De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data

Tian, Xinjie; Long, Yan; Wang, Jiao; Zhang, Jingwen; Wang, Yanyan; Liu, Weimin; Peng, Yufa; Yuan, Qianhua; Pei, Xinwu

doi:10.1371/journal.pone.0131455

Cited by 27 publications

(24 citation statements)

References 52 publications

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“…; N50 = 1147 bp, average length = 715 bp) [65], and sugarcane ( Saccharum officinarum ; N50 = 1177 bp) [66]. Additionally, the GC content of the assembled unitranscripts (49%) was slightly higher compared to those obtained previously in A. donax (45.60% [10] and 47.70%; [11]), but it was similar to that observed in P. australis using Illumina sequencing (49.9%) [64].…”

Section: Discussionmentioning

confidence: 99%

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Evangelistella

Valentini

Ludovisi

et al. 2017

Biotechnol Biofuels

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Background Arundo donax has attracted renewed interest as a potential candidate energy crop for use in biomass-to-liquid fuel conversion processes and biorefineries. This is due to its high productivity, adaptability to marginal land conditions, and suitability for biofuel and biomaterial production. Despite its importance, the genomic resources currently available for supporting the improvement of this species are still limited.ResultsWe used RNA sequencing (RNA-Seq) to de novo assemble and characterize the A. donax leaf transcriptome. The sequencing generated 1249 million clean reads that were assembled using single-k-mer and multi-k-mer approaches into 62,596 unique sequences (unitranscripts) with an N50 of 1134 bp. TransDecoder and Trinotate software suites were used to obtain putative coding sequences and annotate them by mapping to UniProtKB/Swiss-Prot and UniRef90 databases, searching for known transcripts, proteins, protein domains, and signal peptides. Furthermore, the unitranscripts were annotated by mapping them to the NCBI non-redundant, GO and KEGG pathway databases using Blast2GO. The transcriptome was also characterized by BLAST searches to investigate homologous transcripts of key genes involved in important metabolic pathways, such as lignin, cellulose, purine, and thiamine biosynthesis and carbon fixation. Moreover, a set of homologous transcripts of key genes involved in stomatal development and of genes coding for stress-associated proteins (SAPs) were identified. Additionally, 8364 simple sequence repeat (SSR) markers were identified and surveyed. SSRs appeared more abundant in non-coding regions (63.18%) than in coding regions (36.82%). This SSR dataset represents the first marker catalogue of A. donax. 53 SSRs (PolySSRs) were then predicted to be polymorphic between ecotype-specific assemblies, suggesting genetic variability in the studied ecotypes.ConclusionsThis study provides the first publicly available leaf transcriptome for the A. donax bioenergy crop. The functional annotation and characterization of the transcriptome will be highly useful for providing insight into the molecular mechanisms underlying its extreme adaptability. The identification of homologous transcripts involved in key metabolic pathways offers a platform for directing future efforts in genetic improvement of this species. Finally, the identified SSRs will facilitate the harnessing of untapped genetic diversity. This transcriptome should be of value to ongoing functional genomics and genetic studies in this crop of paramount economic importance.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0828-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Evangelistella

Valentini

Ludovisi

et al. 2017

Biotechnol Biofuels

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“…However, the genes specifically expressed in green tissues in common wild rice have not been reported. Previously, we sequenced the transcriptome of common wild rice and identified root-specific and drought-related genes [ 30 ]. In this study, we used this dataset to screen for genes with green tissue-specific expression and cloned the promoter sequence of one of these genes, OrGSE ( O. rufipogon GREEN SPECIAL EXPRESS).…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of a Green-Tissue Promoter from Common Wild Rice (Oryza rufipogon Griff.)

Xue

Long

Zhao

et al. 2018

IJMS

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Promoters play a very important role in the initiation and regulation of gene transcription. Green-tissue promoter is of great significance to the development of genetically modified crops. Based on RNA-seq data and RT-PCR expression analysis, this study screened a gene, OrGSE (GREEN SPECIAL EXPRESS), which is expressed specifically in green tissues. The study also isolated the promoter of the OrGSE gene (OrGSEp), and predicted many cis-acting elements, such as the CAAT-Box and TATA-Box, and light-responding elements, including circadian, G-BOX and GT1 CONSENSUS. Histochemical analysis and quantification of GUS activity in transgenic Arabidopsis thaliana plants expressing GUS under the control of OrGSEp revealed that this promoter is not only green tissue-specific, but also light-inducible. The ability of a series of 5’-deletion fragments of OrGSEp to drive GUS expression in Arabidopsis was also evaluated. We found that the promoter region from −54 to −114 is critical for the promoter function, and the region from −374 to −114 may contain core cis-elements involved in light response. In transgenic rice expressing GUS under the control of OrGSEp, visualization and quantification of GUS activity showed that GUS was preferentially expressed in green tissues and not in endosperm. OrGSEp is a useful regulatory element for breeding pest-resistant crops.

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“…Liu et al demonstrated that CWR could be used to modify the stomatal conductance and membrane stability, which are related to drought resistance in cultivars rice [6]. Based on high-throughput sequencing, there were 901 contig responses to drought stress [7]. Therefore, there are abundant drought resistant-gene resources in CWR, providing excellent resources that can contribute to increasing the rice resistance, productivity, and quality [8].…”

Section: Introductionmentioning

confidence: 99%

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

et al. 2017

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BackgroundDrought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality.ResultsIn this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where ‘R’ indicates the root tissue and ‘L’ indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress.ConclusionOur results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon.

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De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data

Cited by 27 publications

References 52 publications

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock

Isolation and Characterization of a Green-Tissue Promoter from Common Wild Rice (Oryza rufipogon Griff.)

Identification of microRNAs in Response to Drought in Common Wild Rice (Oryza rufipogon Griff.) Shoots and Roots

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