Skip to main content

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

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

Gene name Length (bp) Trait Reference Raw assembly Local de novo reassembly
Query Identity (%) Query Identity (%) Number of haplotypes
coverage (%) coverage (%)
GW5 435 Grain width Shomura et al. 2008 [13] 100 90 100 100 5
Weng et al. 2008 [30]
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 - - -
  1. 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