New insights into homoeologous copy number variations in the hexaploid wheat genome

Abstract

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

Homoeolog Inference Methods Requiring Bidirectional Best Hits or Synteny Miss Many Pairs

“…A GO enrichment indicated that they have general, metabolic functions. This is in line with other studies, for example, in the allohexaploid Triticum aestivum , where homoeologs conserved at a 1:1:1 ratio were expressed at a higher level and a higher breadth than those homoeologs that had experienced duplication or loss ( Juery et al 2020 ).…”

Transcription factor retention through multiple polyploidization steps in wheat

“…One reason for the lower divergence in TF homoeolog expression patterns in hexaploid wheat is that the polyploidization event is much more recent than previously studied paleopolyploidization events. Alternatively, this difference may be because wheat does not show biased genome fractionation ( Juery et al 2021 ) and has negligible global subgenome expression dominance ( Harper et al 2016 ; Ramírez-González et al 2018 ) unlike many other studied allopolyploid species.…”

Transposable elements are associated with genome-specific gene expression in bread wheat

“…To identify TE insertions within gene bodies (exons\ introns) in the Chinese Spring bread wheat cultivar (CS42), we integrated data from two publicly available databases (Appels et al, 2018;Juery et al, 2020). The name, homoeologous group IDs, assignment to one of the five chromosomal regions (R1, R2a, C, R2b, and R3), and the start and stop positions of 70,818 wheat genes belonging to 6,320 dyads (12,640 genes belongs to homoeologous groups that underwent elimination of a single gene), 18,390 triads (55,170 genes), and 752 tetrads (3,008 genes, belongs to homoeologous groups that underwent duplication of a single gene) were retrieved from Juery et al (2020) and integrated with the IWGSC RefSeq v1.0 assembly coordinates for TEs (Appels et al, 2018) using python 3.7 (Guttag, 2021) scripts. Prior to the data integration, the IWGSC RefSeq v1.0 assembly annotations for TEs were organized using pandas, a Python package used for data analysis (Reback et al, 2021), and filtered to include only repeats defined as "repeat region" (nested repeats and repeat fragments were removed).…”