International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 40 Research Report Open Access Phylogenetic and Evolutionary Trajectories of Ananas: Evidence from Whole-Genome Data Zhonggang Li 1 YepingHan 2 1 Tropical Specialty Crops Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572026, Hainan, China 2 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: yeping.han@jicat.org International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1 doi: 10.5376/ijmeb.2025.15.0004 Received: 27 Dec., 2024 Accepted: 03 Feb.,2025 Published: 16 Feb., 2025 Copyright © 2025 Li and Han, 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: Li Z.G., and Han Y.P., 2025, Phylogenetic and evolutionary trajectories of ananas: evidence from whole-genome data, International Journal of Molecular Evolution and Biodiversity, 15(1): 40-50 (doi: 10.5376/ijmeb.2025.15.0004) Abstract Pineapple (Ananas comosus) is a tropical plant. It belongs to the Poales group and split off early in its evolution. Thanks to whole-genome sequencing, scientists can now study the pineapple and related plants in more detail. Research using both mitochondrial and nuclear DNA shows that all Ananas species come from a single common ancestor. It also helps place pineapple clearly within the Bromeliaceae family. This study looks at how comparing genomes helps us understand how important traits in pineapple evolved. The results show that the pineapple genome has not had a recent whole-genome duplication. But other changes, like sudden increases in transposons and repeated copies of certain genes, have changed many gene families. These discoveries show that having full genome data has made pineapple a useful plant for studying how monocots have evolved over time. Keywords Pineapple; Phylogenomics; CAM photosynthesis; Gene family evolution; Genome sequencing 1 Introduction The genus Ananas, which includes the common pineapple (Ananas comosus), is made up of small bromeliad plants. These plants come from the Neotropical region. Pineapple is the second most produced and traded tropical fruit in the world. People value it for its sweet taste and many uses. Besides its farming importance, pineapple has some special traits. It uses water very efficiently because it performs crassulacean acid metabolism (CAM). Most pineapple types also grow without seeds and are propagated asexually (Chen et al., 2019). Pineapple has a small genome-about 563 Mb per haploid-which makes it useful for research. It also sits at a basic position in the plant order Poales, so it is a good plant for studying how monocots evolved and adapted. Ananas belongs to the family Bromeliaceae, an early-diverging lineage within the Poales, providing a phylogenetic reference for comparative evolutionary studies with major cereal crops (e.g., Poaceae) and other bromeliads (Ouyang et al., 2022; Yow et al., 2022). All species in the genus Ananas are native to the Americas and include only a few taxa, such as Ananas comosus and its wild relatives Ananas bracteatus, Ananas ananassoides, etc. Prior to the genomic era, phylogenetic relationships within the genus were primarily inferred from morphological traits and a limited number of DNA markers, leaving species boundaries and hybridization events unresolved. This study presents the currently available pineapple genome data and focuses on the evolutionary processes of several important traits in pineapple, such as CAM photosynthesis, reproductive strategies, fruit development, and its ability to cope with stress. The study emphasizes how genomic changes-such as alterations in chromosome regions, duplicated segments, or active transposable elements-lead to distinct differences among plants. By integrating data from population genomics and trait mapping, this study identifies genes related to domestication and breeding strategies. It also discusses future research priorities for pineapple, highlighting how pineapple serves as a good model for studying monocotyledons and how its genomic data can support the improvement of vegetatively propagated crops.
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