Exploring the rice dispensable genome using a metagenome-like assembly strategy

Table 1 Alignment results of the cloned genes absent from the Nipponbare genome to the dispensable genomes

Gene name	Length (bp)	Trait	Reference	Raw assembly		Local de novo reassembly
				Query	Identity (%)	Query	Identity (%)	Number of haplotypes
				coverage (%)	Identity (%)	coverage (%)	Identity (%)	Number of haplotypes
GW5	435	Grain width	Shomura et al. 2008 [13]	100	90	100	100	5
GW5	435	Grain width	Weng et al. 2008 [30]	100	90	100	100	5
Sub1A	1663	Submergence tolerance	Xu et al. 2006 [14]	100	99	100	100	7
Xa27	342	Blight resistance	Gu et al. 2005 [32]	100	100	100	100	16
PSTOL1	975	Phosphorus starvation tolerance	Gamuyao et al. 2012 [35]	100	97	100	100	13
Pikm1-TS	6319	Blast resistance	Ashikawa et al. 2008 [15]	100	99	17	99	3
Pikm2-TS	3229	Blast resistance	Ashikawa et al. 2008 [15]	100	99	100	99	7
OsHKT2	1781	Na⁺- and K⁺-coupled transporter	Horie et al. 2001 [34]	95	95	62	97	19
Pib	10,322	Blast resistance	Wang et al. 1999 [31]	33	80	-	-	-
SNORKEL1	1487	Deepwater response	Hattori et al. 2009 [33]	7	83	-	-	-
SNORKEL2	1179	Deepwater response	Hattori et al. 2009 [33]	12	82	-	-	-

Length is the length of the reported sequence of the gene. Query coverage (%) is the percentage of the reported sequence matched by a dispensable sequence from raw assembly or local de novo reassembly. Identity (%) is the percentage of the reported sequence identical with a dispensable sequence from raw assembly or local de novo reassembly. Number of haplotypes is the number of haplotypes constructed with the local de novo reassembly

ISSN: 1474-760X