文献类型：期刊文献

英文题名：Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in Camellia

作者：Hu, Zhikang[1,2,3] Lyu, Tao[1,3] Yan, Chao[1,4] Wang, Yupeng[1,2] Ye, Ning[2] Fan, Zhengqi[3] Li, Xinlei[3] Li, Jiyuan[3] Yin, Hengfu[1,3]

第一作者：Hu, Zhikang

通信作者：Yin, HF[1]

机构：[1]Chinese Acad Forestry, Res Inst Subtrop Forestry, State Key Lab Tree Genet & Breeding, Hangzhou, Zhejiang, Peoples R China;[2]Nanjing Forestry Univ, Coll Informat Sci & Technol, Nanjing, Peoples R China;[3]Chinese Acad Forestry, Res Inst Subtrop Forestry, Key Lab Forest Genet & Breeding, Hangzhou, Zhejiang, Peoples R China;[4]Chinese Acad Forestry, Expt Ctr Subtrop Forestry, Fenyi, Jiangxi, Peoples R China

年份：2020

卷号：17

期号：7

起止页码：966-976

外文期刊名：RNA BIOLOGY

收录：;WOS:【SCI-EXPANDED(收录号:WOS:000604471400006)】；

基金：This work was supported by Nonprofit Research Projects (CAFYBB2017SZ001) of Chinese Academy of Forestry, and National Science Foundation of China (NSFC Grant 31870578). We are grateful to two anonymous reviewers for critical comments on this work. And we would like to thank Dr. Y-J Liu of Chinese Academy of Forestry for helpful comments on the bioinformatic analyses.

语种：英文

外文关键词：Alternative splicing; single-molecule sequencing; phased small interfering RNA; polyadenylation; Camellia; lipoxygenase

摘要：Direct single-molecule sequencing of full-length transcripts allows efficient identification of gene isoforms, which is apt to alternative splicing (AS), polyadenylation, and long non-coding RNA analyses. However, the identification of gene isoforms and long non-coding RNAs with novel regulatory functions remains challenging, especially for species without a reference genome. Here, we present a comprehensive analysis of a combined long-read and short-read transcriptome sequencing in Camellia japonica. Through a novel bioinformatic pipeline of reverse-tracing the split-sites, we have uncovered 257,692 AS sites from 61,838 transcripts; and 13,068 AS isoforms have been validated by aligning the short reads. We have identified the tissue-specific AS isoforms along with 6,373 AS events that were found in all tissues. Furthermore, we have analysed the polyadenylation (polyA) patterns of transcripts, and found that the preference for polyA signals was different between the AS and non-AS transcripts. Moreover, we have predicted the phased small interfering RNA (phasiRNA) loci through integrative analyses of transcriptome and small RNA sequencing. We have shown that a newly evolved phasiRNA locus from lipoxygenases generated 12 consecutive 21 bp secondary RNAs, which were responsive to cold and heat stress in Camellia. Our studies of the isoform transcriptome provide insights into gene splicing and functions that may facilitate the mechanistic understanding of plants.