Dinabandhu

rate, CHS the lowest rate by experimenting six Ipomoea species. Rausher et

al . (2008) concluded that difference in the rate of nonsynonymous substitution

between upstream enzymes ANS and UFGT and down srteam enzyme CHS is

not because of rate of adaptive substitution but because of selective constraint.

Oberholzer (2000) reported that a new copy of CHS gene is evolved into the

poaceae genome 15 to 25 million years interval and the rate of protein evolution is

increased after duplication of the gene. Clegg et al . (1997) analysed three nuclear

gene families chalcone synthase ( CHS ), ribulose-1,5-bisphosphate carboxylase

( RBC S), and the gene alcohol dehydrogenases ( ADH ) and found that duplication

and divergence in function appears to be relatively common for CHS genes in

evolution of flowering plants. They also suggested that adaptive evolution has

played an important role in driving divergence following gene duplication

events and recombination is a pervasive force at all levels of plant evolution.

Additionally, the nucleotide diversity across a genome is the source of most of

the phenotypic variation (Buckler et al ., 2002) although plant lineages differ in

mutation rates, research has yet to show the connection between the mutation

rate and extent of gene diversity (Muse, 2000). Nucleotide diversity provides

a snap shot of evolution at its most basic level. Nucleotide diversity reflects a

rich history of selection, migration, recombination, and mating systems (Muse,

2000). Balancing selection and/or frequency-dependent selection may also play

an important role in increasing diversity at specific loci within a genome (Oleksyk

et al ., 2001). Comparative sequence analysis is a valuable tool to determine the

nature of the evolved functions that make one species different from another

(Bennetzen, 2000). Though different crops species of solanaceae and poaceae

are scientifically and economically very important, the comparative analysis with

respect to anthocyanin pathway genes between these two families has not been

reported yet. Therefore, comparative sequence analysis between different species

of solanaceae and poaceae will unravel the evolutionary relationship between

these two important families.

Materials and Methods

The released tomato genome was downloaded from and anthocyanin genes

were predicted by using BLAST (http://blast.ncbi.nlm.nih.gov/ Blast.cgi) and

FGENESH (www.softberry.com) gene prediction programme. The predicted

genes were BLAST searched against NCBI non redundant (nr) database (http://

blast.ncbi.nlm.nih.gov/ Blast.cgi) to retrieve orthologs from monocots (poaceae)

and dicots (solanaceae) present in whole plant kingdom. Synonymous and non-

synonymous substitution rate (McDonald and Kreitman analysis- McDonald

and Kreitman (1991), DNA divergence and conserved DNA regions, codon

usage bias were calculated by using DnaSP version-5.10 software (www.ub.edu/

dnasp/). Ka (the number of nonsynonymous substitutions per nonsynonymous

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International Journal of Bioinformatics and Biological Sciences : v.2 n.3&4. Dec. 2014