Generating a Phased Genome Assembly of the Hexaploid Sweetpotato Cultivar, ‘New Kawogo’

Sweet potato is among the most important staple crops. Sweet potato cultivars rich in Vitamin A have been produced and promoted in areas where childhood Vitamin A deficiency is common. Sweet potato improvement is challenged by a lack of knowledge of the genetic and molecular basis of key agronomic traits. This research project aims to generate a phased genome assembly of the hexaploid sweet potato cultivar, ‘New Kawogo’. PacBio HiFi sequencing was used to produce highly accurate long reads and the reads were assembled into phased contigs with Hifiasm, a de novo assembler that produces haplotype-resolved genome assemblies by integrating chromatin conformation capture (Hi-C) sequencing data. Due to the complexity of the hexaploid sweet potato genome, chimeric contigs resulting from erroneously connected sequences from different haplotypes were present in the initial assembly. By taking advantage of the phased genetic maps, Hi-C contact maps and genome synteny, misassemblies were corrected in the ‘New Kawogo’ assembly. These corrected contigs have been used to produce a haplotype-resolved chromosome-level genome assembly of ‘New Kawogo’, which provides a valuable resource for the discovery of genetic controls of important traits and genomics-assisted improvement of sweet potato. This assembly serves as a foundation for the genetics and biology of ‘New Kawogo’ and will accelerate sweet potato breeding.

I am grateful for the opportunity to conduct summer research in the Fei lab at BTI under Shan Wu’s mentorship. Being part of the team working on the phased genome assembly of the hexaploid sweet potato cultivar ‘New Kawogo’ has been immensely rewarding, as this research supports biofortification efforts to promote Vitamin A-rich cultivars in regions of the world affected by childhood Vitamin A deficiency. I expanded my knowledge of genomics, including genetic markers, Hi-C contact signals, and genome synteny. The guidance and collaborative environment have greatly enriched my learning and research skills. With the help of my mentor and the BTI BCBC bioinformatics course, I learned the basics of UNIX, coding in R, and bioinformatics tools like BLAST, Seqkit, and BUSCO. I am also grateful for the REU programs, such as weekly seminars and the DGS Graduate School Panel, which helped me learn about and decide to pursue higher studies.