Comprehensive transcriptome analysis reveals genes in response to water deficit in the leaves of Saccharum narenga (Nees ex Steud.) hack

Abstract

BackgroundSugarcane is an important sugar and energy crop that is widely planted in the world. Among the environmental stresses, the water-deficit stress is the most limiting to plant productivity. Some groups have used PCR-based and microarray technologies to investigate the gene expression changes of multiple sugarcane cultivars under water stress. Our knowledge about sugarcane genes in response to water deficit is still poor.ResultsA wild sugarcane type, Saccharum narenga, was selected and treated with drought stress for 22 days. Leaves from drought treated (DTS) and control (CK) plants were obtained for deep sequencing. Paired-end sequencing enabled us to assemble 104,644 genes (N50 = 1605 bp), of which 38,721 were aligned to other databases, such as UniProt, NR, GO, KEGG and Pfam. Single-end and paired-end sequencing identified 30,297 genes (> 5 TPM) in all samples. Compared to CK, 3389 differentially expressed genes (DEGs) were identified in DTS samples, comprising 1772 up-regulated and 1617 down-regulated genes. Functional analysis showed that the DEGs were involved in biological pathways like response to blue light, metabolic pathways and plant hormone signal transduction. We further observed the expression patterns of several important gene families, including aquaporins, late embryogenesis abundant proteins, auxin related proteins, transcription factors (TFs), heat shock proteins, light harvesting chlorophyll a-b binding proteins, disease resistance proteins, and ribosomal proteins. Interestingly, the regulation of genes varied among different subfamilies of aquaporin and ribosomal proteins. In addition, DIVARICATA and heat stress TFs were first reported in sugarcane leaves in response to water deficit. Further, we showed potential miRNAs that might be involved in the regulation of gene changes in sugarcane leaves under the water-deficit stress.ConclusionsThis is the first transcriptome study of Saccharum narenga and the assembled genes are a valuable resource for future research. Our findings will improve the understanding of the mechanism of gene regulation in sugarcane leaves under the water-deficit stress. The output of this study will also contribute to the sugarcane breeding program.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1428-9) contains supplementary material, which is available to authorized users.

RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

“…In Saccharum narenga, 175 genes encoding auxin-related proteins were identified in the leaves in response to drought treatment. DEGs encoding auxin response factors and auxininduced proteins were up-regulated in sugarcane leaves in response to water deficit, and genes encoding indole-3-acetic acid were down-regulated in leaves from drought-treated samples compared to the control [73]. A halophyte is able to complete its life cycle at a high salt concentration.…”

Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans

“…Metabolic processes are organic processes (in a cell or organism) that are necessary for life and important features identified during infection of sugarcane by S. scitamineum [20] and in Saccharum narenga (Nees ex Steud.) in response to water deficit [31]. The majority of downregulated DEGs (>5000) were attributed to categories related to single-organism process, single-organism cellular process, single-organism metabolic process, catalytic activity, and membrane (cellular component) in response of the sugarcane to X. albilineans infection.…”

Comparative Transcriptome Analysis between a Novel Allohexaploid Cotton Progeny CMS Line LD6A and Its Maintainer Line LD6B

“…We further analyzed the DEGs in different categories that might be related to CMS, toxic proteins, HATs (histone acetyltransferase) related proteins, TCA cycle related proteins, transcription factors, and some other proteins [6,[17][18][19][20]].…”

“…Several metabolic pathways which influence biological processes that cause CMS via the action of mitochondrial genes coupled with nuclear genes were identified [16]. Studies have been done regarding global transcriptional networks from big data analysis to explore CMS genes, which have been shown to be associated with the tricarboxylic acid (TCA) cycle, respiratory electron transport chain, oxidative phosphorylation and toxic proteins [6,[17][18][19][20].…”