Recombination map construction method using ONT sequence
Although meiotic recombination is a key step shared by eukaryotes, the rate of recombination varies at different taxonomic levels. The construction of high-resolution genome-wide recombination maps will help us understand the variability patterns of recombination rates and their molecular basis. ONT...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | MethodsX |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2215016122003430 |
| _version_ | 1827917767798423552 |
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| author | Zuoquan Chen Lei Xie Xi Tang Zhiyan Zhang |
| author_facet | Zuoquan Chen Lei Xie Xi Tang Zhiyan Zhang |
| author_sort | Zuoquan Chen |
| collection | DOAJ |
| description | Although meiotic recombination is a key step shared by eukaryotes, the rate of recombination varies at different taxonomic levels. The construction of high-resolution genome-wide recombination maps will help us understand the variability patterns of recombination rates and their molecular basis. ONT sequencing technology has the characteristics of long read length, high throughput, and reasonable cost, and can be used as a data source for the construction of whole-gene recombination landscapes. In order to construct the genome-wide recombination map of an individual conveniently and accurately, we developed a method to construct the recombination landscape based on the third-generation sequencing technology, Oxford Nanopore Sequencing. Here we detail a step-by-step approach to efficiently and accurately construct genome-wide recombination maps using ONT pooled sequencing data. The main contents include compression homopolymers and alignment; acquisition of high-quality variants; estimation of recombinant molecules by the sliding window method; and construction of recombinant maps. The results of simulation data validation show that our method has high sensitivity and specificity at moderate heterozygous variant density and sequencing depth. This method provides a new way of constructing high-resolution individual genome recombination maps using long read sequences, and has important reference significance for the study of recombination rate variation. |
| first_indexed | 2024-03-13T03:33:09Z |
| format | Article |
| id | doaj.art-2a71aa5b0838424e87a10c8b311da2a9 |
| institution | Directory Open Access Journal |
| issn | 2215-0161 |
| language | English |
| last_indexed | 2024-03-13T03:33:09Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | MethodsX |
| spelling | doaj.art-2a71aa5b0838424e87a10c8b311da2a92023-06-24T05:16:50ZengElsevierMethodsX2215-01612023-01-0110101969Recombination map construction method using ONT sequenceZuoquan Chen0Lei Xie1Xi Tang2Zhiyan Zhang3State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaState Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaState Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaCorresponding author: Dr. Zhiyan Zhang, Jiangxi Agricultural University State Key Laboratory for Pig Genetic Improvement and Production Technology, China.; State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, ChinaAlthough meiotic recombination is a key step shared by eukaryotes, the rate of recombination varies at different taxonomic levels. The construction of high-resolution genome-wide recombination maps will help us understand the variability patterns of recombination rates and their molecular basis. ONT sequencing technology has the characteristics of long read length, high throughput, and reasonable cost, and can be used as a data source for the construction of whole-gene recombination landscapes. In order to construct the genome-wide recombination map of an individual conveniently and accurately, we developed a method to construct the recombination landscape based on the third-generation sequencing technology, Oxford Nanopore Sequencing. Here we detail a step-by-step approach to efficiently and accurately construct genome-wide recombination maps using ONT pooled sequencing data. The main contents include compression homopolymers and alignment; acquisition of high-quality variants; estimation of recombinant molecules by the sliding window method; and construction of recombinant maps. The results of simulation data validation show that our method has high sensitivity and specificity at moderate heterozygous variant density and sequencing depth. This method provides a new way of constructing high-resolution individual genome recombination maps using long read sequences, and has important reference significance for the study of recombination rate variation.http://www.sciencedirect.com/science/article/pii/S2215016122003430Recombination map construction method using ONT sequence |
| spellingShingle | Zuoquan Chen Lei Xie Xi Tang Zhiyan Zhang Recombination map construction method using ONT sequence MethodsX Recombination map construction method using ONT sequence |
| title | Recombination map construction method using ONT sequence |
| title_full | Recombination map construction method using ONT sequence |
| title_fullStr | Recombination map construction method using ONT sequence |
| title_full_unstemmed | Recombination map construction method using ONT sequence |
| title_short | Recombination map construction method using ONT sequence |
| title_sort | recombination map construction method using ont sequence |
| topic | Recombination map construction method using ONT sequence |
| url | http://www.sciencedirect.com/science/article/pii/S2215016122003430 |
| work_keys_str_mv | AT zuoquanchen recombinationmapconstructionmethodusingontsequence AT leixie recombinationmapconstructionmethodusingontsequence AT xitang recombinationmapconstructionmethodusingontsequence AT zhiyanzhang recombinationmapconstructionmethodusingontsequence |