RT Journal Article
SR Electronic
T1 Generation and comparative analysis of full-length transcriptomes in sweetpotato and its putative wild ancestor <em>I. trifida</em>
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 112425
DO 10.1101/112425
A1 Yonghai Luo
A1 Na Ding
A1 Xuan Shi
A1 Yunxiang Wu
A1 Ruyuan Wang
A1 Lingquan Pei
A1 Ruoyu Xu
A1 Shuo Cheng
A1 Yongyan Lian
A1 Jingyan Gao
A1 Aimin Wang
A1 Qinghe Cao
A1 Jun Tang
YR 2017
UL http://biorxiv.org/content/early/2017/03/30/112425.abstract
AB Sweetpotato [Ipomoea batatas (L.) Lam.] is one of the most important crops in many developing countries and provides a candidate source of bioenergy. However, neither high-quality reference genome nor large-scale full-length cDNA sequences for this outcrossing hexaploid are still lacking, which in turn impedes progress in research studies in sweetpotato functional genomics and molecular breeding. In this study, we apply a combination of second-and third-generation sequencing technologies to sequence full-length transcriptomes in sweetpotato and its putative ancestor I. trifida. In total, we obtained 53,861/51,184 high-quality transcripts, which includes 34,963/33,637 putative full-length cDNA sequences, from sweetpotato/I. trifida. Amongst, we identified 104,540/94,174 open reading frames, 1476/1475 transcription factors, 25,315/27,090 simple sequence repeats, 417/531 long non-coding RNAs out of the sweetpotato/I. trifida dataset. By utilizing public available genomic contigs, we analyzed the gene features (including exon number, exon size, intron number, intron size, exon-intron structure) of 33,119 and 32,793 full-length transcripts in sweetpotato and I. trifida, respectively. Furthermore, comparative analysis between our transcript datasets and other large-scale cDNA datasets from different plant species enables us assessing the quality of public datasets, estimating the genetic similarity across relative species, and surveyed the evolutionary pattern of genes. Overall, our study provided fundamental resources of large-scale full-length transcripts in sweetpotato and its putative ancestor, for the first time, and would facilitate structural, functional and comparative genomics studies in this important crop.