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

Science China(Life Sciences) 2023年第8期66卷 1711-1724页

作者： Yan Yang Xingpeng Wen Zhiguo Wu Kun Wang Yuxian Zhu Institute for Advanced Studies Wuhan UniversityWuhan 430072China College of Life Sciences Wuhan UniversityWuhan 430072China Hubei Hongshan Laboratory Wuhan 430072China TaiKang Center for Life and Medical Sciences RNA InstituteRemin HospitalWuhan UniversityWuhan 430072China

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.

关键词： RNA-seq intergenic transcripts long terminal repeat epigenetic modification nucleosomes

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