Transcriptome of High-Sucrose Sugarcane Variety GT35

Huang, Dongliang; Gao, Yurong; Gui, Yiyun; Chen, Zhongliang; Qin, Cui-Xian; Wang, Miao; Liao, Qing; Yang, Li‐Tao; Li, Yang–Rui

doi:10.1007/s12355-015-0420-z

Cited by 30 publications

(18 citation statements)

References 49 publications

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“…The average length and N50 of the assembled unigenes was higher than those observed for S . spontaneum (801 bp and 1,337 bp) and sugarcane variety GT35 (460 bp and 640 bp) using similar sequencing technologies 21 , 22 , demonstrating the high quality of our sugarcane transcriptomic sequences. In total, more than 43,308 unigenes (46.51%) were over 500 bp in length, 25,486 (27.37%) over 1,000 bp, and 12,278 (13.19%) longer than 2,000 bp (Table 1 ).…”

Section: Resultsmentioning

confidence: 73%

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

Wang

Shang

et al. 2018

Sci Rep

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Sugarcane (Saccharum officinarum L.) is an important crop for sugar production and bioenergy worldwide. In this study, we performed transcriptome sequencing for six contrasting sugarcane genotypes involved in leaf abscission, tolerance to pokkah boeng disease and drought stress. More than 465 million high-quality reads were generated, which were de novo assembled into 93,115 unigenes. Based on a similarity search, 43,526 (46.74%) unigenes were annotated against at least one of the public databases. Functional classification analyses showed that these unigenes are involved in a wide range of metabolic pathways. Comparative transcriptome analysis revealed that many unigenes involved in response to abscisic acid and ethylene were up-regulated in the easy leaf abscission genotype, and unigenes associated with response to jasmonic acid and salicylic acid were up-regulated in response to the pokkah boeng disease in the tolerance genotype. Moreover, unigenes related to peroxidase, antioxidant activity and signal transduction were up-regulated in response to drought stress in the tolerant genotype. Finally, we identified a number of putative markers, including 8,630 simple sequence repeats (SSRs) and 442,152 single-nucleotide polymorphisms (SNPs). Our data will be important resources for future gene discovery, molecular marker development, and genome studies in sugarcane.

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Section: Resultsmentioning

confidence: 73%

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

Wang

Shang

et al. 2018

Sci Rep

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“…The deltaCt method [ 26 ] describes the ΔCt approach, which requires less use of specialist programs and biomaterials by comparing pairs of candidate genes [ 8 ]. With increasing demand for sugarcane production, a growing number of RNA-seq trials have been conducted to identify genes that are associated with specific biological processes such as sugar accumulation [ 33 ], fiber content [ 34 ], and stress responses [ 3 , 4 , 23 – 25 ]. Smut disease, which is caused by Sporisorium scitamineum , is one of the major fungal affecting sugarcane growth, often resulting in a 3%–7% reduction in sugar content [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system

et al. 2018

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BackgroundSugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the normalization of data on gene expression involving the sugarcane-S. scitamineum interaction system; however, no report that addresses criteria in selecting these reference genes has been published to date.ResultsIn this study, 10 sugarcane genes and eight S. scitamineum genes were selected as candidate PCR reference genes in the sugarcane-S. scitamineum interaction system. The stability and reliability of these 18 candidate genes were analyzed in smut-resistant (NCo376) and -susceptible (YC71–374) genotypes using the statistical algorithms geNorm, NormFinder, BestKeeper, and deltaCt method. Subsequently, the relative expression levels of the sugarcane chitinase I-3 gene and S. scitamineum chorismate mutase gene were determined to validate the applicability of these sugarcane and S. scitamineum PCR reference genes, respectively. We finally found that the acyl-CoA dehydrogenase gene (ACAD), serine/arginine repetitive matrix protein 1 gene (SARMp1), or their combination (ACAD + SARMp1) could be utilized as the most suitable reference genes for normalization of sugarcane gene expression in sugarcane bud tissues after S. scitamineum infection. Similarly, the inosine 5′-monophosphate dehydrogenase gene (S10), the SEC65-signal recognition particle subunit gene (S11), or their combination (S10 + S11) were suitable for normalization of S. scitamineum gene expression in sugarcane bud tissues.ConclusionsThe PCR reference genes ACAD, SARMp1, S10, and S11 may be employed in gene transcriptional studies involving the sugarcane-S. scitamineum interaction system.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4854-z) contains supplementary material, which is available to authorized users.

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“…We used the Iso-Seq method for exploring the transcriptomic complexity of this cultivar, in particular long transcripts. KK3 PacBio-isoforms are substantially longer (N50 = 3,611 bp) than previous sugarcane transcriptomic studies employing second-generation sequencing platforms, in which the N50 ranged from 640–1,385 bp ( 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 ). The high complexity of the sugarcane transcriptome hinders de novo assembly of long transcripts from short-read data, such that longer transcripts are under-represented.…”

Section: Discussionmentioning

confidence: 73%

“…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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Transcriptome of High-Sucrose Sugarcane Variety GT35

Cited by 30 publications

References 49 publications

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

Transcriptomic characterization and potential marker development of contrasting sugarcane cultivars

Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system

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

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