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bioRxiv · 10.1101/2023.07.15.549003

In silico characterization and phylogenetic analysis of Elaeocarpus ganitrus based on ITS2 barcode sequence

Kushwaha, J.·Joshi, A.
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Abstract

Plant molecular systematics relies on using DNA barcodes for studying the evolutionary relationship between species Sequences of the nuclear internal transcribed spacer (ITS) regions have been used widely in molecular phylogenetic studies because of their high variability compared to plastid sequences. Elaeocarpus is a diverse genus within the family Elaeocarpaceae and is widely distributed worldwide among tropical and subtropical climatic zones. Elaeocarpus ganitrus has important medicinal and religious values in India. However, Elaeocarpus ganitrus evolutionary relationship with other Elaeocarpus species is not much explored, especially at the molecular and phylogenetic levels. The present research successfully amplified the nuclear gene ITS2, sequenced and submitted it to NCBI Genbank after using Basic Local Alignment Search Tool (BLAST). Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) resulted in different numbers of molecular operational taxonomic units (MOTUs). The lowest score of ASAP (4.5) segregated the sequences into 31 MOTUs with the Threshold dist. value of 0.003524. This study establishes an evolutionary relationship between Elaeocarpus ganitrus and other species belonging to the same genus through the neighbor-joining method. The 38 Elaeocarpus samples were clustered into seven major groups based on ITS2 sequence: Group I is represented by Elaeocarpus ganitrus along with Elaeocarpus sylvestris, Elaeocarpus glabripetalus, Elaeocarpus duclouxii, Elaeocarpus decipiens, and Elaeocarpus zollingeri. Group II is characterized by Elaeocarpus austroyunnanensis and Elaeocarpus glaber. Group III comprises Elaeocarpus sphaericus, Elaeocarpus angustifolius, Elaeocarpus grandis, Elaeocarpus ptilanthus, and Elaeocarpus sphaerocarpus. Three accessions of Elaeocarpus hookerianus are placed in group IV. Elaeocarpus largiflorens and Elaeocarpus thelmae represent group V. Groupr VI contains three species: Elaeocarpus sylvestris, Elaeocarpus dubius, and Elaeocarpus johnsonii. Group VII comprises five species which include Elaeocarpus glabripetalus, Elaeocarpus rugosus, Elaeocarpus tuberculatus, Elaeocarpus hainanensis, and Elaeocarpus angustifolius. The study concludes with the possibility of correctly using the ITS2 gene to identify, discriminate, and documentation of Elaeocarpus ganitrus and other species of the same genus.

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Kushwaha, J., Joshi, A.. 2023-07-15. In silico characterization and phylogenetic analysis of Elaeocarpus ganitrus based on ITS2 barcode sequence. https://doi.org/10.1101/2023.07.15.549003

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