InGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants Due to Genome Complexities

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2021 Mar 12

PMID 33711466

Citations 10

Authors

Qichao Lian

Yamao Chen

Fang Chang

Ying Fu

Ji Qi

Affiliations

Soon will be listed here.

Abstract

Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies. Genome complexities, including large-scale structural variations, bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants, as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms. It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies. Here, we present an efficient and effective framework, inGAP-family, to discover, filter, and visualize DNA polymorphisms and structural variants (SVs) from alignment of short reads. Applying this method to polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant genomes or quantitative trait loci. In addition, inGAP-family provides a user-friendly graphical interface for detecting polymorphisms and SVs, further evaluating predicted variants and identifying mutations related to genotypes. It is accessible at https://sourceforge.net/projects/ingap-family/.

Citing Articles

Enhanced recombination empowers the detection and mapping of Quantitative Trait Loci.

Capilla-Perez L, Solier V, Gilbault E, Lian Q, Goel M, Huettel B Commun Biol. 2024; 7(1):829.

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A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.

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Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.

Fernandes J, Naish M, Lian Q, Burns R, Tock A, Rabanal F Genome Biol. 2024; 25(1):30.

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SCEP1 and SCEP2 are two new components of the synaptonemal complex central element.

Vrielynck N, Peuch M, Durand S, Lian Q, Chambon A, Hurel A Nat Plants. 2023; 9(12):2016-2030.

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Meiotic recombination is confirmed to be unusually high in the fission yeast .

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