Genomics and Applied Biology 2024, Vol.15, No.6, 320-332 http://bioscipublisher.com/index.php/gab 322 diversity. For instance, gene-targeting marker techniques can classify and characterize species, ensuring the conservation of their genetic integrity (Abouseadaa et al., 2020). Effective conservation strategies must also address the impacts of human activities and promote sustainable practices to maintain genetic diversity. 3 Advances in Genomic Studies of Cactaceae 3.1 Sequencing and assembly of organelle genomes in Cactaceae Significant progress has been made in the study of organelle genomes in Cactaceae, particularly in chloroplast and mitochondrial genomes. For instance, Oulo et al. (2020) were the first to sequence the chloroplast genome of Rhipsalis baccifera, providing valuable data on the phylogenetic relationships within Cactaceae. Yu et al. (2023) investigated the chloroplast genomes of 35 genera in the subfamily Cactoideae, deepening the understanding of evolutionary relationships. Similarly, Köhler et al. (2023) assembled the chloroplast genomes of 43 species of the tribe Opuntieae, one of the most diverse and important lineages of the Cactaceae. Their study revealed the dynamic nature of plastome evolution across closely related lineages. The results showed significant variation in plastome length, structure, and content, particularly with respect to the contraction and expansion of the inverted repeat (IR) region, as well as the pseudogenization or loss of certain genes (Figure 1). This genomic variation is closely related to plant evolution and species identification. Studies by Liu et al. (2021) and Qin et al. (2022) on the chloroplast genomes of pitaya revealed a conserved quadripartite structure but highlighted genome size variations among species, uncovering genetic diversity. These studies also identified phenomena such as gene loss, rearrangement, and pseudogene formation, providing new insights into the evolutionary mechanisms and adaptive strategies of pitaya. Figure 1 Phylogenetic inference of tribe Opuntieae based on plastome sequences with the maximum likelihood (ML) criterion, with the major plastome evolution features mapped on the tree (Adopted from Köhler et al., 2023) Image caption: (A) Inference based on the full plastome sequences (genes and intergenic regions, raw alignment). (B) Inference based on chloroplast genes (raw alignment). (C) Inference based on plastome genes trimmed with Gblocks (no gaps allowed). Phylogenetic nodes have full bootstrap support (100), except when depicted; incongruent nodes across different datasets are highlighted by red circles (Adopted from Köhler et al., 2023)
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