Abstract
BackgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale.ResultsHere, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes—the old landrace Chinese Spring and the elite Swiss spring wheat line ‘CH Campala Lr22a’. Both chromosomes were assembled into megabase-sized scaffolds. There is a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations reveals four large indels of more than 100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the molecular mechanisms that caused these indels. Three of the large indels affect copy number of NLRs, a gene family involved in plant immunity. Analysis of SNP density reveals four haploblocks of 4, 8, 9 and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Gene content across the two chromosomes was highly conserved. Ninety-nine percent of the genic sequences were present in both genotypes and the fraction of unique genes ranged from 0.4 to 0.7%.ConclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations and gene content. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.
Highlights
Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives
Two-way comparison of Chinese spring and CH Campala Lr22a allows identification of large structural variations Previously, 10,344 sequence scaffolds were produced from isolated chromosome 2D of CH Campala Lr22a by using Chicago long-range linkage [21, 32]
It was previously found that repetitive sequences were collapsed and less complete in the Chicago assembly, which explains the smaller size of the CH Campala Lr22a pseudomolecule compared to the IWGSC RefSeq v1.0 pseudomolecule [32]
Summary
Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the dynamics of wheat genomes on a megabase scale. The first ‘early’ whole genome assemblies of hexaploid wheat and its diploid wild relatives were based on short-read sequencing approaches These assemblies provided an insight into the gene space of wheat, but they were highly fragmented and incomplete [7,8,9,10].
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