Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus
This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (Eleginops maclovinus), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the E. maclovinus genome, the dataset includes a description of circadian rhy...
Main Author: | |
---|---|
Format: | Software |
Language: | unknown |
Published: |
2023
|
Subjects: | |
Online Access: | https://zenodo.org/record/7829978 https://doi.org/10.5281/zenodo.7829978 |
id |
ftzenodo:oai:zenodo.org:7829978 |
---|---|
record_format |
openpolar |
spelling |
ftzenodo:oai:zenodo.org:7829978 2023-06-11T04:05:58+02:00 Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus Rivera-Colón, Angel 2023-05-30 https://zenodo.org/record/7829978 https://doi.org/10.5281/zenodo.7829978 unknown doi:10.5061/dryad.qbzkh18nt doi:10.5281/zenodo.7829977 https://zenodo.org/communities/dryad https://zenodo.org/record/7829978 https://doi.org/10.5281/zenodo.7829978 oai:zenodo.org:7829978 info:eu-repo/semantics/openAccess https://opensource.org/licenses/LGPL-3.0 notothenioids circadian rhythm genome assembly comparative genomics info:eu-repo/semantics/other software 2023 ftzenodo https://doi.org/10.5281/zenodo.782997810.5061/dryad.qbzkh18nt10.5281/zenodo.7829977 2023-05-30T23:06:00Z This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (Eleginops maclovinus), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the E. maclovinus genome, the dataset includes a description of circadian rhythm orthologs for E. maclovinus, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis. All assembly and annotation files are gzipped, but are otherwise standard bioinformatic formats (i.e., FASTA for genome assembly and coding/amino acid sequences, GTF for annotation, AGP for scaffolding). In addition, bioinformatic scripts for data generation and analysis are in Python (*.py) or Bash (*.sh, but might require the installation of additional, open-source software (e.g., wtdbg2, BRAKER) See links for a description of the FASTA (http://www.ncbi.nlm.nih.gov/blast/fasta.shtml), and GTF (https://useast.ensembl.org/info/website/upload/gff.html), and AGP (https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/) file format specifications. File format Specification File Suffix1 Description *.fa Genome assembly in nucleotide FASTA format. *.agp Assembly structure in AGP format. *.gtf Genome annotation in GTF format. *.cds.fa Genomic sequence for all annotated protein-coding genes in nucleotide FASTA format. *.protein.fa Protein sequence for all annotated protein-coding genes in amino acid FASTA format. 1Does not include the gzipped compression suffix (*.gz).Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1645087Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 11-42158 An E. maclovinus specimen was collected from the Puerto Natales, Chile in January 2018. HMW DNA was extracted and sequenced using PacBio Sequel II and a Hi-C library. A contig-level genome ... Software Antarc* Antarctic Zenodo Antarctic The Antarctic Patagonia |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
notothenioids circadian rhythm genome assembly comparative genomics |
spellingShingle |
notothenioids circadian rhythm genome assembly comparative genomics Rivera-Colón, Angel Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
topic_facet |
notothenioids circadian rhythm genome assembly comparative genomics |
description |
This dataset contains the genome assembly and associated annotation of the Patagonian Blennie (Eleginops maclovinus), the closest extant taxon to the Antarctic notothenioid radiation. In addition to the characterization of the E. maclovinus genome, the dataset includes a description of circadian rhythm orthologs for E. maclovinus, other notothenenioid taxa, and teleost outgroups, as well as a copy of the bioinformatic scripts used for the assembly, annotation, and other downstream analysis. All assembly and annotation files are gzipped, but are otherwise standard bioinformatic formats (i.e., FASTA for genome assembly and coding/amino acid sequences, GTF for annotation, AGP for scaffolding). In addition, bioinformatic scripts for data generation and analysis are in Python (*.py) or Bash (*.sh, but might require the installation of additional, open-source software (e.g., wtdbg2, BRAKER) See links for a description of the FASTA (http://www.ncbi.nlm.nih.gov/blast/fasta.shtml), and GTF (https://useast.ensembl.org/info/website/upload/gff.html), and AGP (https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/) file format specifications. File format Specification File Suffix1 Description *.fa Genome assembly in nucleotide FASTA format. *.agp Assembly structure in AGP format. *.gtf Genome annotation in GTF format. *.cds.fa Genomic sequence for all annotated protein-coding genes in nucleotide FASTA format. *.protein.fa Protein sequence for all annotated protein-coding genes in amino acid FASTA format. 1Does not include the gzipped compression suffix (*.gz).Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1645087Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 11-42158 An E. maclovinus specimen was collected from the Puerto Natales, Chile in January 2018. HMW DNA was extracted and sequenced using PacBio Sequel II and a Hi-C library. A contig-level genome ... |
format |
Software |
author |
Rivera-Colón, Angel |
author_facet |
Rivera-Colón, Angel |
author_sort |
Rivera-Colón, Angel |
title |
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
title_short |
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
title_full |
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
title_fullStr |
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
title_full_unstemmed |
Supplementary data for: Chromosome-level genome assembly and circadian gene repertoire of the Patagonia blennie Eleginops maclovinus |
title_sort |
supplementary data for: chromosome-level genome assembly and circadian gene repertoire of the patagonia blennie eleginops maclovinus |
publishDate |
2023 |
url |
https://zenodo.org/record/7829978 https://doi.org/10.5281/zenodo.7829978 |
geographic |
Antarctic The Antarctic Patagonia |
geographic_facet |
Antarctic The Antarctic Patagonia |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.5061/dryad.qbzkh18nt doi:10.5281/zenodo.7829977 https://zenodo.org/communities/dryad https://zenodo.org/record/7829978 https://doi.org/10.5281/zenodo.7829978 oai:zenodo.org:7829978 |
op_rights |
info:eu-repo/semantics/openAccess https://opensource.org/licenses/LGPL-3.0 |
op_doi |
https://doi.org/10.5281/zenodo.782997810.5061/dryad.qbzkh18nt10.5281/zenodo.7829977 |
_version_ |
1768377676561645568 |