Eriobotrya Belongs to Rhaphiolepis (Maleae, Rosaceae): Evidence From Chloroplast Genome and Nuclear Ribosomal DNA Data.

Jun Wen,De-Yuan Hong,Guang-Ning Liu,Bin-Bin Liu

doi:10.3389/fpls.2019.01731

Abstract

The Eriobotrya-Rhaphiolepis (ER) clade consists of about 46 species distributed in East and Southeast Asia. Although Eriobotrya and Rhaphiolepis have been supported to form a clade, the monophyly of Eriobotrya and Rhaphiolepis at the genus level has never been well tested and their phylogenetic positions in Maleae still remain uncertain. This study aims to reconstruct a robust phylogeny of the ER clade in the framework of Maleae with a broad taxon sampling and clarify the phylogenetic relationship between Eriobotrya and Rhaphiolepis. This study employed sequences of the whole plastome (WP) and entire nuclear ribosomal DNA (nrDNA) repeats assembled from the genome skimming approach and included 83 samples representing 76 species in 32 genera of Rosaceae, especially Maleae. The Maximum Likelihood (ML) and Bayesian Analysis (BI) based on three datasets, i.e., WP, coding sequences of plastome (CDS), and nrDNA, strongly supported the paraphyly of Eriobotrya, within which Rhaphiolepis was nested. Our plastid tree supported the sister relationship between the ER clade and Heteromeles, and the nrDNA tree, however, did not resolve the phylogenetic placement of the ER clade in Maleae. Strong incongruence between the plastid and the nuclear trees is most likely explained by hybridization events, which may have played an important role in the evolutionary history of the ER clade. Molecular, morphological, and geographic evidence all supports the merge of Eriobotrya with Rhaphiolepis, which has the nomenclatural priority. We herein transferred 36 taxa of Eriobotrya to Rhaphiolepis. We also proposed a new name, Rhaphiolepis loquata B.B.Liu & J.Wen, for the economically important loquat, as the specific epithet “japonica” was pre-occupied in Rhaphiolepis.

Highlights

Rosaceae is a widely distributed and economically important plant family currently classified into three subfamilies: Rosoideae, Dryadoideae, and Amygdaloideae (Morgan et al, 1994; Potter et al, 2007)
The chloroplast genome of Rhaphiolepis indica was 159,466 bp in length with a classic quadripartite structure that comprised of inverted repeat's pairs (Figure 2), and that of Eriobotrya japonica had the same structure as R. indica with a length of 159,156 bp (Supplementary Figure 1)
The 79 concatenated coding sequences (CDS) sequences from 83 plastomes were generated an aligned matrix of 67,961 bp in length, which was split into 25 sets of sites with the same best scheme for each data block for the subsequent Maximum Likelihood (ML) and Bayesian Analysis (BI) analysis

Summary

Introduction

Rosaceae is a widely distributed and economically important plant family currently classified into three subfamilies: Rosoideae, Dryadoideae, and Amygdaloideae (Morgan et al, 1994; Potter et al, 2007). The apple tribe includes a number of commercially important fruits, such as apples (Malus domestica (Suckow) Borkh.), pears (Pyrus L. spp.), loquats (Eriobotrya japonica (Thunb.) Lindl.), as well as some ornamentals, e.g. serviceberries The phylogenetic relationships among the members of Maleae have never been resolved confidently using either the morphological characteristics (Phipps et al, 1991; Aldasoro et al, 2005) or the limited plastid and/or nuclear sequences (Campbell et al, 1995; Verbylaitė et al, 2006; Campbell et al, 2007; Li et al, 2012; Lo and Donoghue, 2012; Sun et al, 2018)

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