IC4R009-Genome-2014-24578372

Project Title

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

The Background of This Project

• The researchers 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 reference Nipponbare sequence is particularly useful for evolutionary and functional studies, its use for extensive analysis of genome diversity remains limited because of considerable inter- and intra-species and even intrasubspecies chromosomal rearrangements, such as insertionsanddeletions,duplications,inversions,translocations, and transpositions.

Plant Culture & Treatment

• The researchers sequenced the whole genome of Kasalath rice by using two NGS platforms, Illumina (GAIIx and HiSeq2000) for short reads and Roche 454 (GS FLX Titanium and GS FLXþ Titanium) for long reads.
• The researchers performed de novo assembly and chromosomal mapping of the NGS read seq sequences.
• The researchers carried out the transcriptome analysis with RNA-Seq data obtained from young leaves and panicles of Kasalath by using the GAIIx for annotation of expressed sequences.
• Comparative analysis oftheKasalathsequenceandthoseofotherricecultivars confirmed its value as a new reference genome to facilitate future evolutionary and functional genomic studies in rice.

Research Findings

• Sequence alignment by MUMmer revealed SNPs at 2787250 nucleotide sites between Kasalath and Nipponbare (alignment length of 278.75Mb) and 2216 251 nucleotide sites between Kasalath and 93-11 (alignment length of 259.00 Mb) (Table 2).

• The researchers found that most of the SNPs resided in non-genic regions. Only 5.1% (142366) of the total SNPs detected between Nipponbare and Kasalath were located within protein-coding regions (Fig. 1).

'Figure 1.Distribution pattern of SNPs detected between the genomes of Nipponbare and Kasalath cultivars.'

• The distribution pattern of deletion sizes in Kasalath against Nipponbare displayed two peaks if deletions of ,1 kb were ignored (Fig. 2 and Supplementary Fig. S2). The first and the largest peak appeared at 4 kb (3–5 kb), in which 58.5% of nucleotides were from repetitive sequences. The second peak was at 12–13 kb (11–14 kb), in which up to 62.7% of the nucleotides were from repetitive sequences.

Figure 2.Size distribution and sequence classification of large deletions in Kasalath in comparison with Nipponbare.

Figure S2.Detection of large indels (≥100 bp) between the Kasalath and Nipponbare genomes. (A) An insertion in Kasalath. (B) An insertion in Nipponbare

Labs working on this Project

• Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan *Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
• Department of Bioscience, Faculty of Applied Bioscience,Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan.

Corresponding Author

• jzwu@affrc.go.jp
• Tel. þ81 29-838-6148. Fax. þ81 29-838-6028.