Biology subjects

Gomez Garrido, J.

Publications and source records attributed to Gomez Garrido, J..

3 recordsLinked to original sources

bioRxiv2026

Manta and devil ray genome assemblies uncover signatures of pelagic adaptation

Manta and devil rays (Mobulidae) are iconic marine megafauna highly adapted to life in the open ocean, with forward-facing mouths, enlarged pectoral fins and specialised filter-feeding apparatus. These innovations have enabled mobulids to occupy vast pelagic habitats, yet the genetic changes underlying them remain poorly understood. Here we use a combination of chromatin conformation capture, PacBio HiFi and Nanopore long-reads to generate highly contiguous annotated chromosome-level reference genomes for two mobulid species: the Atlantic pygmy devil ray (Mobula hypostoma) and the Atlantic manta ray (Mobula yarae). The assemblies span 3.5 and 4.0 Gb, with contig N50s of 23.3 and 7.3 Mb, respectively. We combine these into a Progressive Cactus whole genome alignment with benthic batoid outgroups to characterise the landscape of structural variation and identify candidate molecular regions associated with pelagic adaptation. This approach revealed that over 1.5 million structural rearrangements occurred along the ancestral mobulid lineage, with deletions encompassing three times more sequence compared to the benthic sister lineage. Genes affected by mobulid specific deletions were significantly enriched for neurogenesis pathways linked to craniofacial patterning, with several deletions overlapping the putative promoter sequences of craniofacial and roof of mouth development genes. Our findings highlight candidate developmental pathways through which ancestral deletions may have driven mobulid adaptations, while the high-quality genome resources provide a foundation for comparative and functional studies in Chondrichthyes.

evolutionary biology↗

bioRxiv2019

Transposons played a major role in the diversification between the closely related almond (Prunus dulcis) and peach (P. persica) genomes: Results from the almond genome sequence

Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.

genomics↗

bioRxiv2018

De novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate

Introduction Introduction Methods Results and Discussion Conclusion Data and materials References Most amphibian species exhibit a complex life-cycle including two or more life stages separated by an ontogenetic switch point such as hatching or metamorphosis. Adaptations to divergent environments can require the modification of the timing of such switch points and the relative investment in growth and differentiation between subsequent stages [1]. Such alterations of developmental trajectories, however, often have substantial repercussions at several organismal levels, from physiology to morphology and even genomic structure. Adaptive divergence in developmental rate tracking aquatic habitats of different duration in spadefoot toads is a well-known example of this. Spadefoot toads from Europe and ...

genomics↗