Plastid genome sequencing reveals biogeographical structure and extensive population genetic variation in wild populations of Phalaris arundinacea L. in north‐western Europe

Abstract

New and comprehensive collections of the perennial rhizomatous reed canary grass (Phalaris arundinacea) were made in NW Europe along north-to-south and east-to-west clines from Denmark, Germany, Ireland, Poland, Sweden and the United Kingdom. Rhizome, seed and leaf samples were taken for analysis and genetic resource conservation. A subsample covering the geographical range was characterized using plastid genome sequencing and SNP discovery generated using a long-read PCR and MiSeq sequencing approach. Samples were also subject to flow cytometry and all found to be tetraploid. New sequences were assembled against a Lolium perenne (perennial ryegrass) reference genome, and an average of approximately 60% of each genome was aligned (81 064 bp). Genetic variation was high among the 48 sequenced genotypes with a total of 1793 SNPs, equating to 23 SNPs per kbp. SNPs were subject to principal coordinate and Structure analyses to detect population genetic groupings and to examine phylogeographical pattern. Results indicate substantial genetic variation and population genetic structuring of this allogamous species at a broad geographical scale in NW Europe with plastid genetic diversity organized more across an east-to-west than a north-to-south cline.

Genetic diversity of phalaris arundinacea populations in relation to river regulation in the Merkys basin, Lithuania

“…arundinacea contrasts with analogous data for P . arundinacea populations sampled in different ways and greater distances (Anderson et al, ; Barth et al, ; Jakubowski et al, ; Jakubowski et al, ; Jakubowski, Jackson, et al, ; Nelson et al, ; Perdereau et al, ). In our study, molecular variance within populations was lower (69%) compared with the same parameter (74.5%) obtained for SSR loci of cultivars and wild accessions of P .…”

“…In our study, molecular variance within populations was lower (69%) compared with the same parameter (74.5%) obtained for SSR loci of cultivars and wild accessions of P . arundinacea sampled on the global scale (Jakubowski, Jackson, et al, ), 85% obtained for ISSR loci of populations sampled on the global scale (Anderson et al, ), or for others used for SSR loci (Barth et al, ; Perdereau et al, ). This lowered variation in the Merkys populations could be due to close proximity and shared gene flow in this wind‐pollinated species.…”

“…An advantage of studying P . arundinacea is the large set of molecular markers applied (Anderson et al, ; Barth, Jankowska, Hodkinson, Vellani, & Klaas, ; Bloju, Boldura, Samfira, & Popescu, ; Casler et al, ; Jakubowski, Casler, & Jackson, ; Jakubowski, Jackson, Johnson, Hu, & Casler, ; Jakubowski, Casler, & Jackson, ; Jakubowski, Jackson, & Casler, ; Lavergne & Molofsky, ; Nelson et al, ; Perdereau, Klaas, Barth, & Hodkinson, ), providing tested methodological approaches for further research.…”

Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

“…Thirty accessions were collected from each of the ten locations per country. Seed, rhizomes and herbarium voucher specimens were collected and stored following Perderau et al [46]. Not all plants were sequenced to determine nuclear and plastome variation because of time and money constraints.…”

“…Thus, representative subsets of 88 plants, grown from rhizome, were sampled for GBS and 48 accessions for plastome sequencing (Table 1). DNA was extracted and quantified from fresh or dried leaf tissue following [46,47]. Flow cytometry was undertaken to determine ploidy using leaves from grown-up plants.…”