Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress

Abstract

BackgroundArabidopsis pumila is native to the desert region of northwest China and it is extraordinarily well adapted to the local semi-desert saline soil, thus providing a candidate plant system for environmental adaptation and salt-tolerance gene mining. However, understanding of the salt-adaptation mechanism of this species is limited because of genomic sequences scarcity. In the present study, the transcriptome profiles of A. pumila leaf tissues treated with 250 mM NaCl for 0, 0.5, 3, 6, 12, 24 and 48 h were analyzed using a combination of second-generation sequencing (SGS) and third-generation single-molecule real-time (SMRT) sequencing.ResultsCorrection of SMRT long reads by SGS short reads resulted in 59,328 transcripts. We found 8075 differentially expressed genes (DEGs) between salt-stressed tissues and controls, of which 483 were transcription factors and 1157 were transport proteins. Most DEGs were activated within 6 h of salt stress and their expression stabilized after 48 h; the number of DEGs was greatest within 12 h of salt stress. Gene annotation and functional analyses revealed that expression of genes associated with the osmotic and ionic phases rapidly and coordinately changed during the continuous salt stress in this species, and salt stress-related categories were highly enriched among these DEGs, including oxidation–reduction, transmembrane transport, transcription factor activity and ion channel activity. Orphan, MYB, HB, bHLH, C3H, PHD, bZIP, ARF and NAC TFs were most enriched in DEGs; ABCB1, CLC-A, CPK30, KEA2, KUP9, NHX1, SOS1, VHA-A and VP1 TPs were extensively up-regulated in salt-stressed samples, suggesting that they play important roles in slat tolerance. Importantly, further experimental studies identified a mitogen-activated protein kinase (MAPK) gene MAPKKK18 as continuously up-regulated throughout salt stress, suggesting its crucial role in salt tolerance. The expression patterns of the salt-responsive 24 genes resulted from quantitative real-time PCR were basically consistent with their transcript abundance changes identified by RNA-Seq.ConclusionThe full-length transcripts generated in this study provide a more accurate depiction of gene transcription of A. pumila. We identified potential genes involved in salt tolerance of A. pumila. These data present a genetic resource and facilitate better understanding of salt-adaptation mechanism for ephemeral plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5106-y) contains supplementary material, which is available to authorized users.

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…We determined that the mean length of the avocado nonredundant transcripts was2330 bp, implying that our sequences were long enough to represent full-length transcripts. Additionally, this mean length was in between the mean lengths obtained for other species, including Z. bungeanum (3414 bp) [32], T. pretense (2789 bp) [34], M. sativa (1706 bp) [37], Z. planispinum (1781 bp) [38], C. sinensis (1781 bp) [40], and Arabidopsis pumila (2194 bp) [57]. Moreover, the 76,345 nonredundant transcripts derived from the 25.79 Gb clean PacBio SMRT data produced in this study may facilitate future research on the physiology, biochemistry, and molecular genetics of avocado and related species.…”

Full-length transcriptome sequencing reveals a low-temperature-tolerance mechanism in Medicago falcata roots

“…The approach of combining NGS and SMRT has become increasingly popular in researching plant responses to adverse environments for providing high-quality and increasingly complete assemblies at the transcriptome level [26][27][28]. SMRT can generate full-length or long sequences, and the high error rate can be overcome using short and high-accuracy NGS reads [19,22].…”

“…The following pathway was "Arginine and proline metabolism". Arginine and proline metabolism is one of the central pathways for the biosynthesis of the amino acids arginine and proline [27]. Proline accumulation is a well-known measure for alleviating abiotic stress in plants [61].…”

“…Next-generation sequencing (NGS) technology (RNA-Seq) can provide expression profiles of either coding or noncoding RNAs and generate digital data of gene expression that enable rapid and cost-effective genomic and transcriptomic studies for most major crops, including rice [23], wheat [24], and grape [25]. The approach of combining NGS and SMRT sequencing has been applied to generate comprehensive information frequently at the transcriptional level, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance [26][27][28]. The changes in genes responding to low-temperature stress revealed by transcriptome analyses are mainly separated into three parts.…”

Transcriptome profiling of spike provides expression features of genes related to terpene biosynthesis in lavender

“…In this study, we used the DESeq2R package (v1.10.1) 35 to analyse the differentially expressed transcripts between two phases within and across two lavender cultivars at three different developmental stages. The analysis methods of DEGs and TFs were the same as that of Yang et al 34 , so we will not elaborate on this here. A brief description is as follows: using the p.adjust function to adjust the resulting P-values to control the false discovery rate; genes with an adjusted P-value less than 0.05 were considered to be differentially expressed; taking an absolute value of log 2 (Group1/Group2) ≥ 1 as the threshold for judging significant DEGs between different developmental stages; using the GOseq R packages 34 to conduct GO enrichment analysis; and using the KOBAS 38 software (v2.0.12) to analyse the KEGG enrichment pathway of DEGs.…”