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 

作者机构：Institute for Advanced StudiesWuhan UniversityWuhan 430072China College of Life SciencesWuhan UniversityWuhan 430072China Hubei Hongshan LaboratoryWuhan 430072China TaiKang Center for Life and Medical SciencesRNA InstituteRemin HospitalWuhan UniversityWuhan 430072China 

出 版 物：《Science China(Life Sciences)》 (中国科学（生命科学英文版）)

年 卷 期：2023年第66卷第8期

页      面：1711-1724页

核心收录：

学科分类：09[农学] 0901[农学-作物学] 

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) 

主　　题：RNA-seq intergenic transcripts long terminal repeat epigenetic modification nucleosomes 

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 *** genome is occupied by *** 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 *** sequence depths increased from 4 to 100 G,a total of 10,284 novel intergenic transcripts(intergenic genes)were *** 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 *** of these intergenic transcripts possessed no transcription activation markers,while the majority of the regular genic genes possessed at least one such *** 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 *** 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 *** 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 *** characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.