L. Filipe C. Castro

The paper analyzes the evolution of CLDN18 across vertebrates, showing gene loss, alternative splicing, and regulatory changes linked to stomach loss and pleiotropy.

The paper identifies convergent gene loss in the chemical defensome across marine mammals, highlighting adaptation to aquatic environments and reduced detoxification capacity.

The paper identifies a mutation in the MC1R gene responsible for seasonal camouflage in least weasels and shows it was maintained by spatially varying selection.

The paper identifies the independent loss of ghrelin and Mboat4 in snakes, chameleons, and toadhead agamas, linking it to adaptations in energy metabolism.

The paper investigates the evolution of sperm energetics in mammals by analyzing gene duplication and loss of Atp1a4, revealing its role in sodium-dependent glucose uptake and subsequent pseudogenization in three lineages.

The paper presents a phased whole genome assembly for Atlantic bluefin tuna using PacBio HiFi and Omni-C scaffolding, enabling improved phylogenomic and evolutionary studies.

The paper introduces GLossDB, a curated database of gene loss events in vertebrates, focusing on cetaceans and other taxa, with searchable features and supporting evidence.

PseudoChecker2 and PseudoViz automate and visualize gene loss detection across species using genomic data.

The paper provides a de novo transcriptome assembly and gene expression analysis for the vulnerable freshwater fish Thymallus ligericus, offering a foundational resource for future conservation and research.

The paper examines neuropeptide-receptor gene alterations in cetaceans, finding species-specific mutations and gene loss linked to their unique physiological adaptations.

The paper identifies novel mitochondrial genome structural arrangements in deep-sea hatchetfish and Antarctic notothenioid fishes, revealing rare inversions and compositional asymmetry changes.

The paper presents an improved genome assembly for Margaritifera margaritifera using long-read and short-read sequencing, resulting in a more contiguous and accurate reference genome.

The paper presents the first genome assembly of the Iberian dolphin freshwater mussel Unio delphinus using PacBio HiFi technology, resulting in a highly contiguous genome.

The paper presents a de novo transcriptome assembly of the annelid worm Hediste diversicolor using Illumina sequencing, resulting in a comprehensive resource for biological studies.

This study identifies sex-dependent gene expression patterns in a pig model of renal ischemia-reperfusion injury, revealing temporal and sexual dimorphism in injury and recovery processes.

The paper presents a high-quality genome assembly for the Atlantic chub mackerel, providing a resource for studying its biology and fisheries management.

This study assembles and analyzes the gonad transcriptome of Paracentrotus lividus, identifying sex-related and lipid biosynthesis genes through differential expression analysis.

The paper uses genomic analysis to determine whether the pineal gland in Xenarthra is functional or vestigial, finding that melatonin synthesis and signaling genes are independently eroded and lost.

The paper presents the first draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera using Illumina sequencing technologies.

The paper traces the evolutionary expansion, retention, and loss of the ACSBG gene family in vertebrates, identifying a new lineage ACSBG3 and duplication in the Theria ancestor.