Oryza sativa Japonica Group cultivars

Overview

Asian cultivated rice is a staple food for half of the world population. With a genome size of ~390 Mb (n=12), rice has the smallest genome among the domesticated cereals, making it particularly amenable to genomic studies. In 2020, a reanalysis of the population structure analysis showed that rice could be subdivided into a total of 15 subpopulations (XI-1A, XI-1B1, XI-1B2, XI-2B, XI-2A, XI-3B1, XI-3A, XI-3B2, GJ-trop1, GJ-trop2, GJ-subtrp, GJ-tmp, cA2, cA1 and cB) and 4 admixed populations (GJ-adm, XI-adm, admixed and cA-adm). Then 16 rice cultivar varieties were selected based on genetic diversity and origin that could represent the 15 subpopulations and the largest admixed population, i.e. XI-adm. The collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice. Oryza sativa cv. IRGC 135833 (variety cv. Azucena) (collected from: Philippines) is selected as the representative of GJ-trop1 subpopulation, in which the accessions are mostly collected from Indonesia, Philippines, United States of America, Cote d'Ivoire, and Brazil.

Notes of Subpopulations: cA = circum-Aus; cB = circum-Basmati; GJ= Geng-japonica where trop = tropical, subtrp = subtropical; XI = Xian-indica

Assemblies

Scientists from the University of Arizona, King Abdullah University of Science and Technology, International Rice Research Institute, and Huazhong Agricultural University generated Oryza sativa cv. IRGC 135833 (variety cv. Azucena) genome high quality reference (n=12), which is one of the 16 PSRefSeqs and represents GJ-trop1 subpopulation.

The whole DNA was sequenced by >100 X PacBio Sequel cells. The genome assemblies were carried out by multiple assemblers, i.e. mecat2, canu and falcon. The pseudomolecule of each chromosome was constructed using the nucleotide sequence of multiple assemblies by Genome Puzzle Master by using Minghui63 as a guide. The final assembly was polished by >100 X PacBio corrected reads and > 100 X Illumina clean reads.

Annotation

Done by Ware Lab researchers at Cold Spring Harbor Laboratory. Initial protein-coding genes were generated with the MAKER-P pipeline using line-specific RNA-seq transcript and full-length transcripts from Zhou et al (2020). Non-overlapping ab initio models were added using SNAP, Augustus, and FGENESH gene predictors. The combined gene models were improved for structure including UTR extensions using line-specific full-length transcripts and rice ESTs from GenBank. Final models were quality checked using GFF3toolkit and canonical transcripts assigned with TRaCE (Olsen and Ware 2020).