RecView: an interactive R application for locating recombination positions using pedigree data
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 a...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-11-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-023-09807-2 |
| _version_ | 1797453836105809920 |
|---|---|
| author | Hongkai Zhang Bengt Hansson |
| author_facet | Hongkai Zhang Bengt Hansson |
| author_sort | Hongkai Zhang |
| collection | DOAJ |
| description | 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 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 ). |
| first_indexed | 2024-03-09T15:27:38Z |
| format | Article |
| id | doaj.art-c9bedff50b9843c28c0e552e520158db |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:27:38Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c9bedff50b9843c28c0e552e520158db2023-11-26T12:25:48ZengBMCBMC Genomics1471-21642023-11-0124111010.1186/s12864-023-09807-2RecView: an interactive R application for locating recombination positions using pedigree dataHongkai Zhang0Bengt Hansson1Department of Biology, Lund UniversityDepartment of Biology, Lund UniversityAbstract 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 ).https://doi.org/10.1186/s12864-023-09807-2RecombinationCrossoverNon-crossoverR ShinyNext generation sequencingSNP |
| spellingShingle | Hongkai Zhang Bengt Hansson RecView: an interactive R application for locating recombination positions using pedigree data BMC Genomics Recombination Crossover Non-crossover R Shiny Next generation sequencing SNP |
| 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 | Recombination Crossover Non-crossover R Shiny Next generation sequencing SNP |
| url | https://doi.org/10.1186/s12864-023-09807-2 |
| work_keys_str_mv | AT hongkaizhang recviewaninteractiverapplicationforlocatingrecombinationpositionsusingpedigreedata AT bengthansson recviewaninteractiverapplicationforlocatingrecombinationpositionsusingpedigreedata |