TITLE:
Molecular Footprint of Kenya’s Gene Bank Repositories Based on the cp-Genome Signatures
AUTHORS:
Okoth Patrick, Muoma John, Omayio Dennis, Barasa Mustafa, Angienda Paul
KEYWORDS:
DNA Barcoding, Molecular Phylogeny, Molecular Diversity, Plastid Markers, Genome Signatures, Genotyping, NCBI
JOURNAL NAME:
American Journal of Molecular Biology,
Vol.8 No.4,
October
30,
2018
ABSTRACT: While the mutational processes that subsume biological
diversity can be revealed in great detail through phylogenetic inferencing using
plastid markers, few studies document their use. Accurate phylogenic inference can
provide a framework for addressing a host of important evolutionary questions including
a context to reconstruct molecular evolution of an organism. Despite the obvious
utility of plastid markers in illuminating biological enquiry, many important questions
still abound. The use of cp-DNA gene sequence
data for phylogenetic inference can have an enormous impact on plant phylogenetics
and systematics. The repertoire of genetic diversity of Kenya’s Gene Bank repositories
can be explored based on cp-genome signatures.
This is because cp-DNA-based mutational
changes are an important additional tool to the previous evidence available on plant
evolution yet to be explored in biodiversity studies in Kenya. Taken together, these
evolutionary changes can inspire development of realistic algorithms for phylogenetic
inferencing based on molecular data. Phylogenetic reconstructions are at the very
core of molecular evolution. Comparative sequence analyses of plastid markers can
have utility beyond the study of phylogeny. The pattern of nucleotide substitution
observed over evolutionary time can reflect functional constraints imposed due to
natural selection. In line with this, it is possible to detect subtle anatomical
variations associated with small fitness effects that can account for genetic diversity
at varietal level. The lack of sequence information in Kenyan cowpea has limited
the robust advancement of molecular markers use in dissecting diversity based on
the putative plastid markers[1]. The present
study sought to generate and upscale novel technologies such as genomics, DNA barcoding
and bio-informatics in understanding molecular diversity of cowpea accessions from
the Gene Bank of Kenya and ecotypes. A total of 298 sequences of cowpea germplasm
conserved as in situ and ex situ in Kenya but sourced from phylogeographically diverse settings were examined
and their genetic profiles were characterized and evaluated using molecular tools.
The Gene Bank materials were purposefully sampled to develop subsets representative
of the diversity in the genepool’s collection. We present an extensive study on
characterizing the genetic diversity of cp-DNA
gene sequence data for the cowpea accessions from the Nation Gene Bank of Kenya.
The comparative sequence analyses and phylogenetic clustering of seven plastid markers
widely used in the DNA barcoding of land plants provide insights on the molecular
evolution of this vascular plant. The detailed and in-depth genome characterization
herein greatly enriches the genetic profile of this important crop, which can help
in reconstructing realistic models of mutational process during plant evolutionary
history. This study addressed this gap by employing a DNA barcode library for cowpea
to determine the loci that yield the best species resolution. As well, this study
examined the efficacy of custom DNA barcode loci for identification success, and
compared phylogenetic diversity measures between sites and among variants.