Author:
Phillips Aaron L.,Ferguson Scott,Watson-Haigh Nathan S.,Jones Ashley W.,Borevitz Justin O.,Burton Rachel A.,Atwell Brian J.
Abstract
AbstractOryza 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.
Funder
Deputy Vice-Chancellor (Research) Discretionary Fund
Centre of Excellence in Plant Energy Biology, Australian Research Council
Publisher
Springer Science and Business Media LLC
Reference68 articles.
1. Stein, J. C. et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat. Genet. 50, 285–296 (2018).
2. Brar, D. S. & Khush, G. S. Wild relatives of rice: A valuable genetic resource for genomics and breeding research. In The Wild Oryza Genomes (eds Mondal, T. K. & Henry, R. J.) 1–25 (Springer, 2018).
3. Atwell, B. J., Wang, H. & Scafaro, A. P. Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Plant Sci. 215–216, 48–58 (2014).
4. Bisht, D. S., Solanke, A. U. & Mondal, T. K. Informatics of wild relatives of rice. In The Wild Oryza Genomes (eds Mondal, T. K. & Henry, R. J.) 27–40 (Springer, 2018).
5. Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967 (2010).
Cited by
4 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献