De novo sequencing and transcriptome analysis of a low temperature tolerant Saccharum spontaneum clone IND 00-1037

Dharshini, S. Akila Parvathy; Mohan, Chakravarthi; Narayan, Jitendra; Manoj, V. M.; Murugan, Naveenarani; Kumar, Ravinder; Ram, Bakshi; Appunu, C.

doi:10.1016/j.jbiotec.2016.05.036

Cited by 43 publications

(24 citation statements)

References 27 publications

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“…The comparative analysis with the de novo assembled contigs from Illumina RNA-Seq reads, allowed us to evaluate the benefits of each of the assemblies in constructing the sugarcane transcriptome. The short-reads from the Illumina platform have been used widely for RNA-Seq differential gene expression analysis [21, 22, 44] since it provides sufficient depth and a lower error rate compared to reads generated from PacBio. However, due to the complexity of the alternative spicing mechanism of eukaryotic cells, recovering full-length transcripts has been a challenge for most of the assemblers using short reads, such as Trinity, SOAPdenovo-Trans or Velvet/OASES.…”

Section: Discussionmentioning

confidence: 99%

“…The transcriptome sequences obtained from second generation sequencing technology (i.e. Illumina RNA-Sequencing, RNA-Seq) have been playing an important role in capturing the diversity in the RNA populations at a greater sequencing depth [10, 21, 22]. However, a precise prediction and identification of the alternative transcript splicing has not been possible.…”

Section: Introductionmentioning

confidence: 99%

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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

et al. 2017

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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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3757-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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“…In addition, expressions of DREB1/CBF, WRKY, and bHLH as well as other TF genes are induced in S. spontaneum when exposed to lowtemperature conditions (Selvarajan et al, 2018). Furthermore, 2,583 and 3,302 genes in S. spontaneum were reported to be up-and downregulated, respectively, during cold stress, including a DREB2 gene with eightfold upregulation (Dharshini et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses

et al. 2020

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Drought and cold stresses are the main environmental factors that affect the yield of sugarcane, and DREB genes play very important roles in tolerance to drought, cold, and other environmental stresses. In this study, bioinformatics analysis was performed to characterize Saccharum spontaneum SsDREB genes. RNA sequencing (RNA-seq) was used to detect the expression profiles of SsDREBs induced by cold and drought stresses. According to our results, there are 110 SsDREB subfamily proteins in S. spontaneum, which can be classified into six groups; 106 of these genes are distributed among 29 chromosomes. Inter-and intraspecies synteny analyses suggested that all DREB groups have undergone gene duplication, highlighting the polyploid events that played an important role in the expansion of the DREB subfamily. Furthermore, RNA-seq results showed that 45 SsDREBs were up-or downregulated under cold stress; 35 of them were found to be involved in responding to drought stress. According to protein-protein interaction analysis, SsDREB100, SsDREB102, and SsDREB105 play key roles during the response to cold stress. These results reveal that functional divergence exists between collinear homologous genes or among common origin genes in the DREB subfamily of S. spontaneum. This study presents a comprehensive analysis and systematic understanding of the precise mechanism of SsDREBs in response to abiotic stress and will lead to improvements in sugarcane.

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“…Previous studies of the sugarcane transcriptome have employed expressed sequence tag (EST) sequencing, and more recently Next Generation Sequencing (NGS). NGS has been applied for sugarcane transcriptomic study using second-generation sequencing platforms ( Cardoso-Silva et al, 2014 ; Dharshini et al, 2016 ; Huang et al, 2016 ; Li et al, 2016 ; Nishiyama Jr et al., 2014 ; Schaker et al, 2016 ; Vicentini et al, 2015 ). Second-generation sequencing of RNA (RNA-Seq) produces short sequence reads (<1,000 nt).…”

Section: Introductionmentioning

confidence: 99%

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

Piriyapongsa

Kaewprommal

Vaiwsri

et al. 2018

PeerJ

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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.

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De novo sequencing and transcriptome analysis of a low temperature tolerant Saccharum spontaneum clone IND 00-1037

Cited by 43 publications

References 27 publications

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

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

Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses

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

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