title: De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers.
abstract: 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.
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: zjpsyu@163.com.
authors.forename: Mina
authors.initials: M
authors.lastname: Yu
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: jjyu@jaas.ac.cn.
authors.forename: Junjie
authors.initials: J
authors.lastname: Yu
authors.affiliation: Life Sciences College of Nanjing Agricultural University, Weigang 1, Nanjing, Jiangsu 210095, China. Electronic address: guchenhao1991@hotmail.com.
authors.forename: Chenhao
authors.initials: C
authors.lastname: Gu
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: nyf1012@163.com.
authors.forename: Yafeng
authors.initials: Y
authors.lastname: Nie
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: chzy@jaas.ac.cn.
authors.forename: Zhiyi
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: yinjsha@163.com.
authors.forename: Xiaole
authors.initials: X
authors.lastname: Yin
authors.affiliation: Institute of Plant Protection, Jiangsu Academy of Agricultural Science, Zhongling Street 50, Nanjing, Jiangsu 210014, China. Electronic address: liuyf@jaas.ac.cn.
authors.forename: Yongfeng
authors.initials: Y
authors.lastname: Liu
mesh_terms: D001203:Ascomycota / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D005819:Genetic Markers; D016681:Genome, Fungal; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Simple sequence repeat; Transcriptome; Villosiclava virens; Virulence associated genes