International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 40-50 http://ecoevopublisher.com/index.php/ijmeb 41 2 Genomic Resources and Data Availability in Ananas Genus 2.1 Assembly of pineapple reference genomes The first pineapple reference genome was made using the F153 variety. But because this species has many repeated sequences and is highly heterozygous, the genome wasn’t very complete. Later, scientists used long-read sequencing and Hi-C technology to assemble a better version for the MD2 variety, which is popular in the market (Yow et al., 2022). This improved genome has a contig N50 of over 2.9 Mb. It also includes about 161 Mb of new or previously incomplete sequences and over 3 000 new genes. Pineapple has 25 chromosomes (2n = 50), and its haploid genome size is about 563 Mb. Compared to grasses, pineapple has experienced fewer ancient whole-genome duplications, keeping an early chromosome structure from the Poales group. 2.2 Resequencing and genetic diversity data One major study resequenced 89 genomes from the Ananas genus. This included both wild and cultivated types. The study found over 7.2 million SNPs and around 920 000 indels (Xu et al., 2018). The cultivated A. comosus samples grouped into known types such as 'Smooth Cayenne', 'Queen', and 'Spanish'. Wild types like A. bracteatus and A. ananassoides formed their own separate groups (Feng et al., 2022). Some types, like ‘Smooth Cayenne’ and ‘Queen’, show signs of mixing from older lineages. But ‘Singapore Spanish’ seems to come from a single domestication without much mixing (Chen et al., 2019; Feng et al., 2022). This is likely due to clonal propagation. However, occasional sexual reproduction still brings new variations into some genetic backgrounds (Chen et al., 2019). 2.3 Functional genomics and organelle genomes Scientists have sequenced the full chloroplast genomes of pineapple and its wild relatives. These genomes are about 162 kb in size and help in phylogenetic studies. One wild type, A. comosus var. erectifolius, is genetically very close to the cultivated pineapple, which agrees with how they are traditionally grouped (Liu et al., 2022). In terms of gene expression, several RNA-seq datasets are available. These cover different tissues like leaves, flowers, and fruits, as well as responses to stress. Some RNA-seq experiments done under day-night cycles found CAM photosynthesis genes controlled by the internal biological clock. In cold-treated pineapples of two different genotypes, many genes related to cold stress were found. These include genes for wax formation and hormone signaling (Yow et al., 2023). Xu et al. (2024) found 21 HSP70 genes in pineapple. Many of these genes respond to heat and drought stress. 2.4 Data repositories and genomic databases The pineapple genomics database (PGD) was created as a public platform for researchers. It includes genome sequences, gene information, genetic markers, and expression data for A. comosus (Xu et al., 2018). PGD provides online tools like genome browsers, search bars, and co-expression networks. Users can check the locations of about 46 000 pineapple genes, search for specific genes, or download SNP marker files from resequencing studies. Pineapple genome data can also be found in public databases like NCBI and Ensembl Plants. Research groups have connected genomic data to important traits like fruit quality and disease resistance, which helps in breeding programs. 3 Phylogenetic Relationships within the Genus Ananas 3.1 Species diversity and classification of ananas The genus Ananas includes only a few species. In the past, many scientists considered it as a single species, A. comosus, with several botanical varieties or closely related species. These commonly include A. comosus (both farmed and wild types), A. bracteatus, A. ananassoides, A. parguazensis, A. lucidus, A. monstrosus, and A. microstachys. However, classification can differ depending on the source. New genetic research supports the idea that Ananas is a single group clearly different from other genera in the Bromeliaceae family. For example, Pseudananas is now often grouped into Ananas as A. sagenaria. All seven or so types in the genus show only small genetic differences, suggesting they split apart not long ago in evolutionary terms. Wild pineapples mostly grow in South America, especially in Brazil, Paraguay, and nearby places. Scientists believe this region is where both the genus and the cultivated pineapple first appeared (Figure 1) (Chen et al., 2019). Human movement spread the cultivated form, A. comosus var. comosus, to other tropical areas. Still, all farmed pineapples belong to this same group.
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