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
Nam V HoangRobert J Henry

Abstract

Despite 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. The 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 th...Continue Reading

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Citations

Nov 28, 2017·BMC Genomics·Prathima P ThirugnanasambandamRobert J Henry
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Datasets Mentioned

BETA
KU214867

Methods Mentioned

BETA
RNA-Seq
cDNA library construction
PCR

Software Mentioned

BLASTN
OASES
TransAbyss
Velvet
tr2aacds
py
LoRDEC
BUSCO ( Benchmarking Universal Single Orthologs )
Perl script
BLASTP

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