Amazona
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA496322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8108620_1.fastq.gz | Fastqsanger.gz | |||
| SRR8108620_2.fastq.gz | Fastqsanger.gz | |||
| SRR8108622_1.fastq.gz | Fastqsanger.gz | |||
| SRR8108622_2.fastq.gz | Fastqsanger.gz | |||
| SRR8108623_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Genomes, annotations and transcriptome of 3 Caribbean Parrots
| PRJNA496322 | ENA
Project description:Changes in parrot diversity after human arrival to the Caribbean
| PRJNA913959 | ENA
Project description:comparing sulfitobacters genomes and comparing functional annotations
| PRJEB48335 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE27022: Microarray studies of darkness stress and bleaching in the Caribbean coral Acropora palmata GSE27024: Microarray studies of darkness stress and bleaching in the Caribbean coral Montastraea faveolata Refer to individual Series
2011-03-22 | E-GEOD-27025 | biostudies-arrayexpress
Project description:Amazon parrots are long-lived birds with highly developed cognitive skills, including vocal learning. Several parrot mitogenomes have been sequenced, but important aspects of their organization and evolution are not fully understood or have limited experimental support. The main aim of the present study was to describe the mitogenome of the blue-fronted Amazon, Amazona aestiva, and compare it to other mitogenomes from the genus Amazona and the order Psittaciformes. We observed that mitogenomes are highly conserved among Amazon parrots, and a detailed analysis of their duplicated control regions revealed conserved blocks. Population level analyses indicated that the specimen analyzed here seems to be close to A. aestiva individuals from Bahia state. Evolutionary relationships of 41 Psittaciformes species and three outgroups were inferred by BEAST. All relationships were retrieved with high support.
| S-EPMC6136379 | biostudies-literature
Project description:With the creation of accurate, chromosome-scale genomes, the next challenge facing the genomics community is the accurate idenfication of transcriptional units, distinguishing them from aberrant transcriptional noise. This has proven to be a challenge as annotation by traditional means, such as short read RNA-seq followed by transcriptome assembly, which is prone to the generation of in-silico artifacts. To address this issue, we took advantage of epigenomic data in the form of ChIP-seq to unbiasedly annotate plant genomes and identify potential annotation issues, as well as identify novel genes. Histone modifications appear in the genome in a reproducible and predictable manner, making them an ideal resource to use in annotation. Trimethylation of histone 3 lysine 4 (H3K4me3), as well as acetylation of histone 3 lysine 56 are well documented to coincide with initiation of transcription by polymerase II (Pol II) at promoter sequences. These initiation marks, paired with marks deposited across the gene body during transcriptional elongation, such as histone 3 lysine 36 tri-methylation (H3K36me3) and histone 3 lysine 4 mono-methylation (H3K4me1), offer a framework to begin identifying complete transcriptional units. We leveraged these data on a genome-wide scale, allowing for identification of annotations discordant with empirical data. In total, 13,159 potential annotation issues were found in Zea mays across three different tissues, which were corroborated using complementary RNA-based approaches. Upon correction and validation, genes were extended by an average of 2,128 base pairs, and the length of discovered novel genes was 1,962 base pairs. Application of this method to five additional plant genomes revealed a variety of novel gene annotations, including 13,836 in Asparagus officianalis, 2,724 in Setaria viridis, 2,446 in Sorghum bicolor, 8,631 in Glycine max, and 2,585 in Phaseolous vulgaris.
2021-04-26 | GSE160944 | GEO
Project description:A unique community-funded project in Puerto Rico has launched whole-genome sequencing of the critically endangered Puerto Rican Parrot (Amazona vittata), with interpretation by genome bioinformaticians and students, and deposition into public online databases. This is the first article that focuses on the whole genome of a parrot species, one endemic to the USA and recently threatened with extinction. It provides invaluable conservation tools and a vivid example of hopeful prospects for future genome assessment of so many new species. It also demonstrates inventive ways for smaller institutions to contribute to a field largely considered the domain of large sequencing centers.
| S-EPMC3626504 | biostudies-literature