Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
Highlights
The genus Fragaria Linnaeus belongs to the family Rosaceae and is comprised of 25 species, including 13 diploids (2n), five tetraploids (4n), one pentaploid (5n), one hexaploid (6n), three octoploids (8n), and two decaploids (10n; Staudt, 1962, 1989, 2009; Davis et al, 2010; Hummer, 2012; Lei et al, 2017)
The total genome sequence lengths of Fragaria species ranged from 155,479 bp (F. viridis) to 155,832 bp (F. daltoniana_3)
The cp genomes presented a typical quadripartite structure including a pair of Inverted repeats (IRs) regions with lengths of 51,872 bp (F. vesca ssp. bracteata) to 51,948 bp (F. corymbosa_JL), separated by a large single-copy region (LSC) region from 85,471 bp (F. viridis) to 85,726 bp (F. daltoniana_3) and a short single-copy region (SSC) region from 18,116 bp (F. viridis) to 18,219 bp (F. moupinensis_XZ)
Summary
The genus Fragaria Linnaeus belongs to the family Rosaceae and is comprised of 25 species, including 13 diploids (2n), five tetraploids (4n), one pentaploid (5n), one hexaploid (6n), three octoploids (8n), and two decaploids (10n; Staudt, 1962, 1989, 2009; Davis et al, 2010; Hummer, 2012; Lei et al, 2017). To the best of our knowledge, there is only one study that has focused on the molecular phylogenetic analysis of Fragaria genus based on whole complete chloroplast genome sequences (Sun et al, 2021), which revealed that 20 Fragaria species were clustered into northern group (eight species), southern group (11 species), and an oldest extant species (one species) based on whole cp genomes This previous study focused on molecular clock analysis and ignored the variation and evolution of whole cp genomes of Fragaria, including, for example, the contraction and expansion of inverted repeats (IRs) regions (Plunkett and Downie, 2000; Kode et al, 2005; Ma et al, 2014; Lei et al, 2016)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
