We assembled a high quality genome of modern leading wheat variety, AK58, which is comprised of 279,861 contigs (N50 = 237.2 Kb) and 159,139 scaffolds (N50 = 28.3 Mb and 715 Mb by using Hi-C technique). The total scaffold length of the assembly (14.8Gb) spans 95.2% of the estimated genome size (15.5Gb). Through a combination of Hi-C technique and a high density genetic map, 97.0% of the genome sequences are anchored to chromosomes. The assembling quality with LAI (LTR Assembling Index) of 14.1 for AK58 (vs 3.2 for Chinese Spring), which satisfied the standard of reference genome (10

TEs play key roles in generating genomic novelty through inducing genomic rearrangements and modifying genes. However, there are limited reports on TE impact on subgenome divergence in polyploidy species and crop improvement. The high quality assembly of hexaploid wheat, AK58, provided an opportunity for investigating the TE’s contribution on subgenome divergence in hexaploid wheat. Our key findings were that (1) Genome size was mainly determined by copy number of TEs which showed strong bias in subgenomic distribution; (2) TEs were found in more than 99% genes throughtout the genome with more than 90% of them in 5’ UTR and 3’UTR regions, "30% in intron regions and only "5% in exon regions; (3) TEs accounted for almost all orthologous gene divergence in structure and function including expression abundance, alternative splicing and coding sequences; (4) There are more new genes and alternative promoters derived from TEs in wheat genome comparing with other crops; (5) Orthologous genes of AK58 showed more orthologous divergent than those of CS.

All the results suggested that changes in the genome were largely driven by TEs which influenced subgenome/orthologous gene divergence and wheat improvement. New genes, diverse genes and their cis-regulatory elements are major forces for adaptive evolution. Therefore, we propose that divergence of subgenomes and orthologous genes and following selection are major drives of polyploidy heterosis, creation and selection of orthologous genes

Ou S, Chen J, Jiang N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 2018,46(21):e126.