AUTHOR=Song Yanhong , Li Chaochao , Liu Lifeng , Hu Panpan , Li Gang , Zhao Xia , Zhou Houcheng 

TITLE=The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1065218

DOI=10.3389/fpls.2022.1065218

ISSN=1664-462X

ABSTRACT=<p>The genus <italic>Fragaria</italic> consists of a rich diversity of ploidy levels with diploid (2x), tetraploid (4x), pentaploid (5x), hexaploidy (6x), octoploid (8x) and decaploid (10x) species. Only a few studies have explored the origin of diploid and octoploid strawberry, and little is known about the roles of tetraploidy and hexaploidy during the evolution of octoploid strawberry. The chloroplast genome is usually a stable circular genome and is widely used in investigating the evolution and matrilineal identification. Here, we assembled the chloroplast genomes of <italic>F</italic>. x <italic>ananassa</italic> cv. ‘Benihoppe’ (8x) using Illumina and HiFi data seperately. The genome alignment results showed that more InDels were located in the chloroplast genomes based on the PacBio HiFi data than Illumina data. We obtain highly accurate chloroplast genomes assembled through GetOrganelle using Illumina reads. We assembled 200 chloroplast genomes including 198 <italic>Fragaria</italic> (21 species) and 2 <italic>Potentilla</italic> samples. Analyses of sequence variation, phylogenetic and PCA analyses showed that <italic>Fragaria</italic> was divided into five groups. <italic>F</italic>. <italic>iinumae</italic>, <italic>F</italic>. <italic>nilgerrensis</italic> and all octoploid accessions formed Group A, C and E separately. Species native to western China were clustered into Group B. Group D consisted of <italic>F</italic>. <italic>virdis</italic>, <italic>F</italic>. <italic>orientalis</italic>, <italic>F</italic>. <italic>moschata</italic>, and <italic>F</italic>. <italic>vesca</italic>. STRUCTURE and haplotype network confirmed that the diploid <italic>F</italic>. <italic>vesca</italic> subsp. bracteata was the last maternal donator of octoploid strawberry. The dN/dS ratio estimated for the protein-coding genes revealed that genes involved in ATP synthase and photosystem function were under positive selection. These findings demonstrate the phylogeny of totally 21 <italic>Fragaria</italic> species and the origin of octoploid species. <italic>F</italic>. <italic>vesca</italic> was the last female donator of octoploid, which confirms the hypothesis that the hexaploid species <italic>F</italic>. <italic>moschata</italic> may be an evolutionary intermediate between the diploids and wild octoploid species.</p>