Cocoa is an economically important product in Colombia. On-farm germplasm evaluations enable the selection of superior genotypes for propagation and distribution across the country. This study examined 12 cocoa samples from Antioquia along with five reference materials, employing 96 single nucleotide polymorphism (SNP) markers. Furthermore, these genetic findings were correlated with physical, chemical, and sensory attributes. Primary coordinate analysis revealed that the majority of samples were hybrids derived from five original germplasm pools, including Criollo, Amelonado, and three Upper Amazon Forastero cocoas. The integral profile of the 12 selected materials was classified into Modern Criollo (Rodriguez-Medina et al., 2019) [3], Forasteros (Rodriguez-Medina et al., 2019) [3], and Trinitarios (Borja Fajardo et al., 2022) [6]. Three key factors were identified to best account for the sample classification: type of variety, functional properties, and quality.

Thrips are small, cosmopolitan pests that attack a wide variety of crops, including avocado (Persea americana Mill.), where they feed on the fruit surface, hindering export quality. In Colombia, 7 thrips species have been identified in avocado where Frankliniella gardeniae (Fg) (Moulton, 1948), F. panamensis (Fp) (Hood, 1925), and Scirtothrips hansoni (Sh) (Mound and Hoddle, 2016) are the most abundant. Despite their economic importance, limited genomic and transcriptomic data are available for these pests. Here, we present the first draft genomes of these species and compare them to the reference genome of Frankliniella occidentalis. The mitochondrial genomes (mitogenomes) of the 3 species differ in size and gene order, with F. gardeniae exhibiting the largest mitochondria. Phylogenetic analysis clustered F. gardeniae and F. panamensis together and S. hansoni with S. dorsalis. Genome assembly revealed differences in genome sizes: 397 Mbp (Fp), 454 Mbp (Sh), and 601 Mbp (Fg), with F. gardeniae having the largest genome. Coverage was 118× for S. hansoni and 35× for the other 2 species. S. hansoni showed the highest sequence count and N50 values. BUSCO analysis estimated genome completeness between 96% and 97.95%. Annotated genes shared among these species included insecticide resistance and metabolism, particularly P450 and CYP family genes, as well as chemosensory genes (Ir). They are promising targets for RNA interference-based studies to enhance pest management strategies thus further studies are required in this issue.

Although gastrulation is a conserved morphogenetic process in animals, the cellular mechanisms underlying it are highly variable. This raises important questions regarding the extent to which conserved or divergent gene regulatory programs (GRNs) control gastrulation in phylogenetically distant taxa. We compared gene expression profiles during gastrulation of Acropora digitifera and Acropora tenuis , species that diverged ∼50 million years ago. Despite the morphological similarity, each species uses divergent GRNs, supporting the concept of developmental system drift. Consistently, orthologous genes showed significant temporal and modular expression divergence, indicating GRN diversification rather than conservation. Yet, we identified a subset of 370 differentially expressed genes that were up-regulated at the gastrula stage in both species, with roles in axis specification, endoderm formation, and neurogenesis, suggesting a conserved regulatory “kernel” for the process. We also identified species-specific differences in paralog usage and alternative splicing patterns that indicate independent peripheral rewiring of this conserved module. Interestingly, although A. digitifera exhibits greater paralog divergence, consistent with neofunctionalization, A. tenuis shows more redundant expression, suggesting the regulatory robustness of developmental programs in this species.