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

Abstract

AbstractSweetpotato (Ipomoea batatas(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-scalede novoassembly of autohexaploid sweetpotato genome sequences. Before constructing the genome, we created chromosome-scale genome sequences inI. trifidausing 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.De novoassemblies were also performed for chloroplast and mitochondrial genomes inI. trifidaand sweetpotato. In total, 34,386 and 175,633 genes were identified on the assembled nucleic genomes ofI. trifidaand 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-scalede novoassembly of the sweetpotato genome. The results are expected to contribute to genomic and genetic analyses of sweetpotato.