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669 results for “comparative genomics”

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dryad36/100

Comparative genomic analysis of chemosensory-related gene families in gastropods

Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and spiders, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann–Pick type C2 (NPC2) proteins, and lipocalins, although much smaller in size. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) large gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a huge number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.

opencc-zeroMay 2023View details →

dryad36/100

Data from: Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481.5 to 1054.6 Mb, with repetitive sequence contents of 21.2 to 50.7%. Concordance rates of orthologs and heterozygosity ratios were between 82.4 and 91.7% and between 1.1 and 2.6, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesized to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.

opencc-zeroOct 2023View details →

dryad36/100