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De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers

文献类型： 外文期刊

作者： Yu, Mina 1 ; Yu, Junjie 1 ; Gu, Chenhao 2 ; Nie, Yafeng 1 ; Chen, Zhiyi 1 ; Yin, Xiaole 1 ; Liu, Yongfeng 1 ;

作者机构： 1.Jiangsu Acad Agr Sci, Inst Plant Protect, Nanjing 210014, Jiangsu, Peoples R China

2.Nanjing Agr Univ, Life Sci Coll, Nanjing 210095, Jiangsu, Peoples R China

关键词： Simple sequence repeat;Transcriptome;Villosiclava virens;Virulence associated genes

期刊名称：GENE （ 影响因子：3.688； 五年影响因子：3.329 ）

ISSN：

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收录情况： SCI

摘要： Ustilaginoidea virens is the causal agent of rice false smut, which is a rice disease of increasing importance worldwide that has caused with the quantitative and qualitative rice losses. However, research on the pathogenic mechanism of U. virens is limited. In this study, we reported a de novo assembling, annotation, and characterization of the transcriptome and developed simple sequence repeat (SSR) markers of U. virens. U. virens transcripts of the mycelia and conidia mixture were sequenced using Illumina RNA-seq technology. A total of 52,554,142 clean reads were assembled into 36,496 transcripts representing 18,534 unigenes. Assembled unigenes were annotated through sequence comparison with known protein databases, and 48.48% of the unigenes were without hits in any of these databases. Clusters of orthologous groups for eukaryotic complete genome analysis identified the largest set of genes associated with posttranslational modification, protein turnover and chaperones. Kyoto Encyclopedia of Genes and Genomes pathway analyses identified the number of genes associated with mitogen-activated protein kinase and calcium-calcineurin pathways. The study also identified several putative pathogenicity determinants and candidate effectors in U. virens by using the pathogen-host interaction database. In addition, bioinformatics analysis revealed the presence of 12,298 SSR markers. This study provides a better understanding of the biology of U. virens and is an excellent resource for candidate genes required for pathogenesis discovery.

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