Journal article

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

Chenxi Zhou, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert Mwanga, Awais Khan, Andrew George, Zhangjun Fei, Craig Yencho, David Ellis, Lachlan Coin

Gates Open Research | Published : 2018

Abstract

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 comp..

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University of Melbourne Researchers

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