Dataset / Tabular

Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4

author(s) Zheng, S - Zhang, L - Cenci, A - Rouard, M - Zhang, D - Wang, Y - Tang, W
from Bioversity International
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themes
regions
  • Northern America
  • Americas
  • World
  • Eastern Asia
  • Asia
  • South America
  • Latin America and the Caribbean
citation

Zheng, S.; Zhang, L.; Cenci, A.; Rouard, M.; Zhang, D.; Wang, Y.; Tang, W., 2019, "Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4", https://doi.org/10.7910/DVN/W2M6WG, Harvard Dataverse, V1, UNF:6:RsUfD6KhfTXS6IGEoGeoCA== [fileUNF]

Publications and datasets provided via GARDIAN

Abstract

Musa acuminata (subsp. malaccensis) ‘Pahang’ (AA, ITC0609) obtained from the International Musa Germplasm Transit Centre and Musa AAA Cavendish ‘Brazilian’ (commercial variety, in China) were used in the study. The banana corm central cylinder tissues of Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) inoculation and mock-inoculation were harvested at 0, 1, 7, 14 dpi for transcriptome sampling. Six plants were pooled together for each sample and the experiments were conducted with three independent biological replicates. All samples were frozen immediately in liquid nitrogen and stored at -70°C until RNA extraction. The list of samples is shown in the Table S1. Differentially expressed genes (DEGs) between samples of Pahang (resistant) versus Brazilian (susceptible) before treatment (P_untr vs. B_untr) and Foc TR4 inoculated samples versus mock inoculated samples (P_1dpi vs. P_1dmo, P_7dpi vs. P_7dmo, P_14dpi vs. P_14dmo, B_1dpi vs. B_1dmo, B_7dpi vs. B_7dmo, B_14dpi vs. B_14dmo) were identified using the DESeq R package (v1.18.0). Genes with an adjusted P-value<0.05 were assigned as differentially expressed. A DEG of fold change with an absolute value of log2 ratio>0 in read counts between two libraries was considered up-regulated expression; in contrast, log2 ratio<0 was considered to down-regulated expression. DEGs were further annotated by Gene Ontology (GO) functional enrichment using GOseq (Release2.12), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment using KOBAS (2.0). DEGs were considered significantly enriched with an adjusted P-value <0.05. Paralogous sequences of DEGs were identified in the Musa genome by BLASTp analysis using NCBI nr-protein database. Musa genes having higher scores than genes of other species were considered as paralogs. In order to verify whether identified paralogs were expressed and had any potential interference on the DEG impact, FPKM values of all paralogs were summed and compared among RNA-seq libraries.

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