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Pattern recognition receptors (PRRs) play a crucial role in the host's innate immune system. Among the PPRs, the RIG-I-like (RLRs) and NOD-like receptors (NLRs) are two important subgroups. To understand the role of RLRs (RIG-I, MDA5, LGP2) and NLRs (NOD1, NLRC3, NLRX1, NOD2) in reptilian evolution, we identified six genes from reptilian genomes. A total of 168 putative genes were identified from 28 reptile species, including 141 intact genes, 25 partial genes and two pseudogenes. Interestingly, the NOD2 gene was absent in all reptile species. Phylogenetic results showed that all genes were divided into four major clades corresponding to their traditional taxonomic groups, indicating that these genes are conserved in reptiles. Evolutionary analyses detected positive selection in six genes. Most of the positively selected sites (50/76) were located in known functional domains, reflecting their critical and particular contributions to host defense during reptilian evolution. Branch model analysis showed that NLRs were under different evolutionary forces, while the RLRs were not, suggesting that semiaquatic species and terrestrial species faced different environmental pathogens, leading to different adaptations. Moreover, the positively selected sites identified in MDA5 using the branch-site model among semiaquatic reptiles, suggested their involvement in adaptation to semiaquatic environments.
Pubmed ID: 31129211
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Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.
View all literature mentionsSoftware for the automated evaluation of behavior in a range of pre-clinical and neuroscience applications in basic and clinical psychopharmacology. Applications include phenotype characterization and studying the behavioral effects of pharmacologic substances.
View all literature mentionsRepository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study. Through their association with DataCite, each dataset will be assigned a DOI that can be used as a standard citation for future use of these data in other articles by the authors and other researchers. Datasets in GigaDB all require a title that is specific to the dataset, an author list, and an abstract that provides information specific to the data included within the set. Detailed information about the data to be submitted is encouraged in ISA-Tab, a format used by the BioSharing and ISA Commons communities that they work with to maintain the highest data and metadata standards in their journal.
View all literature mentionsA free public server for comparative analysis of sequence alignments using state-of-the-art statistical models. This service is brought to you by the viral evolution group at the School Of Medicine of the University of California, San Diego.
View all literature mentionsMultiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation.
View all literature mentionsTool to search translated nucleotide databases using a protein query.
View all literature mentionsWeb server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.
View all literature mentionsPackage of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree.
View all literature mentionsWelcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
