Abstract
Root lesion disease, caused by Pratylenchus coffeae, seriously impairs the growth and yield of ramie, an important natural fiber crop. The ramie defense mechanism against P. coffeae infection is poorly understood, which hinders efforts to improve resistance via breeding programs. In this study, the transcriptome of the resistant ramie cultivar Qingdaye was characterized using Illumina sequence technology. About 46.3 million clean pair end (PE) reads were generated and assembled into 40,826 unigenes with a mean length of 830 bp. Digital gene expression (DGE) analysis was performed on both the control roots (CK) and P. coffeae-challenged roots (CH), and the differentially expressed genes (DEGs) were identified. Approximately 10.16 and 8.07 million cDNA reads in the CK and CH cDNA libraries were sequenced, respectively. A total of 137 genes exhibited different transcript abundances between the two libraries. Among them, the expressions of 117 and 20 DEGs were up- and down-regulated in P. coffeae-challenged ramie, respectively. The expression patterns of 15 candidate genes determined by qRT-PCR confirmed the results of DGE analysis. Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation. The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance.
Highlights
High-throughput sequencing technology, such as Illumina (Solexa) sequencing, 454 pyrosequencing, and ABI SOLiD sequencing, allows us to analyze the transcriptome and whole genome-wide expression profiles of an organism or organ in a particular state, even in the absence of a reference genome
Time-course expression profiles of eight defense-related genes in susceptible and resistant ramie cultivars were different after P. coffeae inoculation
The differential expression of protease inhibitors, pathogenesis-related proteins (PRs), and transcription factors in resistant and susceptible ramie during P. coffeae infection indicated that cystatin likely plays an important role in nematode resistance
Summary
High-throughput sequencing ( called “Next-generation” sequencing) technology, such as Illumina (Solexa) sequencing, 454 pyrosequencing, and ABI SOLiD sequencing, allows us to analyze the transcriptome and whole genome-wide expression (digital gene expression, DGE) profiles of an organism or organ in a particular state, even in the absence of a reference genome. It produces more comprehensive information and is faster than other available technology. Zhang et al used DGE to study maize resistance to Sporisorium reilianum f. Zeae by comparing transcriptional changes in the roots of resistant and susceptible cultivar after pathogen infection [1]
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