Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Gates Open Research

article

Awais Khan¹  Andrew W. George³  Zhangjun Fei⁴  G. Craig Yencho⁵  David Ellis¹  Lachlan J. M. Coin⁶  Chenxi Zhou⁶  Tania Duarte⁶  Rocio Silvestre¹  Genoveva Rossel¹  Robert O. M. Mwanga¹ 

[1] International Potato Center;Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University;Data61, CSIRO, Ecosciences Precinct;Boyce Thompson Institute, Cornell University;Department of Horticulture, North Carolina State University;Institute for Molecular Bioscience, University of Queensland

关键词: chloroplast;    sweetpotato;    genome assembly;    Oxford Nanopore sequencing;    Illumina sequencing;    phylogenetic analysis;    Convolvulaceae Ipomoea;   

DOI  :  10.12688/gatesopenres.12856.2

学科分类：电子与电气工程

来源: American Journal Of Pharmtech Research

【 摘 要 】

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as a reference, we constructed complete cp genome assemblies for a further 17 sweetpotato cultivars from East Africa and an I. triloba line using Illumina WGS data. Analysis of the sweetpotato cp genomes demonstrated the presence of two distinct subpopulations in East Africa. Phylogenetic analysis of the cp genomes of the species from the Convolvulaceae Ipomoea section Batatas revealed that the most closely related diploid wild species of the hexaploid sweetpotato is I. trifida. Conclusions: Nanopore long reads are helpful in construction of cp genome assemblies, especially in solving the two long inverted repeats. We are generally able to extract cp sequences from WGS data of sufficiently high coverage for assembly of cp genomes. The cp genomes can be used to investigate the population structure and the phylogenetic relationship for the sweetpotato.

【 授权许可】

CC BY