Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1226273 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32426623_1.fastq.gz | Fastqsanger.gz | |||
| SRR32426623_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species.
2015-01-08 | GSE54339 | GEO
Project description:To comprehend the drivers underlying venom variation in ants, we selected 15 Neotropical species and recorded a range of traits, including ecology, morphology, and venom bioactivity. Principal component analysis of both morphological and venom bioactivity traits revealed that stinging ants display two functional strategies. Additionally, phylogenetic comparative analysis indicated that venom function (predatory, defensive, or both) and mandible morphology significantly correlate with venom bioactivity and amount, while pain-inducing activity trades off with insect paralysis. Further analysis of the venom biochemistry of the 15 species revealed switches between cytotoxic and neurotoxic venom compositions in some species. This study highlights the fact that ant venoms are not homogenous, and for some species, there are major shifts in venom composition associated with the diversification of venom ecological functions.
2024-10-16 | PXD050348 | Pride
Project description:Extensive sex-biased expression has been seen in multiple surveys D. melanogaster. We were interested in broadly sampling sex-biased expression of orthologs and species- or lineage-specific genes in the Drosophila genus. To appropriately assay gene expression in multiple species, we used custom microarrays designed against each of six species that broadly sample the phylogenetic space represented by the newly completed genomes (D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis) and an array designed against D. melanogaster to determine the overall patterns of sex-biased expression in those species and their chromosome linkage. Keywords: other
2007-11-08 | GSE6640 | GEO
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.
2020-10-19 | PXD020530 | Pride
Project description:Nosema is a diverse fungal genus of microsporidian unicellular, obligate symbionts of insects and other arthropods. We performed a comparative genomic analysis of N. muscidifuracis, a Nosema species infecting parasitoid wasp genus Muscidifurax, with six other genome-sequenced Nosema species. A sequence motif containing at least three consecutive Cs was significantly enriched immediately upstream of the start codon in all seven Nosema genomes. Interestingly, this motif is present in ~90% of highly expressed genes, compared to ~20% in lowly expressed genes N. muscidifuracis, which may function as a cis-regulatory element for gene expression control and regulation. Our study provides new insights into the gene regulation evolution in Nosema.
2023-11-26 | GSE248484 | GEO
Project description:New genus and species of Pleosporales
| PRJEB30530 | ENA