Genomics and Applied Biology 2024, Vol.15, No.6, 320-332 http://bioscipublisher.com/index.php/gab 323 The assembly of mitochondrial genomes in Cactaceae has unveiled key aspects of their genetic structure and function. For example, the mitochondrial genome of Pereskia aculeata spans 515 187 bp and contains 52 unique genes, including protein-coding genes, tRNA genes, and rRNA genes (Zhang et al., 2023). The genome features a significant number of repetitive elements, which play roles in genome recombination. Lu et al. (2023) assembled the mitochondrial genome of Selenicereus monacanthus, revealing a total length of 2 290 019 bp encoding 59 genes. Evolutionary analyses indicated that its mitochondrial genome underwent multiple recombination events, leading to the loss of at least nine protein-coding genes. These studies enhance our understanding of the genetic foundation of pitaya and provide new perspectives on mitochondrial genome evolution in Cactaceae. 3.2 Sequencing and assembly of nuclear genomes in Cactaceae Compared with other economically important crops, genomic studies of Cactaceae plants are relatively underdeveloped, with only a few nuclear genomes sequenced and assembled. These include two pitaya varieties (Guanhuabai and David Bowie), four North American columnar cacti (Pachycereus pringlei, Lophocereus schottii, Stenocereus thurberi, and Pereskia humboldtii), one South American cactus (Cereus fernambucensis), and the iconic giant saguaro cactus (Carnegiae gigantea) (Sanderson et al., 2020; Amaral et al., 2021; Chen et al., 2021; Tamayo-Ordoñez et al., 2023). These genome assemblies have significantly contributed to understanding cactus evolutionary history, adaptation mechanisms, and the identification of key genes involved in important metabolic pathways. Despite these advancements, challenges remain due to high heterozygosity, large amounts of repetitive sequences, and difficulties in DNA or RNA extraction. For instance, the genome of Hylocereus undatus is approximately 1.41 Gb and contains numerous repetitive sequences, complicating high-quality assembly (Chen et al., 2021). However, improvements in sequencing technologies and bioinformatics tools are expected to advance genomic studies in Cactaceae. Methods such as PacBio-SMRT, Illumina HiSeq paired-end sequencing, 10× Genomics, and Hi-C have enabled chromosome-level genome assemblies of pitaya, achieving an N50 scaffold length of ~127.15 Mb. These advancements provide critical support for understanding the nuclear genomes of Cactaceae. 3.3 Advances in transcriptomic studies of Cactaceae Transcriptomic studies have also made remarkable progress in understanding gene expression and the regulation of vital biological processes in Cactaceae. RNA sequencing (RNA-Seq) has proven instrumental in analyzing gene expression, identifying novel transcripts, alternative splicing, and developing molecular markers. Key transcriptomic studies have focused on various aspects of Cactaceae physiology, from root development to stress responses. Hua et al. (2016) conducted the first transcriptomic study on pitaya, marking a new chapter in functional genomics research of this fruit. In the case of the saguaro cactus (Pachycereus pringlei), transcriptomic sequencing identified genes related to root development, providing insights into growth regulation (Rodriguez-Alonso et al., 2018). Additionally, transcriptomic data from pitaya have been used to elucidate the molecular mechanisms underlying its growth, stress responses, and development (Chen et al., 2021). These studies enhance the understanding of cactus biology and support breeding programs aimed at developing superior cultivars. With continuous advancements in sequencing technologies, transcriptomic studies in Cactaceae are expected to expand significantly. This will ultimately enrich our understanding of the genomes, gene functions, and evolutionary processes in Cactaceae, thereby promoting their genetic improvement. 4 Traditional Breeding Methods for Cactaceae Plants 4.1 Hybrid breeding Hybrid breeding is one of the primary traditional breeding methods for Cactaceae plants. By combining desirable traits from different varieties or species, offspring with multiple favorable characteristics can be obtained (Oliveira et al., 2020; Tel-Zur, 2022). For example, in the breeding of dragon fruit (Hylocereus spp.), hybrid breeding is often used to improve fruit size, color, and flavor (Ding, 2021). Through artificial pollination between different types of dragon fruit, breeders can combine the high disease resistance of red-fleshed dragon fruit with the high
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