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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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Molecular Diversity of a Seemingly Altitude Restricted <i>Ustilago kamerunensis</i>Isolates in Kenya: A Pathogen of Napier Grass

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American Journal of Molecular Biology 2018年第2期8卷 119-143页

作者： Dennis O. Omayio David M. Musyimi Francis N. Muyekho Samuel I. Ajanga Charles A. O. Midega Clabe S. Wekesa patrick okoth Innocent W. Kariuki Botany Department Maseno University Maseno Kenya Department of Biological Sciences Masinde Muliro University of Science and Technology Kakamega Kenya Industrial Crops Research Institute Kenya Agricultural & Livestock Research Organization Molo Kenya Plant Health Section International Centre for Insect Physiology and Ecology Mbita Kenya Food Crops Research Institute Kenya Agricultural & Livestock Research Organization Muguga Centre Nairobi Kenya

The Central region of Kenya which is the second largest market oriented dairy zone, faces a threat in milk production. The challenge is a disease known as the napier head smut caused by Ustilago kamerunensis. This fungal microorganism is a facultative pathogen which has been reported to cause yield losses in napier grass (Pennisetum purpureum) ranging from 25% to 46% across the affected areas. Additionally, there are reports of the continual spread of the disease into neighbouring county of Nakuru in Rift-Valley region which is the leading milk producing zone in the country. This scenario of spread is worrying combined with observation of variations in damage levels of napier grass clones across the five counties of Central Kenya. These observations led to the hypothesis that possible differences might be existing among the Ustilago kamerunensis variants in Kenya. Further, the differences in biomass yield losses that are within a certain percentage range mentioned-above, seemed to support the existence of possible differences. Therefore, to inform effective integrated management strategies of the pathogen in case it’s co-evolving, this study sought to determine the molecular differences of Ustilago kamerunensis isolates in affected counties using ITS 1 and 2 regions which are spanned by 5.8S ribosomal RNA gene. The Ustilago kamerunensis propagules were systematically collected from affected counties’ hot spot areas for sequencing and phylogenetic analysis. The study revealed the most affected areas to be within the mean altitude level of 1988.17 ± 71.97 metres above sea level. Further, differences in the growth in vitro and molecular characteristics of the seemingly altitude restricted isolates were observed. The Kiambu, Nyandarau and Nakuru counties isolates clustered together, whereas those of Murang’a, Nyeri and Kirinyaga formed another clade. The sequences of sixteen Ustilago kamerunensis isolates were deposited in GenBank with accession numbers ranging from MG7

关键词： Ustilago kamerunensis Diversity Altitude Napier Grass Milk

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