Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development

Khemka, Niraj; Singh, Vikash; Garg, Rohini; Jain, Mukesh

doi:10.1038/srep33297

Cited by 66 publications

(62 citation statements)

References 56 publications

(105 reference statements)

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“…4, B and C; Supplemental Table S3). A large number of lincRNAs expressed in the SAM are consistent with previous observations in chickpea and other plants (Khemka et al, 2016). Overall, samples from the same tissue show similar expression patterns (Fig.…”

Section: The Lincrnas Show Highly Tissue-specific Expressionsupporting

confidence: 90%

“…The observations are consistent with lincRNA studies in other plant species. LincRNAs in rice, cucumber (Cucumis sativus), and chickpea (Cicer arietinum) were reported to be shorter than protein-coding genes (Zhang et al, 2014;Hao et al, 2015;Khemka et al, 2016). LincRNAs in cucumber, maize (Zea mays), and chickpea were reported to have predominantly one exon only Hao et al, 2015;Khemka et al, 2016).…”

Section: Lincrnas Have Distinct Properties When Compared To Protein-cmentioning

confidence: 99%

“…LincRNAs in rice, cucumber (Cucumis sativus), and chickpea (Cicer arietinum) were reported to be shorter than protein-coding genes (Zhang et al, 2014;Hao et al, 2015;Khemka et al, 2016). LincRNAs in cucumber, maize (Zea mays), and chickpea were reported to have predominantly one exon only Hao et al, 2015;Khemka et al, 2016). Also, low expression levels of lincRNAs were observed in Arabidopsis, rice, and maize (Liu et al, 2012;Li et al, 2014;Zhang et al, 2014;Hao et al, 2015).…”

Section: Lincrnas Have Distinct Properties When Compared To Protein-cmentioning

confidence: 99%

“…Best hits were identified by lowest e-value. Coordinates of chickpea (Cicer arietinum) lincRNAs were obtained from Khemka et al (2016), Medicago truncatula lincRNAs from Wang et al (2015b), and Arabidopsis (Arabidopsis thaliana) lincRNA from http:// chualab.rockefeller.edu/gbrowse2/homepage.html. The lincRNA sequences were extracted from genome assemblies (chickpea Cicer_arietinum_GA_v1.0, Medicago Mt4.0v1, and Arabidopsis TAIR9).…”

Section: Sequence-based Similarity Of Lincrnasmentioning

confidence: 99%

“…lncRNAs were long considered little beyond transcriptional noise; however, current evidence points to important roles in diverse biological processes across eukaryotes (van Werven et al, 2012;Ulitsky and Bartel, 2013;Flynn and Chang, 2014). In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), lncRNAs have been shown to be involved in flowering time regulation, reproduction, and root organogenesis (Swiezewski et al, 2009;Cifuentes-Rojas et al, 2011;Heo and Sung, 2011;Ariel et al, 2014;Bardou et al, 2014;Matzke et al, 2015;Wang et al, 2014b;Zhang et al, 2014;Berry and Dean, 2015;Khemka et al, 2016). lncRNAs are found both in the nucleus and cytoplasm, which suggests a diversity of modes of action, including chromatin modification (Heo et al, 2013); acting as decoys preventing access of regulatory proteins, including splicing machinery, and microRNAs to their true RNA and DNA targets (Franco-Zorrilla et al, 2007;Wu et al, 2013;Bardou et al, 2014); and acting as scaffolds for assembly of larger protein-RNA complexes (Lai et al, 2013;Pefanis et al, 2015).…”

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confidence: 99%

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The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

2017

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Long intergenic noncoding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean () is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities. Soybean cultivars have photoperiod requirements restricting its use and productivity. Molecular regulators of these legume-specific developmental processes remain enigmatic. Long noncoding RNAs may play important regulatory roles in soybean growth and development. In this study, over one billion RNA-seq read pairs from 37 samples representing nine tissues were used to discover 6,018 lincRNA loci. The lincRNAs were shorter than protein-coding transcripts and had lower expression levels and more sample specific expression. Few of the loci were found to be conserved in two other legume species (chickpea [] and ), but almost 200 homeologous lincRNAs in the soybean genome were detected. Protein-coding gene-lincRNA coexpression analysis suggested an involvement of lincRNAs in stress response, signal transduction, and developmental processes. Positional analysis of lincRNA loci implicated involvement in transcriptional regulation. lincRNA expression from centromeric regions was observed especially in actively dividing tissues, suggesting possible roles in cell division. Integration of publicly available genome-wide association data with the lincRNA map of the soybean genome uncovered 23 lincRNAs potentially associated with agronomic traits.

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Section: The Lincrnas Show Highly Tissue-specific Expressionsupporting

confidence: 90%