Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing

PeerJ

article

Jittima Piriyapongsa¹  Pavita Kaewprommal¹  Sirintra Vaiwsri¹  Songtham Anuntakarun¹  Warodom Wirojsirasak²  Prapat Punpee²  Peeraya Klomsa-ard²  Philip J. Shaw¹  Wirulda Pootakham¹  Thippawan Yoocha¹  Duangjai Sangsrakru¹  Sithichoke Tangphatsornruang¹  Sissades Tongsima¹  Somvong Tragoonrung¹ 

[1] National Center for Genetic Engineering and Biotechnology ,(BIOTEC), National Science and Technology Development Agency;Mitr Phol Sugarcane Research Center Co., Ltd.

关键词: Sugarcane;    Full-length transcripts;    Transcriptome;    Single-molecule long-read sequencing;    Iso-Seq;    PacBio sequencing;    Khon Kaen 3;    KK3;   

DOI  :  10.7717/peerj.5818

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundSugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for sugarcane were generated using second-generation sequencing platforms, which provide short reads. The de novo assembled transcripts from these data are limited in length, and hence may be incomplete and inaccurate, especially for long RNAs.MethodsWe generated a transcriptome dataset of leaf tissue from a commercial Thai sugarcane cultivar Khon Kaen 3 (KK3) using PacBio RS II single-molecule long-read sequencing by the Iso-Seq method. Short-read RNA-Seq data were generated from the same RNA sample using the Ion Proton platform for reducing base calling errors.ResultsA total of 119,339 error-corrected transcripts were generated with the N50 length of 3,611 bp, which is on average longer than any previously reported sugarcane transcriptome dataset. 110,253 sequences (92.4%) contain an open reading frame (ORF) of at least 300 bp long with ORF N50 of 1,416 bp. The mean lengths of 5′ and 3′ untranslated regions in 73,795 sequences with complete ORFs are 1,249 and 1,187 bp, respectively. 4,774 transcripts are putatively novel full-length transcripts which do not match with a previous Iso-Seq study of sugarcane. We annotated the functions of 68,962 putative full-length transcripts with at least 90% coverage when compared with homologous protein coding sequences in other plants.DiscussionThe new catalog of transcripts will be useful for genome annotation, identification of splicing variants, SNP identification, and other research pertaining to the sugarcane improvement program. The putatively novel transcripts suggest unique features of KK3, although more data from different tissues and stages of development are needed to establish a reference transcriptome of this cultivar.

【 授权许可】

CC BY