Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes

Abstract

Background: Whiteflies threaten agricultural crop production worldwide, are polyphagous in nature, and transmit hundreds of plant viruses. Little is known how whitefly gene expression is altered due to feeding on plants infected with a semipersistently transmitted virus. Tomato chlorosis virus (ToCV; genus Crinivirus, family Closteroviridae) is transmitted by the whitefly (Bemisia tabaci) in a semipersistent manner and infects several globally important agricultural and ornamental crops, including tomato.

Results: To determine changes in global gene regulation in whiteflies after feeding on tomato plants infected with a crinivirus (ToCV), comparative transcriptomic analysis was performed using RNA-Seq on whitefly (Bemisia tabaci MEAM1) populations after 24, 48, and 72 h acquisition access periods on either ToCV-infected or uninfected tomatoes. Significant differences in gene expression were detected between whiteflies fed on ToCV-infected tomato and those fed on uninfected tomato among the three feeding time periods: 447 up-regulated and 542 down-regulated at 24 h, 4 up-regulated and 7 down-regulated at 48 h, and 50 up-regulated and 160 down-regulated at 72 h. Analysis revealed differential regulation of genes associated with metabolic pathways, signal transduction, transport and catabolism, receptors, glucose transporters, α-glucosidases, and the uric acid pathway in whiteflies fed on ToCV-infected tomatoes, as well as an abundance of differentially regulated novel orphan genes. Results demonstrate for the first time, a specific and temporally regulated response by the whitefly to feeding on a host plant infected with a semipersistently transmitted virus, and advance the understanding of the whitefly vector-virus interactions that facilitate virus transmission.

Conclusion: Whitefly transmission of semipersistent viruses is believed to require specific interactions between the virus and its vector that allow binding of virus particles to factors within whitefly mouthparts. Results provide a broader understanding of the potential mechanism of crinivirus transmission by whitefly, aid in discerning genes or loci in whitefly that influence virus interactions or transmission, and subsequently facilitate development of novel, genetics-based control methods against whitefly and whitefly-transmitted viruses.

Keywords: Bemisia tabaci MEAM1 (biotype B); Crinivirus; Gene expression; Orphan genes; RNA-Seq; Semipersistent transmission; Tomato chlorosis virus; Whitefly.

Fig. 1

Differentially expressed genes (DEGs) in whitefly, Bemisia tabaci MEAM1 following feeding on ToCV-infected (ToCV whiteflies) or uninfected (virus-free whiteflies) tomato plants for 24, 48, and 72 h; a Number of DEGs detected between ToCV whiteflies and virus-free whiteflies at three different feeding time points; b Venn-diagram showing unique and common DEGs in whitefly after feeding on ToCV-infected or uninfected tomato plants at three different feeding time points; c Principle component analysis (PCA) plot generated from 18 samples derived from virus free (healthy) or ToCV-whiteflies with three AAPs of 24, 48, and 72 h

Fig. 2

Summary of the KEGG reference pathways associated with up-regulated (a) and down-regulated genes (b) from whiteflies fed on ToCV-infected tomato (ToCV whiteflies) for 24 h. Bars represent the percentage of the total KEGG annotated transcripts (92 genes out of a total of 447 up-regulated genes and 272 genes out of a total of 542 down-regulated genes) in the ToCV whiteflies at 24 h compared to virus-free whiteflies

Fig. 3

Summary of the KEGG reference pathways associated with up-regulated (a) and down-regulated genes (b) from whiteflies fed on ToCV-infected tomato (ToCV whiteflies) for 72 h. Bars represent the percentage of the total KEGG annotated transcripts (24 genes out of a total of 50 up-regulated genes and 43 genes out of a total of 160 down-regulated genes) in the ToCV whiteflies at 72 h compared to virus-free whiteflies

Fig. 4

RT-qPCR validation of selected genes differentially regulated in ToCV whiteflies after feeding periods of 24, 48, or 72 h compared to virus-free (VF) whiteflies (Bemisia tabaci MEAM1). Each experiment contained three independent biological replications and three technical replications per biological replicate