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RecView: an interactive R application for locating recombination positions using pedigree data
BACKGROUND: Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chrom...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10676570/ https://www.ncbi.nlm.nih.gov/pubmed/38007417 http://dx.doi.org/10.1186/s12864-023-09807-2 |
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author | Zhang, Hongkai Hansson, Bengt |
author_facet | Zhang, Hongkai Hansson, Bengt |
author_sort | Zhang, Hongkai |
collection | PubMed |
description | BACKGROUND: Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes. RESULTS: We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions. CONCLUSIONS: RecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub (https://github.com/HKyleZhang/RecView.git). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09807-2. |
format | Online Article Text |
id | pubmed-10676570 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-106765702023-11-25 RecView: an interactive R application for locating recombination positions using pedigree data Zhang, Hongkai Hansson, Bengt BMC Genomics Software BACKGROUND: Recombination reshuffles alleles at linked loci, allowing genes to evolve independently and consequently enhancing the efficiency of selection. This makes quantifying recombination along chromosomes an important goal for understanding how selection and drift are acting on genes and chromosomes. RESULTS: We present RecView, an interactive R application and its homonymous R package, to facilitate locating recombination positions along chromosomes or scaffolds using whole-genome genotype data of a three-generation pedigree. RecView analyses and plots the grandparent-of-origin of all informative alleles along each chromosome of the offspring in the pedigree, and infers recombination positions with either of two built-in algorithms: one based on change in the proportion of the alleles with specific grandparent-of-origin, and one on the degree of continuity of alleles with the same grandparent-of-origin. RecView handles multiple offspring and chromosomes simultaneously, and all putative recombination positions are reported in base pairs together with an estimated precision based on the local density of informative alleles. We demonstrate RecView using genotype data of a passerine bird with an available reference genome, the great reed warbler (Acrocephalus arundinaceus), and show that recombination events can be located to specific positions. CONCLUSIONS: RecView is an easy-to-use and highly effective application for locating recombination positions with high precision. RecView is available on GitHub (https://github.com/HKyleZhang/RecView.git). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09807-2. BioMed Central 2023-11-25 /pmc/articles/PMC10676570/ /pubmed/38007417 http://dx.doi.org/10.1186/s12864-023-09807-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Zhang, Hongkai Hansson, Bengt RecView: an interactive R application for locating recombination positions using pedigree data |
title | RecView: an interactive R application for locating recombination positions using pedigree data |
title_full | RecView: an interactive R application for locating recombination positions using pedigree data |
title_fullStr | RecView: an interactive R application for locating recombination positions using pedigree data |
title_full_unstemmed | RecView: an interactive R application for locating recombination positions using pedigree data |
title_short | RecView: an interactive R application for locating recombination positions using pedigree data |
title_sort | recview: an interactive r application for locating recombination positions using pedigree data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10676570/ https://www.ncbi.nlm.nih.gov/pubmed/38007417 http://dx.doi.org/10.1186/s12864-023-09807-2 |
work_keys_str_mv | AT zhanghongkai recviewaninteractiverapplicationforlocatingrecombinationpositionsusingpedigreedata AT hanssonbengt recviewaninteractiverapplicationforlocatingrecombinationpositionsusingpedigreedata |