Fosu-Nyarko John, Nicol Paul, Naz Fareeha, Gill Reetinder, Jones Michael G K
Plant Biotechnology Research Group, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia.
NemGenix Pty Ltd, Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, Australia.
PLoS One. 2016 Jan 29;11(1):e0147511. doi: 10.1371/journal.pone.0147511. eCollection 2016.
The beet cyst nematode, Heterodera schachtii, is a major root pest that significantly impacts the yield of sugar beet, brassicas and related species. There has been limited molecular characterisation of this important plant pathogen: to identify target genes for its control the transcriptome of the pre-parasitic J2 stage of H. schachtii was sequenced using Roche GS FLX. Ninety seven percent of reads (i.e., 387,668) with an average PHRED score > 22 were assembled with CAP3 and CLC Genomics Workbench into 37,345 and 47,263 contigs, respectively. The transcripts were annotated by comparing with gene and genomic sequences of other nematodes and annotated proteins on public databases. The annotated transcripts were much more similar to sequences of Heterodera glycines than to those of Globodera pallida and root knot nematodes (Meloidogyne spp.). Analysis of these transcripts showed that a subset of 2,918 transcripts was common to free-living and plant parasitic nematodes suggesting that this subset is involved in general nematode metabolism and development. A set of 148 contigs and 183 singletons encoding putative homologues of effectors previously characterised for plant parasitic nematodes were also identified: these are known to be important for parasitism of host plants during migration through tissues or feeding from cells or are thought to be involved in evasion or modulation of host defences. In addition, the presence of sequences from a nematode virus is suggested. The sequencing and annotation of this transcriptome significantly adds to the genetic data available for H. schachtii, and identifies genes primed to undertake required roles in the critical pre-parasitic and early post-parasitic J2 stages. These data provide new information for identifying potential gene targets for future protection of susceptible crops against H. schachtii.
甜菜孢囊线虫（Heterodera schachtii）是一种主要的根部害虫，对甜菜、芸苔属植物及相关物种的产量有重大影响。对这种重要的植物病原体的分子特征研究有限：为了确定其防治的靶标基因，利用罗氏GS FLX对甜菜孢囊线虫寄生前J2阶段的转录组进行了测序。平均PHRED得分>22的97%的 reads（即387,668条）分别用CAP3和CLC基因组学工作台组装成37,345个和47,263个重叠群。通过与其他线虫的基因和基因组序列以及公共数据库中的注释蛋白进行比较，对转录本进行注释。注释后的转录本与大豆孢囊线虫（Heterodera glycines）的序列比与苍白球孢囊线虫（Globodera pallida）和根结线虫（Meloidogyne spp.）的序列更为相似。对这些转录本的分析表明，2918个转录本的一个子集在自由生活和植物寄生线虫中是共同的，这表明该子集参与线虫的一般代谢和发育。还鉴定出一组148个重叠群和183个单拷贝，它们编码先前已鉴定的植物寄生线虫效应子的假定同源物：已知这些对于线虫在组织中迁移或从细胞取食期间寄生宿主植物很重要，或者被认为参与逃避或调节宿主防御。此外，提示存在来自一种线虫病毒的序列。该转录组的测序和注释显著增加了甜菜孢囊线虫可用的遗传数据，并鉴定出在关键的寄生前和寄生后早期J2阶段承担所需作用的基因。这些数据为确定未来保护易感作物免受甜菜孢囊线虫侵害的潜在基因靶标提供了新信息。
