Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton  

作　　者：Yan Yang Xingpeng Wen Zhiguo Wu Kun Wang Yuxian Zhu 

机构地区：[1]Institute for Advanced Studies,Wuhan University,Wuhan 430072,China [2]College of Life Sciences,Wuhan University,Wuhan 430072,China [3]Hubei Hongshan Laboratory,Wuhan 430072,China [4]TaiKang Center for Life and Medical Sciences,RNA Institute,Remin Hospital,Wuhan University,Wuhan 430072,China

出　　处：《Science China(Life Sciences)》2023年第8期1711-1724,共14页中国科学（生命科学英文版）

基　　金：supported by the National Key Research and Development Program of China(2022YFF1001400);the National Natural Science Foundation of China(31690090,32200286,32070207);Foundation of Hubei Hongshan Laboratory(2021hszd014);Hubei Provincial Natural Science Foundation of China(2021CFA055,2021BBA102);the China Postdoctoral Science Foundation(2022TQ0240,2022M722470)。

摘　　要：Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81%transposable elements(TEs),while only 57%of the 735-Mb G.raimondii genome is occupied by TEs.In this study,we investigated whether there were unknown transcripts associated with TE or TE fragments and,if so,how these new transcripts were evolved and regulated.As sequence depths increased from 4 to 100 G,a total of 10,284 novel intergenic transcripts(intergenic genes)were discovered.On average,approximately 84%of these intergenic transcripts possibly overlapped with the long terminal repeat(LTR)insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels.Most of these intergenic transcripts possessed no transcription activation markers,while the majority of the regular genic genes possessed at least one such marker.Genes without transcription activation markers formed their+1 and-1 nucleosomes more closely(only(117±1.4)bp apart),while twice as big spaces(approximately(403.5±46.0)bp apart)were detected for genes with the activation markers.The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content.Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7million years ago(MYA)for all eudicot genomes or 13.7 MYA for the Gossypium family,respectively,while the intergenic transcripts evolved around 1.6 MYA,resultant of the last LTR insertion.The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.

关 键 词：RNA-SEQ intergenic transcripts long terminal repeat epigenetic modification NUCLEOSOMES 

分 类 号：S562[农业科学—作物学]