Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

Abstract

Summary Ascochyta blight ( AB ) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes ( DEG s). These DEG s were mainly related to pathogenesis‐related proteins, disease resistance genes like NBS ‐ LRR , cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 mi RNA s which included 478 known and 173 novel mi RNA s. A total of 297 mi RNA s were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 mi RNA s. The combined analysis of both small RNA and transcriptome datasets identified 12 mi RNA ‐ mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post‐transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

“…Key miRNA-mRNA modules with antagonistic regulatory patterns subject to different stresses were discovered based on the integrated multi-omics analysis [ 66 , 67 , 70 , 71 ]. miRNA-mRNA interactions of these modules were evidenced by three sequencing datasets (miRNA expression evidenced by sRNA-seq results, mRNA expression evidenced by transcriptome-seq results, and miRNA-guided mRNA cleavage evidenced by degradome-seq results).…”

“…This could only be achieved with a multi-omics analysis that collectively analyzes datasets of sRNA-seq, mRNA-seq, and degradome-seq at the same time. Previous research has successfully employed such a multi-omics approach in species like rice, maize, and chickpea [ 66 , 67 , 68 , 69 ]. However, it has not been previously undertaken in durum wheat.…”

Genome-wide transcriptome and physiological analyses provide new insights into peanut drought response mechanisms

“…Therefore, this study reports the identification of drought tolerance sources in the genetic background of Valencia-type peanuts. Furthermore, in recent years, the RNA-seq approach has been successfully used to understand the mechanisms behind various biotic and abiotic stresses in different crop species 16,17 . The availability of genome sequence information of diploid progenitors of cultivated peanut 18,19 facilitates to understand the genomic complexity of the different traits in peanut.…”

Screening and identification of miRNAs related to sexual differentiation of strobili in Ginkgo biloba by integration analysis of small RNA, mRNA, and degradome sequencing

“…The combined analysis of multiple sequencing could present itself as a versatile tool to analyze the mechanisms of plant life process. The complex mechanism of Ascochyta blight resistance in chickpea were analyzed by means of multi-group sequencing combination [37]. In Camellia, miR172-AP2 and miR156-SPLs regulatory pairs were identi ed as key regulatory nodes to promote the diversity of double ower forms by the multi-group analysis [38].…”