Two gap-free reference genomes and a global view of the centromere architecture in rice

Abstract

Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gapfree reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which $41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.

gcaPDA: a haplotype-resolved diploid assembler

“…We selected a rice F 1 hybrid by crossing two inbred lines MH63 and ZS97 as test sample. Gap-free reference genomes are available for both parents [ 25 ] which could be used to benchmark the phased diploid assemblies. In total, 23 Gb PacBio HiFi reads, with an average read length of 14.9 Kb of the rice hybrid was generated (Additional file 1 : Table S6).…”

From Green Super Rice to green agriculture: Reaping the promise of functional genomics research

“…In particular, the high-quality (now gap-free) reference genomes of two xian/indica varieties, Minghui 63 and Zhenshan 97, the parents of the elite rice hybrid Shanyou 63, were released in 2016 (http://rice.hzau.edu.cn/). Comparative analysis revealed a surprisingly large number of structural variations (SVs) between these two reference genomes (Zhang et al, 2016;Song et al, 2021). Recently, more than 60 complete rice genome sequences were generated (Zhao et al, 2018b;Thudi et al, 2021).…”

Improved 93-11 Genome and Time-Course Transcriptome Expand Resources for Rice Genomics

“…If two adjacent contigs overlapped with the two ends of long reads, respectively, then the gap between the two contigs were closed using the reads. (VI) Mummer (version 4.0) (Delcher et al, 2003) with the default setting was used to align the contigs on the three genomes [Nipponbare (Kawahara et al, 2013), ZS97, and MH63 (Song et al, 2021)] to detect the potentially adjacent contigs. If one unlocated contig is adjacent to a contig in the interaction map along as supported by PacBio reads, and the unlocated contig was put back into the map.…”

“…For decades, the rice cultivar 93-11, which is one of the main indica cultivars grown across China, has served as a reference genome for molecular breeding research (Yu et al, 2002). Recently, with the development of sequencing technology and the dramatic decrease in its cost, several chromosome-level assemblies of various rice cultivars have been reported, including telomere to telomere assemblies of ZS97 and MH63 (Du et al, 2017;Choi et al, 2020;Song et al, 2021). The assembly data reveals the complex genetic diversity that give rise to desirable domestication traits.…”