Whole-Genome Sequencing Revealed a Late-Maturing Isogenic Rice Koshihikari Integrated with Hd16 Gene Derived from an Ise Shrine Mutant

Table 1

Summary of resequencing data by next-generation sequencing.

	Seq by Illumina HiSeq 4000		Mapping to the ref. genome		Mapping status
Library name	Reads obtained (bp)	Bases generated (bp)	Reads unmapped/mapped; ratio (%)	Ref. bases cover; ratio (%)	median	mean	Depth median	Depth mean
Koshihikari_1	66,135,729	6,679,708,629	0.005884119	99.03155997	153	113.783	30	~35.67571
Koshihikari_2	66,135,729	6,679,708,629
Koshihikari Hd-i_1	114,244,160	11,538,660,160	0.003406305	99.18284484	184	160.232	30	~61.51913
Koshihikari Hd-i_2	114,244,160	11,538,660,160

A whole-genome analysis by next-generation sequencing was conducted on Koshihikari and the late-maturation isogenic Koshihikari (BC₄F₂), which was integrated with the late-maturation gene derived from Isehikari. First, the read sequences gained by NGS from Koshihikari genome were mapped by using the Nipponbare genome as a reference sequence. As a result, a 372,912,445 bp long consensus sequence of the Koshihikari genome was constructed at the average depth of 35.68 with 99.0% cover ratio. Next, by using the consensus sequence of Koshihikari as a reference, the read sequences gained from late-maturation isogenic Koshihikari were assembled at 99.1% cover ratio with the average depth of 61.52.