A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

BMC Genomics

Research Article

Agnelo Furtado¹  Robert J. Henry¹  Patrick J. Mason¹  Nam V. Hoang²  Lakshmi Kasirajan³  Prathima P. Thirugnanasambandam³  Annelie Marquardt⁴  Frederik C. Botha⁴ 

[1] Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, 4072, St. Lucia, QLD, Australia;Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, 4072, St. Lucia, QLD, Australia;College of Agriculture and Forestry, Hue University, Hue, Vietnam;Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, 4072, St. Lucia, QLD, Australia;ICAR - Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, India;Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Room 2.245, Level 2, The John Hay Building, Queensland Biosciences Precinct [#80], 306 Carmody Road, 4072, St. Lucia, QLD, Australia;Sugar Research Australia, 4068, Indooroopilly, QLD, Australia;

关键词: Sugarcane;    Polyploid transcriptome;    Transcriptome assembly;    De novo;    Isoform sequencing;    Hybrid assembly;    SUGIT database;   

DOI  :  10.1186/s12864-017-3757-8

 received in 2016-10-04, accepted in 2017-05-03,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundDespite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum gene indices (SoGI), expressed sequence tags (ESTs) and de novo assembled transcript contigs from short-reads; hence knowledge of the sugarcane transcriptome is limited in relation to transcript length and number of transcript isoforms.ResultsThe sugarcane transcriptome was sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample derived from leaf, internode and root tissues, of different developmental stages, from 22 varieties, to explore the potential for capturing full-length transcript isoforms. A total of 107,598 unique transcript isoforms were obtained, representing about 71% of the total number of predicted sugarcane genes. The majority of this dataset (92%) matched the plant protein database, while just over 2% was novel transcripts, and over 2% was putative long non-coding RNAs. About 56% and 23% of total sequences were annotated against the gene ontology and KEGG pathway databases, respectively. Comparison with de novo contigs from Illumina RNA-Sequencing (RNA-Seq) of the internode samples from the same experiment and public databases showed that the Iso-Seq method recovered more full-length transcript isoforms, had a higher N50 and average length of largest 1,000 proteins; whereas a greater representation of the gene content and RNA diversity was captured in RNA-Seq. Only 62% of PacBio transcript isoforms matched 67% of de novo contigs, while the non-matched proportions were attributed to the inclusion of leaf/root tissues and the normalization in PacBio, and the representation of more gene content and RNA classes in the de novo assembly, respectively. About 69% of PacBio transcript isoforms and 41% of de novo contigs aligned with the sorghum genome, indicating the high conservation of orthologs in the genic regions of the two genomes.ConclusionsThe transcriptome dataset should contribute to improved sugarcane gene models and sugarcane protein predictions; and will serve as a reference database for analysis of transcript expression in sugarcane.

【 授权许可】

CC BY   
© The Author(s). 2017