Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

Abstract

The full-length single-molecular sequencing and short reads Illumina sequencing were combined to generate the transcripts of adzuki bean with high-quality. A total of 17,636 loci and 60,454 transcripts were detected in this study. To characterize the drought-responsive genes during seed germination in adzuki bean, two varieties, i.e., tolerant and sensitive to drought stress, were selected to conduct analysis of alternative splicing dynamics (AS) and differentially expressed genes (DEGs) by combining the newly assembled draft genome and public adzuki bean reference genome. AS analysis indicated that both the two varieties underwent a little more AS events under control conditions than under drought stress. Among the AS events, IR (intron retention) predominately accounted for 34.3%, whereas AD (alternative donor site) was the least frequent with 15.8%. Meanwhile, 562 long non-coding RNAs, 409 fusion genes and 1208 transcription factors were identified. Moreover, a total of 5,337 DEGs were identified in comparison of the two varieties with drought or control treatments. Notably, 82 DEGs were discovered in the two varieties under drought stress, which might be the candidate in regulation of seed germination to answer for different drought tolerance. The DEGs encoded proteins involved in primary or second metabolism, plant hormone signal transduction, transcript or translation processes, ubiquitin proteasome system, transcription factor, transporters, and so on. The results facilitate to increase the knowledge about the mechanism of drought tolerance during crop seed germination, and provide reference for the breeding of drought-tolerant adzuki bean.

Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis

“…At the same time, DEGs with the same expression pattern were also enriched in amino acid metabolism, carbohydrate metabolism, signaling and cellular processes, ion channels, and other KEGG pathways, which suggests that there is an obvious co-regulatory system between NaCl and PEG induced osmotic response pathways. These findings are similar to those previously observed in Arabidopsis [ 44 ], alfalfa [ 1 ], rice [ 45 ], and red bean [ 13 ]. These results showed that when I. lactea var.…”

“…chinensis under drought and salt stress. Moreover, due to the obvious disadvantages of second-generation sequencing, such as the short length of sequencing reads and unreliable assembly results, the accuracy of transcriptome abundance calculation is reduced to a large extent [ 12 , 13 ].…”

Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development

“…The application of long-read technologies to the exploration of the lncRNA repertoire in plants has been demonstrated for several plant species, including Oryza sativa L. ssp. japonica [ 27 ], Populus simonii [ 28 ], P. qiongdaoensis [ 29 ], poplar “Nanlin 895” [ 30 ], Trifolium pratense [ 31 ], Cardamine violifolia [ 32 ], and Vigna angularis [ 33 ]. These studies demonstrated that long-read sequencing can be used to obtain a comprehensive catalogue of lncRNAs.…”

iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean

“…The mass spectrometry data were transformed into MGF files with Proteome Discovery 1.2 (Thermo, Pittsburgh, PA, USA) and analyzed using Mascot search engine (Matrix Science, London, UK; version 2.3.2). Mascot database was set up for protein identification using Vigna angularis L reference genome 47 ( ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/190/045/GCF_001190045.1_Vigan1.1/ ), Vigna angularis L data in NCBI nr/Swiss-Prot/Uniprot/IPI database, and the PacBio SMRT and illumina sequencing data published by Zhu et al 18 . Mascot was searched with a fragment ion mass tolerance of 0.050 Da and a parent ion tolerance of 10.0 PPM.…”

“…Several bZIP genes were reported in response to drought and salt stress in Vigna radiata and V. angularis by whole-genome sequencing and quantitative real-time PCR analysis 17 . We previously selected a drought-tolerant variety and a drought-sensitive variety through the drought tolerance identification of adzuki bean seeds, and identified 82 differentially expressed genes (DEGs) in the germinating seeds between drought tolerant and drought sensitive variety of adzuki bean under drought stress by PacBio SMRT and Illumina Sequencing 18 . It provided a ideal materials for investigating protein expression patterns of two varieties under drought stress.…”