Analyses of the root-knot nematode (Meloidogyne graminicola) transcriptome during rice (Oryza spp.) infection

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa (Nipponbare) and O. glaberrima (TOG5681) infection were characterized at different time after infection. M. graminicola RNA-Seq data were retrieved from 14 (7 × 2 replicates) cDNA libraries obtained from pre-parasitic M. graminicola stage-two juveniles (J2s), and from O. sativa cv Nipponbare (susceptible) or O. glaberrima TOG5681 (resistant) plants challenged with M. graminicola. Root tips and galls, when formed, were collected at 2, 4, or 8 dpi. Time points 2, 4, and 8 dpi were chosen to focus on the early stages of the interaction, when gene expression differences may determine the nature of interaction between both partners. We generated a de novo M. graminicola transcriptome composed of 44,137 sequences. We compared the M. graminicola transcriptomes before and during infection to identify M. graminicola genes differentially expressed at 2, 4 and 8 days after infection of susceptible (Nipponbare) or resistant (TOG5681) rice.

植物寄生线虫禾谷根结线虫（Meloidogyne graminicola）对水稻（Oryza sativa）栽培造成严重危害。近缘物种光稃稻（Oryza glaberrima）对该线虫的抗性可阻碍其二龄幼虫（stage-two juveniles，J2s）的根侵入，并终止线虫后续的发育进程。本研究针对该线虫在侵染水稻（栽培稻品种Nipponbare）与光稃稻TOG5681过程中表达的基因，于侵染后不同时间点开展了表征分析。禾谷根结线虫的RNA测序（RNA-Seq）数据取自14个（7组2次生物学重复）互补DNA（cDNA）文库，这些文库分别来源于寄生前期的禾谷根结线虫二龄幼虫（J2s），以及被该线虫侵染的感病栽培稻品种Nipponbare或抗病光稃稻TOG5681植株。若形成根结（gall），则于接种后天数（days post inoculation，dpi）2、4或8天采集根尖与根结样本。选择这三个时间点，旨在聚焦该寄主-病原互作的早期阶段——此时的基因表达差异或可决定双方互作的最终性质。本研究构建了包含44137条序列的禾谷根结线虫从头转录组（de novo transcriptome），并通过比较该线虫在侵染前与侵染过程中的转录组，鉴定出了在侵染感病稻Nipponbare或抗病稻TOG5681后2、4、8天时差异表达的禾谷根结线虫基因。