The power of chromosome-scale, haplotype-resolved genomes

Abstract

The assembly of chromosome-scale and haplotype-resolved reference genomes is now more easily attainable, largely due to various improvements in both assembly algorithms and long-read sequencing technologies (see recent review by Michael and VanBuren, 2020 Michael T.P. VanBuren R. Building near-complete plant genomes. Curr. Opin. Plant Biol. 2020; 54: 26-33 Google Scholar ). Due to these technological advancements, there has been a shift away from using highly inbred accessions, in some instances double haploids, to instead assembling the genomes of important reference genotypes. For example, a haplotype-resolved genome was recently assembled for an important cultivated garden strawberry (Fragaria x ananassa) cultivar Royal Royce, which is not only highly heterozygous but also octoploid (8×) ( Hardigan et al., 2021 Hardigan M.A. Feldmann M.J. Pincot D.D.A. Famula R.A. Vachev M.V. Madera M.A. Zerbe P. Mars K. Peluso P. Rank D. et al. Blueprint for phasing and assembling the genomes of heterozygous polyploids: application to the octoploid genome of strawberry. Preprint at bioRxiv. 2021; https://doi.org/10.1101/2021.11.03.467115 Google Scholar ). Similarly, haplotype-phased genomes have been assembled for other important crops, including cassava (Manihot esculenta) ( Hu et al., 2021 Hu W. Ji C. Shi H. Liang Z. Ding Z. Ye J. Ou W. Zhou G. Tie W. Yan Y. et al. Allele-defined genome reveals biallelic differentiation during cassava evolution. Mol. Plant. 2021; 14: 851-854 Google Scholar ) and potato (Solanum tuberosum) ( Hoopes et al., 2022 Hoopes G. Meng X. Hamilton J.P. Achakkagari S.R. de Alves Freitas Guesdes F. Bolger M.E. Coombs J.J. Esselink D. Kaiser N.R. Kodde L. et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. 2022; (S1674-2052, 00003-X)https://doi.org/10.1016/j.molp.2022.01.003 Google Scholar ). This has resulted in the development of new genomic resources that can be directly used in guiding molecular breeding efforts, without worrying about the gene presence-absence variation that exists within a crop or species ( Golicz et al., 2016 Golicz A.A. Batley J. Edwards D. Towards plant pangenomics. Plant Biotechnol. J. 2016; 14: 1099-1105 Google Scholar ; Bayer et al., 2021 Bayer P.E. Scheben A. Golicz A.A. Yuan Y. Faure S. Lee H. Chawla H.S. Anderson R. Bancroft I. Raman H. et al. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. Plant Biotechnol. J. 2021; 19: 2488-2500 Google Scholar ). An additional benefit of having a reference genome of an important cultivar and/or genotype, versus from a highly inbred line, is that valuable insights that are potentially gained from the analysis of genetic variants present among haplotypes are not lost, allowing for additional insights.