RecView : an interactive R application for locating recombination positions using pedigree data
Zhang, Hongkai LU and Hansson, Bengt LU
(2023)
In BMC Genomics
24(1).
- Abstract
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... (More)
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).
(Less)
- author
- Zhang, Hongkai
LU
and Hansson, Bengt
LU
- organization
- publishing date
- 2023-12
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Crossover, Next generation sequencing, Non-crossover, R Shiny, Recombination, SNP
- in
- BMC Genomics
- volume
- 24
- issue
- 1
- article number
- 712
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:38007417
- scopus:85177738120
- ISSN
- 1471-2164
- DOI
- 10.1186/s12864-023-09807-2
- language
- English
- LU publication?
- yes
- id
- c037c327-787e-461b-b734-a053c75ea8fc
- date added to LUP
- 2023-12-20 13:40:06
- date last changed
- 2024-04-18 23:18:54
@article{c037c327-787e-461b-b734-a053c75ea8fc,
abstract = {{<p>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).</p>}},
author = {{Zhang, Hongkai and Hansson, Bengt}},
issn = {{1471-2164}},
keywords = {{Crossover; Next generation sequencing; Non-crossover; R Shiny; Recombination; SNP}},
language = {{eng}},
number = {{1}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Genomics}},
title = {{RecView : an interactive R application for locating recombination positions using pedigree data}},
url = {{http://dx.doi.org/10.1186/s12864-023-09807-2}},
doi = {{10.1186/s12864-023-09807-2}},
volume = {{24}},
year = {{2023}},
}