D5）基因组中频繁出现而在二倍体亚洲棉（Gossypium arboreum，A2）基因组中很少出现的重复元件ICRd motif。进一步探讨了G. raimondii，G.利用荧光原位杂交（FISH）技术对亚洲棉（Gossypium arboreum）和陆地棉（Gossypium hirsutum）、海岛棉（Gossypium barbadense）两个四倍体（AADD）棉花品种的DNA序列进行分析，发现ICRd基序存在于D5和D亚基因组中，而不存在于A2和A亚基因组中。ICRd基序包括两个组成部分，可变串联重复（TR）区域和保守序列（CS）。这两种成分各有数百个重复，均匀分布在D5基因组的13条染色体上。ICRd基序（及其重复序列）被揭示为古老的长末端重复逆转录转座子所共有的保守区域。ICRd基序的鉴定和研究将促进棉花A、D基因组差异的研究，促进棉花基因组进化的研究，并为亚基因组鉴定和基因组组装提供帮助。
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.