Haplotype-resolved genome analyses of a heterozygous diploid potato

Abstract

Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

Hapo-G, Haplotype-Aware Polishing Of Genome Assemblies

“…We downloaded the Nanopore data produced by the authors of a recent article by Zhou et al(24) describing the diploid assembly of Solanum tuberosum (Table 2). The long-read dataset was assembled using the Flye assembler(19) (v2.8.1) with the parameter ‘-g 1600m’ to indicate a genome size of 1600Mb (representing the length of the diploid genome).…”

Resisting Potato Cyst Nematodes With Resistance

“…Thus, more recently, potato genomes have been sequenced from the homozygous diploid inbred potato clone M6 of S. chacoense , which is used as a breeding line and in genetics analysis ( Jansky et al, 2014 ). A heterozygous clone, RH, has also solved haplotype blocks with third generation sequencing technology ( Leisner et al, 2018 ; Zhou et al, 2020 ). These additional genomes will allow a greater resolution and understanding of NB-LRR loci and aid in the isolation and cloning of target genes.…”

“…As sequencing methods continue to improve, so will the outputs for the de novo assembly of genomes or loci of interest, particularly in highly repetitive regions and for the many potato species with high levels of heterozygosity. Indeed, newly emerging and rapidly improving long-read sequencing technologies such as Oxford Nanopore and PacBio, are already starting to provide potential solutions for potato genomics and new potato genomes are being released ( van Lieshout et al, 2020 ; Zhou et al, 2020 ). With these technological advances and the computational tools that facilitate ever more complex analyses, mapping and cloning of resistance genes should become more routine in the future.…”

Computational methods for chromosome-scale haplotype reconstruction

“…Algorithms for long-read sequencing are now able to produce megabase contigs for haplotypes and improve the availability of reference-quality genomes for humans and various other eukaryotic organisms [ 23 , 103 , 104 ]. This technique has been applied to assemble phased sequences of humans [ 55 , 103 ] (Table 1 ), diploid potato [ 105 ], zebra finch [ 54 ], cattle [ 54 ], and goat genomes [ 106 ]. Broadly, the bioinformatic approaches for diploid assembly fall into three classes: collapsed, semi-collapsed, and uncollapsed (Fig.…”