International Journal of Molecular Evolution and Biodiversity 2024, Vol.14, No.3, 105-107 http://ecoevopublisher.com/index.php/ijmeb 105 Scientific Commentary Open Access Genomic Interpretation and Phylogenetic Analysis: Exploring the Origins and Diversity of Hawaiian Mint Species Ben J.L. Zhong Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, Hainan, China Corresponding author: zhongjianli8888@gmail.com International Journal of Molecular Evolution and Biodiversity, 2024, Vol.14, No.3 doi: 10.5376/ijmeb.2024.14.0013 Received: 19 Apr., 2024 Accepted: 21 May, 2024 Published: 27 May, 2024 Copyright © 2024 Zhong, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhong B.J.L., 2024, Genomic interpretation and phylogenetic analysis: exploring the origins and diversity of Hawaiian mint species, International Journal of Molecular Evolution and Biodiversity, 14(3): 105-107 (doi: 10.5376/ijmeb.2024.14.0013) Published on April 10, 2024, by the Department of Biological Sciences at the State University of New York at Buffalo, the School of Biological Sciences at Nanyang Technological University, Singapore, and the Faculty of Biological and Environmental Sciences at the University of Helsinki, Finland, the research findings were published in the journal Nature Communications. Crystal M. Tomlin is the lead author, with Victor A. Albert and Charlotte Lindqvist as corresponding authors. The article is titled “Allopolyploid origin and diversification of the Hawaiian endemic mints”. The study was funded by the School of Biological Sciences at Nanyang Technological University, the National Science Foundation (2139311; 2030871), and the Research Council of Norway (154145). The research produced a chromosome-level reference genome for a representative species, ‘Stenogyne calaminthoides’, and resequenced its 45 close relatives. The study found that these plants evolved through multiple polyploidization events, including an allopolyploid event directly related to North American ancestors, leading to the radiation and diversification of this group in the Hawaiian Islands. 1 Interpretation of Experimental Data Detailed genomic information about Stenogyne calaminthoides and its related species also revealed their complex interactions and diversification strategies during evolution. Figure 1 describes the assembly and structural evolution of the Stenogyne calaminthoides genome in detail. Part (a) displays a physical photograph of the species, providing a visual reference for species morphology. Part (b)’s Hi-C contact map, marked with blue-framed chromosomes, shows the interactions and spatial structure between chromosomes, providing key information for understanding the three-dimensional structure of the genome. Part (c) reveals the distribution of genes and various types of repetitive sequences (such as Copia, Helitron, Gypsy) in the genome, displaying density per 1 Mb area and highlighting homologous regions with different colors, enhancing our understanding of genomic complexity. Part (d) compares the S. calaminthoides genome with grape chromosomes through a fractional deviation plot, showing conservation and variation in genome evolution. Part (e)’s phylogenetic tree discusses the history of polyploidy events within the genus Stenogyne, including unique whole-genome duplication events, which are crucial for understanding their adaptive evolution. Figure 2 depicts the phylogenetic relationships and genetic admixture among Hawaiian mint species and their related groups through two types of phylogenetic trees. The tree on the left is based on a dataset of single nucleotide polymorphisms (SNPs) and analyzed using a maximum likelihood approach, while the tree on the right is based on the coalescent analysis of single-copy nuclear genes, each highlighting the evolutionary relationships and gene flow among species. The figure also includes an ADMIXTURE analysis, which reveals the gene flow and diversity of genetic backgrounds among species, with each color representing different ancestral populations, thus illustrating the complex dynamics of genetic mixing and species formation.
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