A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

Abstract

A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of ‘translational elongation’, ‘translation factor activity’, ‘ribosomal subunit’ and ‘phosphorelay signal transduction’, were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga’s resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

“…Lastly, PR gene responses to whiteflies were compared to data sets in the literature that documented responses to five other aggressors: the cassava mealybug Phenacoccus manihoti; the bacterial blight pathogen Xanthomonas axonopodis pv. manihotis; the fungus causing cassava anthracnose disease Colletotrichum gloeosporioides, Cassava Mosaic Virus (CMV), and Cassava Brown Streak Virus (CBSV) [26][27][28][29][30][31][32][33]. Together, our integrative analyses defined the core transcriptome response of susceptible cassava to whitefly infestation, and revealed key PR gene families (PR-2, -5, -7 and -9) in the responses of cassava to whiteflies, SA, JA, and a variety of other biotic stresses.…”

Cassava breeding and agronomy in Asia: 50 years of history and future directions

“…However, to date, advanced genomic and genetic tools have contributed in describing the crop's genetic diversity (Bradbury et al 2013, de Oliveira et al 2014, Fregene et al 2003, diagnostics of cassava pest and diseases (Bart et al 2012, Legg et al 2011, gene expression studies (Amuge et al 2017, Ballén-Taborda et al 2013, resistance to CMD in African germplasm (Egesi et al 2006, Okogbenin et al 2007, as well as post-harvest physiological deterioration (PPD) gene profiling in cassava roots (Reilly et al 2007, Wilson et al 2017. Therefore, recent developments in genomic research will help facilitate cassava breeding by providing knowledge and tools for attributes or traits for cassava improvement (de Oliveira et al 2012, Wolfe et al 2016.…”

Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress

“…A total of 74 transcriptome-wide RNA-sequencing (RNA-seq) reads, generated from 71 polyA-tail libraries and 3 strand-specific total RNA libraries, were used as expression evidence for the predicted ncRNAs. These were retrieved from cassava SRA accessions SRP101302 [15], SRP042139 [32], SRP076160 [39], and SRP096257 [40] in NCBI and from RNA-seq datasets [41] provided by the Genomic Research Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand. Reads with adapter sequences or those with low quality were trimmed and/or filtered out by Trimmomatic [42].…”

“…The following are available online at http://www.mdpi.com/2073-4425/11/4/366/s1: Figure S1: 56,840 predicted ncRNAs from RNAz tool with P > 0.5; Figure S2: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in cassava RNA-seq data from Li [15]; Figure S3: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in cassava RNA-seq data from Wang [32]; Figure S4: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in cassava RNA-seq data from Wilson [39]; Figure S5: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in cassava RNA-seq data from Pootakham [41]; Figure S6: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in CBSV-resistant cassava RNA-seq data from Amuge [40]; Figure S7: Comparison of expression level between unmatched ncRNAs with known ncRNAs and protein coding genes in CBSV-susceptible cassava RNA-seq data from Amuge [40]; Figure S8: Expression supporting and confidence of potential novel lncRNAs; Figure S9: Comparison of expression level between Me-lncRNAs and protein coding genes in cassava RNA-seq data from Li [15]; Figure S10: Comparison of expression level between Me-lncRNAs and protein coding genes in cassava RNA-seq data from Wang [32]; Figure S11: Comparison of expression level between Me-lncRNAs and protein coding genes in cassava RNA-seq data from Wilson [39]; Figure S12: Comparison of expression level between Me-lncRNAs and protein coding genes in cassava RNA-seq data from Pootakham [41]; Figure S13: Comparison of expression level between Me-lncRNAs and protein coding genes in CBSV-resistant cassava RNA-seq data from Amuge [40]; Figure S14: Comparison of expression level between Me-lncRNAs and protein coding genes in CBSV-susceptible cassava RNA-seq data from Amuge [40]; Figure S15: Volcano plot represents differentially expressed coding genes under cold stress of cassava; ...…”