Illegitimate Recombination Between Homeologous Genes in Wheat Genome

Chao Liu,Shaoqi Shen,Chendan Wei,Xiyin Wang,Fanbo Meng,Pengchuan Sun,He Guo,Xinyu Li,Zhikang Zhang,Jinpeng Wang,Jigao Yu

doi:10.3389/fpls.2020.01076

Abstract

Polyploidies produce a large number of duplicated regions and genes in genomes, which have a long-term impact and stimulate genetic innovation. The high similarity between homeologous chromosomes, forming different subgenomes, or homologous regions after genome repatterning, may permit illegitimate DNA recombination. Here, based on gene colinearity, we aligned the (sub)genomes of common wheat (Triticum aestivum, AABBDD genotype) and its relatives, including Triticum urartu (AA), Aegilops tauschii (DD), and T. turgidum ssp. dicoccoides (AABB) to detect the homeologous (paralogous or orthologous) colinear genes within and between (sub)genomes. Besides, we inferred more ancient paralogous regions produced by a much ancient grass-common tetraploidization. By comparing the sequence similarity between paralogous and orthologous genes, we assumed abnormality in the topology of constructed gene trees, which could be explained by gene conversion as a result of illegitimate recombination. We found large numbers of inferred converted genes (>2,000 gene pairs) suggested long-lasting genome instability of the hexaploid plant, and preferential donor roles by DD genes. Though illegitimate recombination was much restricted, duplicated genes produced by an ancient whole-genome duplication, which occurred millions of years ago, also showed evidence of likely gene conversion. As to biological function, we found that ~40% catalytic genes in colinearity, including those involved in starch biosynthesis, were likely affected by gene conversion. The present study will contribute to understanding the functional and structural innovation of the common wheat genome.

Highlights

Common wheat is one of the most widely grown cereal crops in the world and an essential source of food, its production affects the global economy, and failed harvests could lead to social unrest (Choulet et al, 2014; Wang et al, 2015; Appels et al, 2018)
Two hybridization process made the common wheat genome complicated and made its genome even more complicated is that a grass-common wholegenome duplication having occurred ~100 million years ago produced thousands of duplicated genes in the extant grass genomes (Paterson et al, 2004; Wang et al, 2015; Du et al, 2017)
We revealed gene colinearity between the tetraploid wild wheat, T. turgidum (AtAtBtBt), with the common wheat genome

Summary

Introduction

Common wheat is one of the most widely grown cereal crops in the world and an essential source of food, its production affects the global economy, and failed harvests could lead to social unrest (Choulet et al, 2014; Wang et al, 2015; Appels et al, 2018). The sequencing of its relatives, the diploid Triticum urartu (genotype AdAd; hereafter capital letters to indicate genome types and subscripts to indicate ploidy of organisms carrying them, with d, t, or h to show diploid, tetraploid, or hexaploid, respectively), and Aegilops tauschii (genome DdDd), and the tetraploid wild emmer wheat Irreversible recombination involves the transfer of information from one site to its homeolog, leading to gene transformation (Datta et al, 1997; Kurosawa and Ohta, 2011). Gene conversion involves the unidirectional transfer of genetic material from a ‘donor’ sequence to a homologous ‘acceptor.’ In eukaryotes, it constitutes the main form of homologous recombination initiated by DNA double-strand breaks, as reviewed previously (Chen et al, 2007)

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Conclusion