Abstract
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Here we report the de novo assembly of an indica rice genome Shuhui498 (R498) through the integration of single-molecule sequencing and mapping data, genetic map and fosmid sequence tags. The 390.3 Mb assembly is estimated to cover more than 99% of the R498 genome and is more continuous than the current reference genomes of japonica rice Nipponbare (MSU7) and Arabidopsis thaliana (TAIR10). We annotate high-quality protein-coding genes in R498 and identify genetic variations between R498 and Nipponbare and presence/absence variations by comparing them to 17 draft genomes in cultivated rice and its closest wild relatives. Our results demonstrate how to de novo assemble a highly contiguous and near-complete plant genome through an integrative strategy. The R498 genome will serve as a reference for the discovery of genes and structural variations in rice.
Highlights
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism
We sequenced an F3 population of 364 individuals produced from a cross between rice genome Shuhui498 (R498) and Nip via genotyping-by-sequencing (GBS) technology[26]
We found 8,402 presence variations (PVs) in R498 and 7,119 PVs in Nip at least 500 bp, which include 170 and 92 PVs that are at least kb in R498 and Nip, respectively (Supplementary Data 4)
Summary
A high-quality reference genome is critical for understanding genome structure, genetic variation and evolution of an organism. Real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform generates long reads of up to 40–60 kb with randomly distributed errors[7] This makes SMRT sequencing very suitable for de novo genome assembly under high sequencing depth, and it has been used to assemble complete microbial genomes, high-quality plant draft genomes and significantly improved human and animal reference genomes[8,9,10,11]. We present a cost-effective method for de novo assembly of high-quality reference genomes by leveraging whole-genome shotgun (WGS) SMRT sequencing, pooled fosmid clone sequencing and genetic map construction, and using BioNano genome maps to verify and help correct the assembled sequences. Our method can effectively assemble high-quality complex genomes This R498 assembly provides an extra resource for gene discovery and for studying genetic variations in rice
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