catalog.fa.gz,\u00a0catalog.tags.tsv.gz
\n\nThe files generated by the Stacks operation, by changing the parameters M (M controls the number of mismatches allowed between the two alleles of a heterozygote sample), m (m controls the number of identical reads required to initiate a new putative allele) and n (n controls the number of mismatches allowed between any two alleles of the population).\u00a0Depending on the data set, gapped alignments may provide more loci for the analysis.\u00a0
\n\nmatches.zip
\n\nStacks will generate a matches file for each sample through operation comparison. By analyzing these matches files, you can find the depth of each site.
\n\npopulations.sumstats.tsv
\n\nThe populations program outputs a summary file for each site of the population. Can be grouped according to needs (such as male and female).
\n\nQuasipaa_ boulengeri_Sex_linked_marker
\n\nSex-linked markers were screened with three approaches followed by Brelsford et al. (2017), respectively based on (i) sex differences in allele frequencies, (ii) sex differences in heterozygosity, and (iii) sex-limited occurrence. We used RStudio 1.2.1335 to generate candidate alleles for each individual.
\n\nsequences.zip
\n\nThe primer design method was adopted for four sex-linked\u00a0sites. After amplification in additional samples (10\u264010\u2642) respectively from three populations, the PCR products were sequenced at Sangon Sequencing Center (Shanghai, China).
\nFunding provided by: National Natural Science Foundation of China
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809
Award Number: NSFC-31772439
We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog Quasipaa boulengeri with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations.
", "publication_date": "2020-08-19", "publisher": "Zenodo", "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "CC0 waives copyright interest in a work you've created and dedicates it to the world-wide public domain. Use CC0 to opt out of copyright entirely and ensure your work has the widest reach." }, "icon": "cc-cc0-icon", "id": "cc0-1.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" }, "title": { "en": "Creative Commons Zero v1.0 Universal" } } ], "subjects": [ { "subject": "sex-linked markers" }, { "subject": "spiny frog" }, { "subject": "Quasipaa boulengeri" } ], "title": "Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)" }, "parent": { "access": { "owned_by": { "user": "90070" } }, "communities": { "default": "734b6452-1f40-4db0-b218-08ab1d568b7f", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-02-04T14:03:17.992421+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "734b6452-1f40-4db0-b218-08ab1d568b7f", "links": {}, "metadata": { "curation_policy": "The Dryad collection in Zenodo contains datasets mirrored from the Dryad Digital Repository. If you want your dataset to appear here, submit it through https://datadryad.org. No other datasets will be accepted.
", "description": "Dryad is an international open-access repository of research data, especially data underlying scientific and medical publications. Dryad is a curated general-purpose repository that makes data discoverable, freely reusable, and citable.", "organizations": [ { "id": "00x6h5n95" } ], "page": "Dryad is a community-governed open data publishing and curation repository. Through Dryad and Zenodo's partnership, Zenodo hosts a preservation copy of Dryad datasets, available through this Zenodo Community. For more information or to access the original published datasets, visit https://datadryad.org.
", "title": "Dryad", "type": { "id": "organization" }, "website": "https://datadryad.org" }, "revision_id": 3, "slug": "dryad", "updated": "2024-02-01T21:26:57.292847+00:00" } ], "ids": [ "734b6452-1f40-4db0-b218-08ab1d568b7f" ] }, "id": "3997589", "pids": {} }, "pids": { "doi": { "identifier": "10.5061/dryad.s4mw6m94b", "provider": "external" }, "oai": { "identifier": "oai:zenodo.org:3997590", "provider": "oai" } }, "revision_id": 3, "stats": { "all_versions": { "data_volume": 28397554373.0, "downloads": 1974, "unique_downloads": 1956, "unique_views": 131, "views": 132 }, "this_version": { "data_volume": 28397554373.0, "downloads": 1974, "unique_downloads": 1956, "unique_views": 131, "views": 132 } }, "status": "published", "swh": {}, "updated": "2022-06-03T01:27:30.598302+00:00", "versions": { "index": 1, "is_latest": true } }