A PHYLOGENETIC ANALYSIS OF THE CUCURBITACEAE: EVIDENCES FROM MATK NUCLEOTIDE SEQUENCES

• Published in: International journal of bioinformatics research Vol. 1; no. 2; pp. 47 - 53
• Main Author: Reddy, B Uma
• Format: Journal Article
• Language: English
• Published: 30.12.2009
• Subjects: Bioinformatics; Chloroplasts; Computer programs; Cucurbitaceae; Evolutionary genetics; Introns; Mathematics; matK gene; Momordica; Nucleotide sequence; Nucleotides; Phylogeny; Sicyos; software; Splicing; Transversion
• ISSN: 0975-3087; 0975-9115
• DOI: 10.9735/0975-3087.1.2.47-53

MaturaseK gene (matK) of chloroplast is highly conserved in plant systematics which is involved in Group-II intron splicing. The size of the gene is approximately 1500 base pairs in length, located with in the intron of trnK. In the present study, matK gene from Cucurbitaceae was taken for the analysis of variants, parsimony site, patterns, transition/ transversion rate and phylogeny. The family Cucurbitaceae comprises over 120 genera and 825 species with medicinal values. The matK gene sequences have been withdrawn from GenBank and used for the analysis. The multiple sequence alignments were performed by Genebee-ClustalW. The phylogenetic analyses were carried out by MEGA (Molecular Evolutionary Genetics Analysis) software package based on Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Maximum Parsimony (MP) methods. The results indicated that the Trichosanthes, Austrobryonia, Momordica, Neoalsomitra, Gomphogyne, Sicyos genera showed polyphyletic condition. The overall invariants between the 88 taxa are 28.5%, average composition of nucleotides among taxa are found to be approximately, A-0.30, T-0.37, G-0.15, C-0.17 and the ratio of transition and transversion is 0.824. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intra-generic relationships. From this study, it could be concluded that, the chloroplast matK gene sequences can unambiguously resolve the relationships, as well as provided a good indication of major supra-generic groupings among the selected members of the family Cucurbitaceae.