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.
Highlights
Potato (Solanum tuberosum L.) is the most important tuber crop worldwide
While genome heterozygosity in diploid potato has been surveyed[6,7,8,9], these efforts were limited to bacterial artificial chromosome (BAC) clones and short-read sequences and lacked a genome-wide assessment of haplotype diversity
Current phasing strategies rely on the alignment of sequenced reads to a reference genome to infer regional haplotypes[13,14,15,16,17]; such efforts are limited by the continuity of an available reference assembly
Summary
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. The diploid genome was assembled into scaffolds using Illumina reads (WGS and 10xG data; Supplementary Table 3). In a total of 184 BACs previously assembled and ordered, 126 and 169 BACs mapped to a single fragment on RHgv[1] and RHgv[2], respectively, with 113 and 152 BACs showing perfect collinearity with the scaffolds or unitigs (Supplementary Data 1 and 2).
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