ABSTRACT: The complete mitochondrial genomes and phylogenetic analysis of two Chinese endemic cave fishes, Sinocyclocheilus guilinensis and S. huangtianensis (Cypriniformes: Cyprinidae)
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members. Examination of 2 different eye samples in 2 Sinocyclocheilus species.
Project description:we report a transcriptome-wide comparative investigation between surface and cave species in Sinocyclocheilus. De novo transcriptome assemblies were performed on surface and cave species; then the Sinocyclocheilus contigs were annotated with Gene Ontology. RNA-Seq assays revealed reduced transcription of a series of visual phototransduction and retinal disease related genes in cave-dwelling species compared with surface species. Degeneration of the retina in Sinocyclocheilus cavefish might occur in a lens-independent way by the down-regulation of several transcriptional factors, which have direct roles in retina development and maintenance, such as crx, rorb and Wnt pathway members.
2013-03-31 | GSE40446 | GEO
Project description:Complete mitochondrial genome of the Korean endemic species Coreoleuciscus aeruginos (Cypriniformes, Cyprinidae)
Project description:Spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances being found between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for the phylogenetic reconstruction of ancient fauna previously thought to be unreachable using ancient DNA.
Project description:An archaeological bone fragment from Baishiya Karst Cave, China, was identified as stemming from a hominin through ZooMS (Zooarchaeology by Mass Spectrometry). Shotgun palaeoproteomic analyses were thereafter conducted on the specimen to refine the taxonomic identification and perform phylogenetic analyses. The reconstruted proteome shows that the newly described Baishiya Karst Cave individual, Xiahe 2, is most closely related to the high-coverage published genome from a Denisovan individual.
2024-05-22 | PXD047932 | Pride
Project description:Transcriptome of cave and surface in Sinocyclocheilus
| PRJNA185248 | ENA
Project description:The complete mitochondrial genome and phylogenetic analysis of the vulnerable troglomorphic species Sinocyclocheilus anatirostris