Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea.

Jiyoung Yang,Seung-Chul Kim,Gi-Ho Kang,Jae-Hong Pak

doi:10.3390/ijms21144933

Jiyoung Yang, Seung-Chul Kim + Show 2 more

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https://doi.org/10.3390/ijms21144933

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Abstract

Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 6 of the 75 protein-coding genes have been subject to strong positive selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.

Highlights

The family Rosaceae (Rosid I, Fabidae) comprises approximately 3000 species in 91 genera within three subfamilies (Rosoideae, Amygdaloideae, and Dryadoideae) and includes numerous economically important commercial fruit species, such as Malus, Prunus, Pyrus, Rubus, and Fragaria [1,2,3]
Of the six Rosaceae endemic to Ulleung Island, C. wilsonii is characterized by the longest plastome (159,997 bp), whereas that of P. dickinsii var. glabrata is the shortest
We determined the complete plastome sequences of two species in the family Rosaceae (Potentilla dickinsii var. glabrata and Spiraea insularis) that are endemic to Ulleung Island, Korea

Summary

Introduction

The family Rosaceae (Rosid I, Fabidae) comprises approximately 3000 species in 91 genera within three subfamilies (Rosoideae, Amygdaloideae, and Dryadoideae) and includes numerous economically important commercial fruit species, such as Malus (apples), Prunus (almonds, plums, peaches, cherries, etc.), Pyrus (pears), Rubus (raspberries, blackberries), and Fragaria (strawberries) [1,2,3]. In addition to being a source of important commercial fruit and ornamental/landscaping trees, woody species of Rosaceae provide important habitats and food resources for innumerable forest animals, including birds and mammals [2]. Among the numerous important contributions to the phylogenetic characterization of Rosaceae, the whole plastid phylogenomic approach, based on 142 accessions, representing 87 genera, reported by Zhang et al, is of particular interest because they attempted to reconstruct deep relationships and reveal temporal diversification of the family [10]. On the basis of 125 new transcriptomic and genomic datasets, Xiang et al fully resolved the phylogeny of Rosaceae, revealing numerous whole-genome duplications and providing a foundation for understanding the evolution of fruit-bearing plants in the Rosaceae [6]

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