Sequence Analysis of some species in the genus Amaranthus L. using Ribulose-1.5 - bisphosphate carboxylase/oxygenase (rbcL) genes
DOI:
https://doi.org/10.61308/ZOJA3530Keywords:
Bioinformatics; Amaranthus; rbcL; phylogenetic study; genetic diversity; evolutionAbstract
Bioinformatics is a novel method to investigate evolutionary relationships and genetic diversity among species. This study assessed the evolutionary patterns and genetic diversity of Amaranthus species using ribulose-1.5-bisphosphate carboxylase/oxygenase (rbcL gene). A total of 20 full FASTA-format rbcL gene sequences for accessions of Amaranthus tricolor, A. dubius, A. cruentus, A. viridis, and A. spinosus from different regions were retrieved from the National Center for Biotechnology Information. Multiple sequence alignment was used to determine genetic variations. A phylogenetic tree was constructed using neighbor-joining clustering method while a distant matrix was created using Tamura-Nei genetic distance model. From position 1 to 22 in nucleotide alignment, only accession KX082771.1 from USA, aligns. The exclusive alignment in this region suggests an exceptionally conserved sequence among species, implying a common genetic origin. However, from position 23 to 50, nine different accessions namely MN192576.1, MN204800.1, EF590496.1, GQ248546.1, OQ737000.1, MG246937.1, MN104855.1, MN104858.1, and MN04859.1 align. The phylogenetic tree representing the evolutionary relationships offers insights into the genetic diversity and relatedness of these species within specific regions. The genetic distance matrix shows that sequences within the same region share relatively high similarity scores, indicating a genetic connection likely influenced by their geographic proximity. However, sequences from different regions, exhibit moderate genetic differences, emphasizing the genetic diversity across geographically distinct regions. The observed genetic diversity and evolutionary relationships among accessions of Amaranthus revealed by rbcL genes highlight the unique genetic features of these species in different regions, and therefore should be explored for their genetic improvement and conservation purposes.
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