Plastid markers from whole plastome sequencing for gene-flow studies in the endangered endemic bellflowers of St Helena, Wahlenbergia angustifolia and Wahlenbergia linifolia (Campanulaceae)

Abstract

St Helena is an endemic rich but ecologically devastated island in the South Atlantic Ocean. Many of the endemic plants are extinct or critically endangered. The genus Wahlenbergia is an example. Two species are extinct, one species critically endangered (population <50: Wahlenbergia linifolia) and one species vulnerable (population c. 8800: Wahlenbergia angustifolia). Gene flow between these two remaining species has been suspected. To aid parental analysis of these ultra-rare endemics we used whole genome sequencing to generate large plastome contigs from two individuals of W. angustifolia. These were then used to develop sufficient plastid markers (indels, snps and microsatellites) to enable discrimination of plastotypes within and between species. Ten polymorphic plastid indels ranging between 7 and 19 bp along with three microsatellites and one SNP were selected using this next generation sequencing approach. Nine W. angustifolia and 35 W. linifolia plants were scored for these markers. Seven species-specific markers were found of which five were indels. We identified eight plastotypes within W. angustifolia and one plastotype in W. linifolia. Preliminary results indicate that gene flow has occurred between the two species. The results show the ease with which highly variable plastid markers can be found using next generation sequencing. The indel markers are particularly valuable as these can be scored using cheap and safe agarose gels. The markers will help generate breeding system data that is of direct relevance for the conservation of these species.