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Molecular Footprint of Kenya’s Gene Bank Repositories Based on the <i>cp</i>-Genome Signatures

American Journal of Molecular Biology 2018年第4期8卷 215-244页

作者： Okoth Patrick Muoma John Omayio Dennis Barasa Mustafa angienda paul Department of Biological Sciences Masinde Muliro University of Science and Technology Kakamega Kenya Department of Zoology School of Physical and Biological Sciences Maseno University Private Bag Maseno Kenya Department of Medical Laboratory Sciences (MLS) Masinde Muliro University of Science and Technology Kakamega Kenya

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 conser

关键词： DNA Barcoding Molecular Phylogeny Molecular Diversity Plastid Markers Genome Signatures Genotyping NCBI

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The Potential of DNA Barcode-Based Delineation Using Seven Putative Candidate Loci of the Plastid Region in Inferring Molecular Diversity of Cowpea at Sub-Species Level

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American Journal of Molecular Biology 2016年第4期6卷 138-158页

作者： Patrick Okoth John Muoma Mulaya Emmanuel Wekesa Clabe Dennis O. Omayio paul O. angienda Department of Zoology School of Physical and Biological Sciences Maseno University Maseno Kenya Department of Biological Sciences Masinde Muliro University of Science and Technology Kakamega Kenya Centre for Global Health Research Kenya Medical Research Institute (KEMRI) Kisumu Kenya Department of Biochemistry and Biotechnology Kenyatta University Nairobi Kenya

The novelty and suitability of the mitochondrial gene CO1 in DNA barcoding as a reliable identification tool in animal species are undisputed. This is attributed to its standardized sequencing segment of the mitochondrial cytochrome c oxidase-1 gene (CO1) which has the necessary universality and variability making it a generally acceptable barcode region. CO1 is a haploid single locus that is uniparentally-inherited. Protein-coding regions are present in high-copy numbers making it an ideal barcode. The mitochondrial oxidase subunit I (COI) gene is a robust barcode with a suitable threshold for delineating animals and is not subject to drastic length variation, frequent mononucleotide repeats or microinversions. However, a low nucleotide substitution rate of plant mitochondrial genome [mtDNA] precludes the use of CO1 as a universal plant DNA barcode and makes the search for alternative barcode regions necessary. Currently, there exists no universal barcode for plants. The plastid region reveals leading candidate loci as appropriate DNA barcodes yet to be explored in biodiversity studies in Kenya. Four of these plastid regions are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and three noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbL) which emerge as ideal candidate DNA loci. While different research groups propose various combinations of these loci, there exists no consensus;the lack thereof impedes progress in getting a suitable universal DNA barcode. Little research has attempted to investigate and document the applicability and extend of effectiveness of different DNA regions as barcodes to delineate cowpea at subspecies level. In this study we sought to test feasibility of the seven putative candidate DNA loci singly and in combination in order to establish a suitable single and multi-locus barcode regions that can have universal application in delineating diverse phylogeographic groups of closely related Kenyan cowpea variants. In this study, ou

关键词： DNA Barcoding Plastid Region DNA Sequencing Intergenic Spacers cp DNA Mo-lecular Phylogenetics Intraspecific Infraspecific

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