Phylogeny and Bioinformatics Study on Leaf Tissue Genes for Selected Elite Cultivars of Plantain (Musa paradisiaca L.) in the Rain Forest Ecology of Nigeria
Journal Title: Journal of Advances in Biology & Biotechnology - Year 2017, Vol 15, Issue 3
Abstract
Aims: To show that phylogenetic and bioinformatics study could be very crucial to the survival and adaptation of elite plantain species that are threatened by rapid changes in environment, urbanization, genetic erosion and climate in the rain forest ecology of Nigeria. Study Design: The study is a survey of elite cultivars of plantain in the rain forest ecology of Nigeria, involving laboratory work and use of genetic analysis software for evaluation. Place and Duration of Study: The leaf samples were sourced and collected from the rain forest of Nigeria in 2015 and outsourced to South Africa for laboratory DNA extraction and leaf tissue gene sequencing. Methodology: Apical leaf samples less that 2 day old were collected from each of the 14 elite plantain cultivars, preserved in silica gel nylon and outsourced to South Africa for DNA extraction using the CTAB method and Leaf Tissue genes sequencing using the Sangers method. Sequenced DNA nucleotides were aligned using the Molecular Evolution and Genetic Analysis (MEGA 6.0) software for multiple alignment and ClustalW. Aligned sequenced were pasted in note pad, saved and later pasted in a new window for phylogeny tree construction using the maximum livelihood option. The GOR IV and PHYRE2 softwares were used to determine the secondary and 3D tertiary structure for each elite cultivar. Results: Phylogenetic and bioinformatics study is very crucial to the survival of these elite plantain cultivars in the study geographical locations, which are being threatened by the rapid changes in environment, urbanization, climate change and emerging pests and disease conditions. The results revealed that the elite plantain cultivars have a rooted phylogenetic tree indicating a common ancestry for all. The phylogeny tree showed two internal ancestors and two descendant relatives for the cultivars. The phylogeny tree showed four clusters with four branches and leaves. There was an OUT group made up of cooking bananas with ABB genome which complemented the other cultivars with AAB genome to give the tree a root. Cultivars in the first cluster showed 100G consensus, those on the second cluster showed 69G consensus while those in the third cluster showed 53G consensus. Results of bioinformatics study revealed that the C-G content of 46.04% was higher in cooking bananas and least 35.26% in Ogoni Red cultivar. Number of amino acids was also higher 221 in cooking bananas and least in Ogoni red. However, number of nucleotide was higher in Enugu plantain and least in cooking bananas. The secondary and 3D tertiary structures of all the elite cultivars showed variations their fold structures as well as in their alpha and beta properties. Conclusion: Bioinformatics study, alongside a complete knowledge on the phylogeny of the elite plantain cultivars will scale up and promote conservation efforts for plantain germplasm which do not possess seeds for short, medium and long term storage. The study will also provide baseline information on the phylogeny and bio information that will help in the establishment of biodiversity within the plantain germplasm for future research purpose, food security and income generation.
Authors and Affiliations
Godwin Michael Ubi, Chioma M. Okolo Adilieje, Nneka Constance Ogbonna, Success Kalu Eni
Keywords
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- EP ID EP318259
- DOI 10.9734/JABB/2017/28482
- Views 94
- Downloads 0
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