Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes.
Chenxi Zhou, Tania Duarte, Rocio Silvestre, Genoveva Rossel, Robert OM Mwanga, Awais Khan, Andrew W George, Zhangjun Fei, G Craig Yencho, David Ellis, Lachlan JM Coin
Gates Open Research | Published : 2018
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..View full abstract