A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing

Abstract It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexi...

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Autores principales:	Shi-Yi Chen, Feilong Deng, Xianbo Jia, Cao Li, Song-Jia Lai
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/09ec89a5d0614355a34fbcde67f375e2
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spelling	oai:doaj.org-article:09ec89a5d0614355a34fbcde67f375e22021-12-02T11:50:55ZA transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing10.1038/s41598-017-08138-z2045-2322https://doaj.org/article/09ec89a5d0614355a34fbcde67f375e22017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08138-zhttps://doaj.org/toc/2045-2322Abstract It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.Shi-Yi ChenFeilong DengXianbo JiaCao LiSong-Jia LaiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shi-Yi Chen Feilong Deng Xianbo Jia Cao Li Song-Jia Lai A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
description	Abstract It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.
format	article
author	Shi-Yi Chen Feilong Deng Xianbo Jia Cao Li Song-Jia Lai
author_facet	Shi-Yi Chen Feilong Deng Xianbo Jia Cao Li Song-Jia Lai
author_sort	Shi-Yi Chen
title	A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
title_short	A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
title_full	A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
title_fullStr	A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
title_full_unstemmed	A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
title_sort	transcriptome atlas of rabbit revealed by pacbio single-molecule long-read sequencing
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/09ec89a5d0614355a34fbcde67f375e2
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A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing

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