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UGDR:一种用于检测多倍体和复杂杂交酵母基因组中重组区域的通用管道。

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

机构信息

Institut Curie, UPMC University, Paris, France.

Meiogenix, 27 Rue du Chemin Vert, Paris, France.

出版信息

BMC Bioinformatics. 2022 Dec 21;23(1):555. doi: 10.1186/s12859-022-05113-y.

Abstract

MOTIVATION

In eukaryotes, homologous recombination between the parental genomes frequently occurs during the evolutionary conserved process of meiosis, generating the genetic diversity transmitted by the gametes. The genome-wide determination of the frequency and location of the recombination events can now be efficiently performed by genotyping the offspring's polymorphic markers. However, genotyping recombination in complex hybrid genomes with existing methods remains challenging because of their strain and ploidy specificity and the degree of diversity and complexity of the parental genomes, especially in [Formula: see text] polyploids.

RESULTS

We present UGDR, a pipeline to genotype the polymorphisms of complex hybrid yeast genomes. It is based on optimal mapping strategies of NGS reads, comparative analyses of the allelic ratio variation and read depth coverage. We tested the UGDR pipeline with sequencing reads from recombined hybrid diploid yeast strains and various clinical strains exhibiting different degrees of ploidy. UGDR allows to plot the markers distribution and recombination profile per chromosome.

CONCLUSION

UGDR detects and plots recombination events in haploids and polyploid yeasts, which facilitates the discovery and understanding of the yeast genetic recombination map and identify new out-performing recombinants.

摘要

动机

在真核生物中,亲代基因组之间的同源重组经常发生在进化保守的减数分裂过程中,产生由配子传递的遗传多样性。通过对后代的多态性标记进行基因分型,可以有效地确定重组事件的频率和位置。然而,由于现有方法的菌株和倍性特异性以及亲代基因组的多样性和复杂性程度,在[Formula: see text]多倍体中,对复杂杂交基因组中的重组进行基因分型仍然具有挑战性。

结果

我们提出了 UGDR,这是一种用于对复杂杂交酵母基因组进行基因分型的流水线。它基于 NGS reads 的最佳映射策略,等位基因比例变化和读深度覆盖的比较分析。我们使用来自重组杂交二倍体酵母菌株和表现出不同倍性程度的各种临床菌株的测序reads 测试了 UGDR 流水线。UGDR 允许绘制每个染色体的标记分布和重组图谱。

结论

UGDR 可以检测和绘制单倍体和多倍体酵母中的重组事件,这有助于发现和理解酵母遗传重组图谱,并识别新的表现更好的重组体。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/350a/9773435/25fb36a16e87/12859_2022_5113_Fig1_HTML.jpg

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