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Evolutionary studies in sub-families of Leguminosae family based on
matK
gene
2
relationships from shallow to deep taxonomic levels
(Johnson and Soltis, 1994; Hayashi and Kawano, 2000;
Hilu et al., 2003; Cameron, 2005). In addition to the
importance of
matK
in plant phylogenetics, it is also
the only putative group II intron maturase encoded in
the chloroplast genome (Neuhaus and Link, 1987).
Maturases are enzymes that catalyze the removal of
nonautocatalytic intron from premature RNAs.
Maturases generally contain three domains: a
reverse-transcriptase (RT) domain, domain X (the
proposed functional domain), and a zinc-finger-like
domain (Mohr et al., 1993). The 3′ region of
matK
has
homology to the domain X of mitochondrial group II
intron maturases (Neuhaus and Link, 1987). This
region of
matK
also lacks indels (Hilu and Liang, 1997),
indicating evolutionary constraint and conservation of
function. Among higher plants,
matK
is the only plastid
gene containing this putative maturase domain
(Neuhaus and Link, 1987). The
matK
gene stands out
among plastid genes used in plant systematics in its
distinct mode and tempo of evolution. The rate of
substitution in
matK
is three times higher at the
nucleotide level and is six times higher at the amino
acid level than that of
rbcL
(Johnson and Soltis, 1994;
Olmstead and Palmer, 1994), denoting it as a fast or
rapidly evolving gene (Soltis and Soltis, 2004). The
accelerated rate of amino acid substitution in
matK
is
due to almost even distribution of substitution rates
among the three codon positions compared with most
protein-coding genes where the rates are skewed
toward the third codon position.
Figure 1. Structure of
matK
gene
.
1.2. NCBI (The National Center for Biotechnology
Information)
NCBI is part of the United States National Library of
Medicine (NLM), a branch of the National Institutes of
Health. The NCBI houses a series of databases relevant
to biotechnology and biomedicine. Major databases
include GenBank for DNA sequences, Protein,
Genome, EST etc. All these databases are available
online through the Entrez search engine
(
http://www.ncbi.nlm.nih.gov/
).
1.3. DNA (Deoxyribonucleic acid) / Nucleotide
DNA is a molecule that encodes the genetic
instructions used in the development and functioning
of all known living organisms and many viruses. Along
with RNA and proteins, DNA is one of the three major
macromolecules essential for all known forms of life.
DNA is well-suited for biological information storage,
since the DNA backbone is resistant to cleavage and
the double-stranded structure provides the molecule
with a built-in duplicate of the encoded information
(
http://www.ncbi.nlm.nih.gov/nuccore/
).
1.4. Protein
Proteins are large biological molecules consisting of
one or more chains of amino acids. Proteins perform a
vast array of functions within living organisms,
including catalyzing metabolic reactions, replicating
DNA, responding to stimuli, and transporting
molecules from one location to another
(
http://www.ncbi.nlm.nih.gov/protein/
).
[II]Materials and Methods
Figure 2. Flow chart of methods used in this study.
In this paper we have considered around 266 species
which are found in Gujarat state of India (Sagar Patel et
al., 2013). Further we searched each species in NCBI
database and finally found around 148 species’
information like DNA, Protein and other useful
information of leguminosae family (Sagar Patel et al.,
2014). Further we have only considered
matK
gene
sequences of DNA and Protein sequences.
Evolutionary analysis done in MEGA 5 software with
two different methods one with Maximum Likelihood
(ML) method with Bootstrap method and other method
PLANT GENE AND TRAIT