First steps towards conservation of endemic Salvia in Italy with population genomics

Chiara Paleni ¹, Cristina Puricelli ¹, Camilla Pieri ¹, Silvia Manrique Urpì ², Larissa De Paola ³, Aureliano Bombarely ⁴, Martin Kater ¹, Carla Lambertini ⁵

Museo Orto Botanico di Brera e Erbario, MOBE, Università degli Studi di Milano, Milan, Italy ¹, Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia, Spain ², Groningen Institute for Evolutionary Life Sciences, GELIFES, University of Groningen, Groningen, The Netherlands ³, Instituto de Biologia Molecular y Celular de Plantas, IBMCP (CSIC-UPV), Valencia, Spain ⁴, Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy ⁵

The Salvia genus is well known in botanical gardens for its long, shared history with humans, as medicinal, culinary and aromatic plants; but while domesticated plants like kitchen sage (S. officinalis) and rosemary (S. rosmarinus) enjoy great popularity, their wild relatives are less known. Around 20 species of Salvia grow natively in Italy, of which S. pratensis, one of the most common, is closely related to endemic taxa whose classification has been debated in the past (S. ceratophylloides, S. saccardiana, S. haematodes, S. pratensis subsp. bertolonii). In this project we investigated the geographic distribution of genetic diversity in Salvia populations via a sampling campaign in the entire peninsula, thanks to a network of contributors coordinated by the Botanical Garden of Brera (coming from other botanical gardens, institutions, or individuals). The aim of the study is to create a phylogeny for the genus supported by genome-wide data and verify whether there is genetic isolation between different taxa of the pratensis group that corroborates their species status, to finally develop genetic markers to identify endemics more easily. The long-term goal of the project is to develop ex situ collections that adequately represent the genetic diversity present in natural populations. The collection of dry leaf samples was analysed with the Genotyping-By-Sequencing (GBS) method, which allows to obtain thousands of markers distributed all over the genome. The S. pratensis genome was sequenced and assembled with PacBio HiFi data to serve as a reference and annotated with information on gene locations and function. The results on 155 samples, 14 taxa show separation between the endemic taxa and S. pratensis, which is split in three lineages: one lineage in Northern and Central Italy; S. saccardiana in sympatry but clearly genetically isolated from S. pratensis in Veneto; and a lineage including samples identified as both S. haematodes and S. pratensis coming from southern Italy. Subspecies bertolonii is instead clustering within S. pratensis. Moreover, different levels of ploidy were seen inside the Salvia genus and separation was seen between other groups of related species (S. verbenaca and S. clandestina; S. argentea and S. desoleana, an endemism of Sardinia). More analyses are in progress to include additional samples from the range of S. saccardiana and other populations and species. The results from this project will give a clearer idea of the evolution of this genus in Italy and help identify morphologically similar species with genetic data. The project is a case study for the use of second and third generation sequencing applied to study and conservation of biodiversity in an Italian botanical garden and in nature.

Main author career stage: PhD student

Contribution type: Talk

First choice session: 1. Systematics, phylogenetics, biogeography and evolution

Second choice session: 5. Genetics, genomics, and bioinformatics