RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis

Abstract

Meiotic recombination is an essential biological process that ensures faithful chromosome segregation and promotes parental allele shuffling. Tetrad analysis is a powerful approach to quantify the genetic makeups and recombination landscapes of meiotic products. Here we present RecombineX (https://github.com/yjx1217/RecombineX), a generalized computational framework that automates the full workflow of marker identification, gamete genotyping, and tetrad-based recombination profiling based on any organism or genetic background with batch processing capability. Aside from conventional reference-based analysis, RecombineX can also perform analysis based on parental genome assemblies, which facilitates analyzing meiotic recombination landscapes in their native genomic contexts. Additional features such as copy number variation profiling and missing genotype inference further enhance downstream analysis. RecombineX also includes a dedicate module for simulating the genomes and reads of recombinant tetrads, which enables fine-tuned simulation-based hypothesis testing. This simulation module revealed the power and accuracy of RecombineX even when analyzing tetrads with very low sequencing depths (e.g., 1-2X). Tetrad sequencing data from the budding yeast Saccharomyces cerevisiae and green alga Chlamydomonas reinhardtii were further used to demonstrate the accuracy and robustness of RecombineX for organisms with both small and large genomes, manifesting RecombineX as an all-around one stop solution for future tetrad analysis. Interestingly, our re-analysis of the budding yeast tetrad sequencing data with RecombineX and Oxford Nanopore sequencing revealed two unusual structural rearrangement events that were not noticed before, which exemplify the occasional genome instability triggered by meiosis.

Chromosome‐dependent aneuploid formation in Spo11‐less meiosis

“…From the sequencing results, we observed marked differences in recombination events (Table 1 ). Using the RecombineX tool, we detected 78.5 crossing overs (COs) per tetrad and 110 gene conversions (GCs) per tetrad in the wild‐type strain as reported previously (Li et al, 2022 ), whereas spo11 ∆ cells did not induce any types of recombination. Therefore, nondisjunction of achiasmatic homologs is expected to occur in spo11 ∆.…”

“…The detailed plotting method of SNP plots is indicated in Figures 2 and 3 . Crossing over (COs) and gene conversions (GCs) were detected by the RecombineX package (Li et al, 2022 ).…”

Genomic Adaptations of Saccharomyces Genus to Wine Niche

“…Besides the huge biotechnological impact of hybrids, recent advances in yeast genomics and the development of new methodologies have opened up our understanding about the hybridization potential as a source of genetic diversity [137][138][139][140][141][142]. The diversity offered by the hybrid population has the potential to be used in quantitative genetics analysis in order to unveil the structure of complex traits [143].…”

UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes

“…Indeed, ReCombine [ 9 ] was designed to detect recombination in tetrads and requires a merged reference genome containing both parental genomes with some hard coded parameters making it hard to apply for tetrads of unknown reference genome. Recently, RecombineX [ 10 ], a general automatic framework for polymorphic markers identification, improved the process of gametes genotyping in yeasts and extended the process to green alga. Clearly, UGDR is more suitable for tetrads with unavailable merged reference parent or a parent different than S288C; nevertheless, RecombineX would be more appropriate to analyze genomes from other organisms.…”

“…ReCombine aligns the reads to a merged reference genome (S288C/YJM789) and compares the number of reference versus variant markers using the base alignment quality score. Another generalized framework, RecombineX, has been developed to genotype gametes and draw the recombination profile of tetrads in different organisms including yeasts [ 10 ]. More approaches to precisely track the recombination landscape of diploid yeasts were presented.…”