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NanoCross: A pipeline that detecting recombinant crossover using ONT sequencing data.

Zuoquan Chen¹, Lei Xie¹, Xi Tang¹

¹State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang 330045, China.

|September 29, 2022

Summary

Researchers developed NanoCross, a new script using long-read sequencing to map genome-wide recombination events. This tool enhances understanding of genetic variation and evolution by providing high-resolution recombination maps.

Keywords:

Computational biology ONT sequences Pigs Pipelines Recombination

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Area of Science:

Genetics and Evolutionary Biology
Genomics
Molecular Biology

Background:

Meiotic recombination is essential for eukaryotic reproduction and genetic diversity.
Recombination rates exhibit significant variation across different species and populations.
Understanding the mechanisms driving recombination rate variation is key to deciphering genetic and evolutionary processes.

Purpose of the Study:

To introduce NanoCross, a novel genome-wide identification script for detecting cross-recombination events using Oxford Nanopore (ONT) sequencing data.
To develop a method for constructing high-resolution individual genome recombination maps.
To provide a tool for analyzing variations in individual recombination rates.

Main Methods:

Developed NanoCross script utilizing ONT long-read sequencing data.
Implemented error reduction and homopolymer filtering for ONT sequences.
Constructed individual haplotypes and estimated cross-recombination events per molecule read.
Simulated data to assess the sensitivity and specificity of the NanoCross technique.

Main Results:

NanoCross demonstrated good sensitivity and specificity in simulations under moderate heterozygous variation and sequencing depth.
Generated a high-resolution recombination map for wild boar genomes.
Compared wild boar recombination maps with those from male breeding pig populations, revealing variations.

Conclusions:

NanoCross offers a robust method and script for creating high-resolution individual genome recombination maps using long-read sequencing.
The tool provides a novel approach to investigate variations in individual recombination rates.
This research facilitates deeper insights into the molecular basis and evolutionary significance of meiotic recombination.