Current status in whole genome sequencing and analysis of Ipomoea spp.

Sachiko Isobe,Hideki Hirakawa,Kenta Shirasawa

doi:10.1007/s00299-019-02464-4

Abstract

The recent advances of next-generation sequencing have made it possible to construct reference genome sequences in divergent species. However, de novo assembly at the chromosome level remains challenging in polyploid species, due to the existence of more than two pairs of homoeologous chromosomes in one nucleus. Cultivated sweet potato (Ipomoea batatas (L.) Lam) is a hexaploid species with 90 chromosomes (2n = 6X = 90). Although the origin of sweet potato is also still under discussion, diploid relative species, I. trifida and I. triloba have been considered as one of the most possible progenitors. In this manuscript, we review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, I. trifida, I. triloba and sweet potato (I. batatas). Most of the results of genome assembly suggest that the genomes of sweet potato consist of two pairs and four pairs of subgenomes, i.e., B1B1B2B2B2B2. The results also revealed the relation between sweet potato and other Ipomoea species. Together with the development of bioinformatics approaches, the large-scale publicly available genome and transcript sequence resources and international genome sequencing streams are expected to promote the genome sequence dissection in sweet potato.

Highlights

Genome and gene sequences have become essential information for a wide range of biological studies
In addition to the number of sequenced species, the quality in de novo assembly of genomes has been improved with advances in long reads sequencing technologies, such as the PacBio (Pacific Biosciences, Menlo Park, CA, USA) and Nanopore
We review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, including sweet potato

Summary

Introduction

Genome and gene sequences have become essential information for a wide range of biological studies. Cultivated sweet potato (Ipomoea batatas (L.) Lam) is a hexaploid species with 90 chromosomes (2n = 6X = 90), and the structure of the hexaploid genome has not yet been defined It was first considered an allohexaploid species based on cytological studies (Jones 1967; Magoon et al 1970; Sinha and Sharma 1992). Construction of the reference genome sequence in sweet potato would contribute to advances in genetic, genomic, and physiological studies of the species. In this manuscript, we review the recent results and activities of whole-genome sequencing in the genus Ipomoea series Batatas, including sweet potato. The assembled sequences were not chromosome level, they contributed to the advances in sweet potato studies as the first reference genomes (Shirasawa et al 2017; Si et al 2016; Zhang et al 2017). Each group of 15 pseudomolecules were generated in I. trifida and

Genome sequencing in sweet potato

Future perspectives

Findings

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