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A comparative study on 193 plastomes of Poaceae for validity and implications of individual barcode genes and concatenated protein coding sequences with selected plastomes of grasses from the desert of India

2021; Elsevier BV; Volume: 29; Linguagem: Inglês

10.1016/j.mgene.2021.100921

2214-5400

Pritesh Bhatt, Vrinda S. Thaker,

Genetic diversity and population structure

Poaceae is the fifth largest family and one of the important plant family to mankind economically and ecologically. This family includes most important crop plants like wheat, rice and corn. It also includes forage, bamboo, biofuel and medicinal species. Grasses occupy all diverse habitat from aquatic to terrestrial, temperate to tropical, wetlands to deserts. Poaceae consists of subfamilies i.e. Bambusoideae, Oryzoideae and Pooideae (BOP clade), Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae and Danthonioideae (PACMAD clade), Anomochlooideae, Pharoideae and Puelioideae. From these, Panicoideae and Chloridoideae are among the important subfamilies of Poaceae. From the past, many attempts are there for the phylogeny of Poaceae using one or more barcode genes. In the present, study 9 grass species from Kutch desert were selected and their chloroplast DNA was isolated. It was subjected to high throughput sequencing and from these complete plastomes were assembled. They were annotated by different methods and corrected. For phylogenetic analysis, total of 193 Poaceae species were selected and searched for common concatenated protein coding regions. A total of 82 common protein coding genes were extracted and one concatenated sequence was made for each species. Common barcode genes were also individually extracted and their respective phylogenetic trees were prepared by the maximum likelihood method. Statistical analysis was done using DnaSP using various parameters. In phylogeny, most barcode gives reliable phylogeny but unable to resolve some related groups. Among barcodes, the most useful candidate for Poaceae was found to be matK while resolving power of rpoC2 is the lowest. Concatenated sequence resolves all groups in their particular positions and gives accurate phylogeny. This study gives the utility of concatenated protein coding genes over traditional barcodes to resolve the phylogenetic relationship among different species of Poaceae.