Transcriptome profiling and digital gene expression analysis of sweet potato for the identification of putative genes involved in the defense response against Fusarium oxysporum f. sp. batatas

Abstract

Sweet potato production is constrained by Fusarium wilt, which is caused by Fusarium oxysporum f. sp. batatas (Fob). The identification of genes related to disease resistance and the underlying mechanisms will contribute to improving disease resistance via sweet potato breeding programs. In the present study, we performed de novo transcriptome assembly and digital gene expression (DGE) profiling of sweet potato challenged with Fob using Illumina HiSeq technology. In total, 89,944,188 clean reads were generated from 12 samples and assembled into 101,988 unigenes with an average length of 666 bp; of these unigenes, 62,605 (61.38%) were functionally annotated in the NCBI non-redundant protein database by BLASTX with a cutoff E-value of 10−5. Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were examined to explore the unigenes’ functions. We constructed four DGE libraries for the sweet potato cultivars JinShan57 (JS57, highly resistant) and XinZhongHua (XZH, highly susceptible), which were challenged with pathogenic Fob. Genes that were differentially expressed in the four libraries were identified by comparing the transcriptomes. Various genes that were differentially expressed during defense, including chitin elicitor receptor kinase 1 (CERK), mitogen-activated protein kinase (MAPK), WRKY, NAC, MYB, and ethylene-responsive transcription factor (ERF), as well as resistance genes, pathogenesis-related genes, and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling pathways, were identified. These data represent a sequence resource for genetic and genomic studies of sweet potato that will enhance the understanding of the mechanism of disease resistance.

Transcriptome and digital gene expression analysis unravels the novel mechanism of early flowering in Angelica sinensis

“…In non-model plants, combine these two methods can promote the identification of different expression genes. The combination of transcriptome sequencing and DGE can provide more sensitive and efficient analysis of gene expression changes, and can also promote gene expression comparisons for the sample without reference databases 8 .…”

Comparative proteomic analysis of the sweetpotato provides insights into response mechanisms to Fusarium oxysporum f. sp. batatas

“…From the current research, sets of proteins that are involved in the defense systems of sweetpotato to Fob were identified, their functions of which need to be further exploited. Previously, the same cultivars (JS57 than XZH) and pathogens (Fob) were used to identify disease resistance genes in sweetpotato by performing de novo transcriptome assembly and digital gene expression analysis 27 , but there were few identical genes/proteins found in the study.…”

Transcriptomic analyses revealed the effect of Funneliformis mosseae on genes expression in Fusarium oxysporum

“…Crop root rot caused by Fusarium oxysporum is a typical destructive soil-borne disease [4]. This pathogen has many specialized types and a wide host range, causing more than a 100 diseases in different plants, such as melons, solanaceae, legumes and flowers [5]. This pathogen infects plant roots, causing vascular diseases.…”