Construction of Pseudomolecule Sequences of the aus Rice Cultivar Kasalath for Comparative Genomics of Asian Cultivated Rice

Abstract

Having a deep genetic structure evolved during its domestication and adaptation, the Asian cultivated rice (Oryza sativa) displays considerable physiological and morphological variations. Here, we describe deep whole-genome sequencing of the aus rice cultivar Kasalath by using the advanced next-generation sequencing (NGS) technologies to gain a better understanding of the sequence and structural changes among highly differentiated cultivars. The de novo assembled Kasalath sequences represented 91.1% (330.55 Mb) of the genome and contained 35 139 expressed loci annotated by RNA-Seq analysis. We detected 2 787 250 single-nucleotide polymorphisms (SNPs) and 7393 large insertion/deletion (indel) sites (>100 bp) between Kasalath and Nipponbare, and 2 216 251 SNPs and 3780 large indels between Kasalath and 93-11. Extensive comparison of the gene contents among these cultivars revealed similar rates of gene gain and loss. We detected at least 7.39 Mb of inserted sequences and 40.75 Mb of unmapped sequences in the Kasalath genome in comparison with the Nipponbare reference genome. Mapping of the publicly available NGS short reads from 50 rice accessions proved the necessity and the value of using the Kasalath whole-genome sequence as an additional reference to capture the sequence polymorphisms that cannot be discovered by using the Nipponbare sequence alone.

The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice

“…Alignment of available Kasalath genomic sequence data (Sakai et al, 2014) against the Nipponbare genome sequence (International Rice Genome Sequencing Project, 2005) showed that Kasalath has a 30-kb deletion that includes the TAM1 region on chromosome 12. For several of the tested cultivars from the Japanese and world rice cultivar collections, significant amounts of genomic sequence data are available in the NCBI short read archive (http://www.ncbi.nlm.nih.gov/sra; accession number numbers in Table 2).…”

Rice SNP-seek database update: new SNPs, indels, and queries

“…In addition to Nipponbare (japonica), the SNP-calling pipeline (11) was run on four sequenced rice genomes representing indica and aus, two of the major rice subpopulations: IR 64 (indica) and DJ 123 (aus) (12), Kasalath (aus) (13) and 93-11 (indica) (14). To avoid including redundant SNP positions, a custom pipeline was run on a path alignment of the five genomes computed from the pair-wise alignment between the five reference genomes.…”

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

“…In recent years, tremendous efforts on NGS (next-generation sequencing)-based genome and transcriptome sequencing and advent of advanced computational genomics tools have expedited the generation of enormous genomic and transcript sequence resources for multiple rice accessions representing diverse cultivated and wild populations 1 (Jain et al, 2014; Sakai et al, 2014). Therefore, it is now possible to extend the analysis of in silico polymorphic SSR markers development previously documented between indica (93-11) and japonica (Nipponbare) into a larger set of rice accessions belonging to diverse population groups by comparing their freely accessible genomic sequences at a whole genome level.…”