Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies

Giovanni Cafa; Riccardo Baroncelli; Carol A Ellison; Daisuke Kurose

doi:10.7717/peerj.8739

Impatiens glandulifera (Himalayan balsam) chloroplast genome sequence as a promising target for populations studies

PeerJ. 2020 Mar 24:8:e8739. doi: 10.7717/peerj.8739. eCollection 2020.

Authors

Giovanni Cafa¹, Riccardo Baroncelli², Carol A Ellison¹, Daisuke Kurose¹

Affiliations

¹ CABI Europe, Egham, Surrey, UK.
² University of Salamanca, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Villamayor (Salamanca), Spain.

Abstract

Background: Himalayan balsam Impatiens glandulifera Royle (Balsaminaceae) is a highly invasive annual species native of the Himalayas. Biocontrol of the plant using the rust fungus Puccinia komarovii var. glanduliferae is currently being implemented, but issues have arisen with matching UK weed genotypes with compatible strains of the pathogen. To support successful biocontrol, a better understanding of the host weed population, including potential sources of introductions, of Himalayan balsam is required.

Methods: In this molecular study, two new complete chloroplast (cp) genomes of I. glandulifera were obtained with low coverage whole genome sequencing (genome skimming). A 125-year-old herbarium specimen (HB92) collected from the native range was sequenced and assembled and compared with a 2-year-old specimen from UK field plants (HB10).

Results: The complete cp genomes were double-stranded molecules of 152,260 bp (HB92) and 152,203 bp (HB10) in length and showed 97 variable sites: 27 intragenic and 70 intergenic. The two genomes were aligned and mapped with two closely related genomes used as references. Genome skimming generates complete organellar genomes with limited technical and financial efforts and produces large datasets compared to multi-locus sequence typing. This study demonstrates the suitability of genome skimming for generating complete cp genomes of historic herbarium material. It also shows that complete cp genomes are solid genetic markers for population studies that could be linked to plant evolution and aid with targeting native range and natural enemy surveys for biocontrol of invasive species.

Keywords: Balsaminaceae; Chloroplast genome; Genome skimming; Impatiens glandulifera; Phylogenetic analyses; Whole genome sequencing.

Grants and funding

CABI is an international intergovernmental organization and receives core financial support from our member countries (and lead agencies) including the United Kingdom (Department for International Development), China (Chinese Ministry of Agriculture), Australia (Australian Centre for International Agricultural Research), Canada (Agriculture and Agri-Food Canada), Netherlands (Directorate-General for International Cooperation) and Switzerland (Swiss Agency for Development and Cooperation). Riccardo Baroncelli’s research is supported by the project Escalera de Excelencia CLU-2018-04 co-funded by the P.O. FEDER of Castilla y León, Spain. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.