Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice
Journal
DNA Research
Journal Volume
21
Journal Issue
4
Date Issued
2014-01-01
Author(s)
Hiroaki, Sakai
Hiroyuki, Kanamori
Yuko, Arai Kichise
Mari, Shibata Hatta
Kaworu, Ebana
Youko, Oono
Kanako, Kurita
Hiroko, Fujisawa
Satoshi, Katagiri
Yoshiyuki, Mukai
Masao, Hamada
Takashi, Matsumoto
Yuichi, Katayose
Kyo, Wakasa
Masahiro, Yano
Jianzhong, Wu
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 Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.
Subjects
Comparative genomics | Gain and loss of genes | Genome re-sequencing | Oryza sativa | SNPs and indels
Type
journal article