Chromosomes; Phylogeny; Salinity; Oryza/genetics; Genome, Plant; Genome; Oryza; Statistics and Probability; Information Systems; Education; Computer Science Applications; Statistics, Probability and Uncertainty; Library and Information Sciences
Abstract :
[en] Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.
Disciplines :
Agriculture & agronomy
Author, co-author :
Zhao, Hang ✱; Université de Liège - ULiège > TERRA Research Centre ; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
Wang, Wenzheng ✱; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
Yang, Yirong ✱; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
Wang, Zhiwei ; Université de Liège - ULiège > Gembloux Agro-Bio Tech > Gembloux Agro-Bio Tech ; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
Sun, Jing; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
Yuan, Kaijun; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China ; Duke university, Durham, USA
Rabbi, S M Hisam Al; Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
Khanam, Munnujan; Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
Kabir, Md Shahjahan; Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
Seraj, Zeba I; Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
Rahman, Md Sazzadur ✱; Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh. sazzadur.phys@brri.gov.bd
Zhang, Zhiguo ✱; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhangzhiguo@caas.cn
✱ These authors have contributed equally to this work.
Language :
English
Title :
A high-quality chromosome-level wild rice genome of Oryza coarctata.
Ministry of Science and Technology of the People's Republic of China
Funding text :
This research was funded by National Key Research and Development Program of China (2022YFF1001700). We thank Dr. Hongbing Liu for his comments and suggestions of improvement to the manuscript.
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