Haploid-resolved and chromosome-scale genome assembly in hexa-autoploid sweetpotato (<i>Ipomoea batatas</i>(L.) Lam)

<jats:title>Abstract</jats:title><jats:p>Sweetpotato (<jats:italic>Ipomoea batatas</jats:italic>(L.) Lam) is the world’s seventh most important food crop by production quantity. Cultivated sweetpotato is a hexaploid (2n = 6x = 90), and its genome (B1B1B2B2B2B2) is quite complex due to polyploidy, self-incompatibility, and high heterozygosity. Here we established a haploid-resolved and chromosome-scale<jats:italic>de novo</jats:italic>assembly of autohexaploid sweetpotato genome sequences. Before constructing the genome, we created chromosome-scale genome sequences in<jats:italic>I. trifida</jats:italic>using a highly homozygous accession, Mx23Hm, with PacBio RSII and Hi-C reads. Haploid-resolved genome assembly was performed for a sweetpotato cultivar, Xushu18 by hybrid assembly with Illumina paired-end (PE) and mate-pair (MP) reads, 10X genomics reads, and PacBio RSII reads. Then, 90 chromosome-scale pseudomolecules were generated by aligning the scaffolds onto a sweetpotato linkage map.<jats:italic>De novo</jats:italic>assemblies were also performed for chloroplast and mitochondrial genomes in<jats:italic>I. trifida</jats:italic>and sweetpotato. In total, 34,386 and 175,633 genes were identified on the assembled nucleic genomes of<jats:italic>I. trifida</jats:italic>and sweetpotato, respectively. Functional gene annotation and RNA-Seq analysis revealed locations of starch, anthocyanin, and carotenoid pathway genes on the sweetpotato genome. This is the first report of chromosome-scale<jats:italic>de novo</jats:italic>assembly of the sweetpotato genome. The results are expected to contribute to genomic and genetic analyses of sweetpotato.</jats:p>