Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats

Abstract

Structural variations (SVs) such as copy number and presence–absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

“…In order to mitigate this problem, the interval that harbored a gene to be mapped was first identified using Insertion Site‐Based Polymorphisms (ISBP) markers, which mark junctions between neighboring TEs that are present in both the IWGSC RefSeq v1.0 and IWGSC RefSeq v2.1 assemblies. ISBPs are 150‐mers representing a unique sequence shaped by the junction of a TE and its insertion site (De Oliveira et al, 2020 ; Paux et al, 2010 ; Rimbert et al, 2018 ). Because ISBPs can be derived at each TE extremity, they are extremely abundant and well adapted for identifying corresponding loci across different assembly versions.…”

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

“…Previous studies revealed a partitioning of the wheat genome based on different structural and functional features, including the recombination rate, gene and transposable element (TE) densities, gene expression breadth, histone modifications, as well as gene and TE structural variation rate (Choulet et al., 2014; De Oliveira et al., 2020; IWGSC, 2018; Pingault et al., 2015). Consequently, chromosomes can be divided into five chromosomal compartments: the short arm distal R1, the short arm proximal R2a, the centromeric‐pericentromeric C, the long arm proximal R2b and the long arm distal R3 regions.…”

“…This differential association with active or repressive histones marks have already been reported in other species, such as potato where CNV frequency increased in genes lacking histone marks associated with permissive transcription (Hardigan et al., 2016). In wheat, we showed recently that genes affected by intra‐ and interspecific copy number variations were enriched in H3K27m3 (De Oliveira et al., 2020).…”

“…Presence/absence variation (PAV) analysis was performed as described by De Oliveira et al. (2020). Briefly, sequencing reads from 16 wheat accessions (Montenegro et al., 2017) were mapped on the IWGSC RefSeq v1.0 using BWA‐MEM v0.7.12 (Li & Durbin, 2010).…”

“…To assess if duplications in tetrads occurred within diploids or upon polyploidization, we used GMAP to estimate the number of copies in the diploid and tetraploid ancestor genomes. Presence/absence variation (PAV) analysis was performed as described by De Oliveira et al (2020). Briefly, sequencing reads from 16 wheat accessions (Montenegro et al, 2017) were mapped on the IWGSC RefSeq v1.0 using BWA-MEM v0.7.12 (Li & Durbin, 2010).…”