Sequences analysis
The entire sequence of the atp H genes of B810S and 810S were
determined by comparisons with those of other previously reported rices
(GenBank accession number NC_031333). The atpH gene sequences of
B810S’, 810S’ and other rices (downloaded from Genebank)were aligned by
the computer program Clustal X 1.81. To calculate the sequence
differences between B810S and 810S, the formula D = 1 -
(M/L ) was used. In the formula, different capitals represent
different means, where M is the number of alignment positions at which
the two sequences have a common base , and L is the total number of
alignment positions over which the two sequences are compared. The
Megalign procedure within DNAStar 5.0 (Burland, 2000) was used to
analyze sequence similarities of B810S and other rices which included
810S and other rice gene sequences which are downloaded from Genebank.
Also, to align the variable sites of B810S and 810S, and calculate their
haplotype (Hd) and nucleotide diversity (Pi), the computer program Dna
SP 5.0 was used with default parameters.
Phylogenetic analysis
To infer the phylogenetic relationship of B810S, 810S and other rices, a
phylogenetic tree was re-constructed using the maximum likelihood (ML)
method. ML analyses were performed using PhyML 3.0 (Guindon et al.
2010), and the GTR+I model with its parameters determined by JModeltest
(Posada, 2008). Bootstrap support (BS) for the ML tree was calculated
using 100 bootstrap replicates. In the tree, B810S, 810S and other
members of the Oryzais genus(e.g.,(O.sativa (MK348618),O.coarctata (MG383937), O.
longistaminata (KF359907),O.meridionalis (KF359906), O.barthii (KF359904), O.
glaberrima
(KF359903), O. rufipogon (KF359902), O.
glumipatula (KR364803), O. nivara (AP006728),O.rhizomatis (KX085497), O.eichingeri (KX085496),O.latifolia (MF401451), O. alta (KF359913) andO.officinalis (KF359910)) were considered as the inside-group, andTriticum aestivum was considered as the out-group. Tree View
program version 1.65 was used to draw the phylogenetic tree (Page,
1996).