Comparison of the Whole-Plastome Sequence between the Bonin Islands Endemic Rubus boninensis and Its Close Relative, Rubus trifidus (Rosaceae), in the Southern Korean Peninsula.

Jiyoung Yang,Jae-Hong Pak,Koji Takayama,Seung-Chul Kim

doi:10.3390/genes10100774

Jiyoung Yang, Jae-Hong Pak + Show 2 more

Open Access

https://doi.org/10.3390/genes10100774

Copy DOI

Journal: Genes	Publication Date: Oct 2, 2019
Citations: 9	License type: CC BY 4.0

Affiliation: Kyungpook National University, Sungkyunkwan University

Abstract

Rubus boninensis is a rare endemic species found on the Bonin Islands with a very restricted distribution. It is morphologically most closely related to Rubus trifidus, occurring widely in the southern Korean peninsula and Japan. This species pair provides a good example of anagenetic speciation on an oceanic island in the northwestern Pacific Ocean—R. trifidus as a continental progenitor and R. boninensis as an insular derivative species. In this study, we firstly characterized the complete plastome of R. boninensis and R. trifidus and compared this species pair to another anagenetically derived species pair (R. takesimensis–R. crataegifolius). The complete plastome of R. trifidus was 155,823 base pairs (bp) long, slightly longer (16 bp) than that of R. boninensis (155,807 bp). No structural or content rearrangements were found between the species pair. Eleven hotspot regions, including trnH/psbA, were identified between R. trifidus and R. boninensis. Phylogenetic analysis of 19 representative plastomes within the family Rosaceae suggested sister relationships between R. trifidus and R. boninensis, and between R. crataegifolius and R. takesimensis. The plastome resources generated by the present study will help elucidate plastome evolution and resolve phylogenetic relationships within highly complex and reticulated lineages of the genus Rubus.

Highlights

The Bonin Islands, known as the Ogasawara Islands, consist of 25 small islands (>0.1 km2 )and many islets scattered in the region of 24◦ 14’–27◦ 44’ N and 140◦ 52’–142◦ 15’ E, and are located approximately 1000 km directly south of the Japanese archipelago [1,2]
They were formed during the Paleogene period, their uplift started in the Pleistocene epoch, exposing the landmass above the sea level before the middle Pleistocene epoch [3,4]
We found that the large single copy (LSC) region was the most divergent and the two inverted repeat (IR) regions were highly conserved, and that the non-coding regions were more divergent and variable than the coding regions

Summary

Introduction

The Bonin Islands, known as the Ogasawara Islands, consist of 25 small islands (>0.1 km2 )and many islets scattered in the region of 24◦ 14’–27◦ 44’ N and 140◦ 52’–142◦ 15’ E, and are located approximately 1000 km directly south of the Japanese archipelago [1,2]. The Bonin Islands, known as the Ogasawara Islands, consist of 25 small islands (>0.1 km ). The Bonin Islands consist of two island groups, i.e., Ogasawara Group (Hahajima, Chichijima, and Mukojima) and Volcano Group (Kitaiwojima, Iwojima, and Minamiiwojima). The Ogasawara Group is a group of three aggregated islands, and are aligned from south to north, i.e., Hahajima, Chichijima, and Mukojima. They were formed during the Paleogene period, their uplift started in the Pleistocene epoch, exposing the landmass above the sea level before the middle Pleistocene epoch [3,4]. Of the 369 indigenous vascular plant species, approximately 40% of them are endemic to the Bonin Islands, Genes 2019, 10, 774; doi:10.3390/genes10100774 www.mdpi.com/journal/genes

Objectives

Methods

Results

Conclusion