Department of Food Science, University of Adelaide, Adelaide, SA, Australia.
ARC Centre of Excellence in Plant Energy Biology, Adelaide, SA, Australia.
Sci Rep. 2022 Jun 25;12(1):10823. doi: 10.1038/s41598-022-14893-5.
Oryza australiensis is a wild rice native to monsoonal northern Australia. The International Oryza Map Alignment Project emphasises its significance as the sole representative of the EE genome clade. Assembly of the O. australiensis genome has previously been challenging due to its high Long Terminal Repeat (LTR) retrotransposon (RT) content. Oxford Nanopore long reads were combined with Illumina short reads to generate a high-quality ~ 858 Mbp genome assembly within 850 contigs with 46× long read coverage. Reference-guided scaffolding increased genome contiguity, placing 88.2% of contigs into 12 pseudomolecules. After alignment to the Oryza sativa cv. Nipponbare genome, we observed several structural variations. PacBio Iso-Seq data were generated for five distinct tissues to improve the functional annotation of 34,587 protein-coding genes and 42,329 transcripts. We also report SNV numbers for three additional O. australiensis genotypes based on Illumina re-sequencing. Although genetic similarity reflected geographical separation, the density of SNVs also correlated with our previous report on variations in salinity tolerance. This genome re-confirms the genetic remoteness of the O. australiensis lineage within the O. officinalis genome complex. Assembly of a high-quality genome for O. australiensis provides an important resource for the discovery of critical genes involved in development and stress tolerance.
澳洲野稻是一种原产于季风性北部澳大利亚的野生稻。国际稻基因图谱整合项目强调了它作为 EE 基因组分支唯一代表的重要性。由于其高长末端重复（LTR）逆转座子（RT）含量，组装澳洲野稻基因组之前一直具有挑战性。将 Oxford Nanopore 长读长与 Illumina 短读长相结合，在 850 个 contigs 中生成了高质量的~858 Mbp 基因组组装，长读覆盖度为 46×。参考指导的支架构建增加了基因组的连续性，将 88.2%的 contigs 放置在 12 个假染色体中。将组装的基因组与栽培稻 cv. Nipponbare 基因组进行比对后，我们观察到了一些结构变异。生成了五个不同组织的 PacBio Iso-Seq 数据，以改进 34587 个蛋白质编码基因和 42329 个转录本的功能注释。我们还报告了基于 Illumina 重测序的三个额外澳洲野稻基因型的单核苷酸变异（SNV）数量。尽管遗传相似性反映了地理分离，但 SNV 的密度也与我们之前关于耐盐性变异的报告相关。这个基因组再次证实了澳洲野稻谱系在 O. officinalis 基因组复合体中的遗传隔离。组装高质量的澳洲野稻基因组为发现参与发育和胁迫耐受性的关键基因提供了重要资源。
