Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome

Abstract

BackgroundCitrus blight is a citrus tree overall decline disease and causes serious losses in the citrus industry worldwide. Although it was described more than one hundred years ago, its causal agent remains unknown and its pathophysiology is not well determined, which hampers our understanding of the disease and design of suitable disease management.ResultsIn this study, we sequenced and assembled the draft genome for Swingle citrumelo, one important citrus rootstock. The draft genome is approximately 280 Mb, which covers 74 % of the estimated Swingle citrumelo genome and the average coverage is around 15X. The draft genome of Swingle citrumelo enabled us to conduct transcriptome analysis of roots of blight and healthy Swingle citrumelo using RNA-seq. The RNA-seq was reliable as evidenced by the high consistence of RNA-seq analysis and quantitative reverse transcription PCR results (R2 = 0.966). Comparison of the gene expression profiles between blight and healthy root samples revealed the molecular mechanism underneath the characteristic blight phenotypes including decline, starch accumulation, and drought stress. The JA and ET biosynthesis and signaling pathways showed decreased transcript abundance, whereas SA-mediated defense-related genes showed increased transcript abundance in blight trees, suggesting unclassified biotrophic pathogen was involved in this disease.ConclusionsOverall, the Swingle citrumelo draft genome generated in this study will advance our understanding of plant biology and contribute to the citrus breeding. Transcriptome analysis of blight and healthy trees deepened our understanding of the pathophysiology of citrus blight.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2779-y) contains supplementary material, which is available to authorized users.

The structure and function of the global citrus rhizosphere microbiome

“…The clean reads were further trimmed using Sickle software 70 , and trimmed reads shorter than 80 bp were discarded. The trimmed reads were mapped to the sweet orange 27 , Citrus clementina 28 and Swingle citrumelo 71 genomes using Bowtie2 software 72 to identify and remove the citrus host-originated reads. The 23 rhizosphere and 20 soil samples were separated into 9 groups (Supplementary Figure 2 ) based on their microbial community similarity calculated by Mash 73 , and the pooled metagenomic reads from each group were de novo assembled using Megahit 74 ver.…”

Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome

“…On average, 4.85% of the clean reads were discarded from this trimming step. The trimmed reads were aligned to the Swingle citrumelo genome [ 26 ], sweet orange genome [ 27 ], and Citrus clementina genome [ 28 ] using bowtie2 [ 29 ], and the corresponding mapped reads were removed. Only the reads that did not map to any of the three citrus genomes were retained for further analysis.…”

Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection

“…Currently, two C. sinensis genomes are available but none for P. trifoliate (Adhikari et al 2012;Wang et al 2014). However, draft genome of Swingle citrumelo, which is also a hybrid of C. paradisi Macf and P. trifoliata, is available (Zhang et al 2016) and it could be used as a reference to map the Carrizo citrange reads that correspond to the P. trifoliata genome. To determine the proportions of these two, one parent (C. sinensis) and one step sibling (Swingle) genomes in Carrizo transcriptome, all read samples were separately mapped to these three reference genomes.…”