Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis.

Yunhong Tan,Yu Song,Jing Xin,Zhanghong Dong,Shaohong Qu,Wen-Bin Yu,Sven Landrein,Peiyao Xin,Wenzhi Zhao

doi:10.3389/fgene.2022.831206

Abstract

Eriobotrya (Rosaceae) is an economically important genus with around 30 species. It is widely distributed in tropical and warm temperate regions of Asia, with most of its species in China, Myanmar, and Vietnam. However, Eriobotrya is often confused with the smaller genus Rhaphiolepis, and the phylogenetic relationships between the two genera are controversial. Here we present phylogenetic analyses of 38 newly generated Eriobotrya and Rhaphiolepis nrDNA together with 16 sequences of nrDNA and 28 sequences of ITS obtained from GenBank, representing 28 species of Eriobotrya and 12 species of Rhaphiolepis, in order to reconstruct highly supported relationships for the two genera. Contrary to previous research based on limited sampling, our results highlight the monophyly of Eriobotrya as well as Rhaphiolepis. The topology recovered here is consistent with key morphological synapomorphies such as the persistent sepals in Eriobotrya. Our findings show that increased sampling of taxa can provide a more robust phylogeny through reducing phylogenetic error and increasing overall phylogenetic accuracy.

Highlights

Eriobotrya Lindl. and Rhaphiolepis Lindl., two genera of the tribe Maleae in the family Rosaceae (Kalkman, 2004), include about 30 and 15 species respectively, which are distributed throughout tropical and warm temperate regions from East Asia to tropical Southeast Asia
Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear and four chloroplast regions, and the results showed that Eriobotrya and Rhaphiolepis were sister groups (Li et al, 2012)
The size of the 38 newly determined Eriobotrya and Rhaphiolepis nuclear ribosomal DNA (nrDNA) sequences ranged from 6,775 bp

Summary

INTRODUCTION

Eriobotrya Lindl. and Rhaphiolepis Lindl., two genera of the tribe Maleae in the family Rosaceae (Kalkman, 2004), include about 30 and 15 species respectively, which are distributed throughout tropical and warm temperate regions from East Asia to tropical Southeast Asia. The latest research shows that multiple ancient hybridization and chloroplast capture events within Eriobotrya in the Yunnan-Guizhou Plateau (Chen et al, 2021) This makes the taxonomic study of Eriobotrya more complicated. Six chloroplast DNA (cpDNA) regions, two GBSSI genes (1A and 2B), and nrITS sequences supported a sister relationship between Eriobotrya and Rhaphiolepis (Campbell et al, 2007). Phylogenetic relationships among 88 genera of Rosaceae were investigated using nucleotide sequence data from six nuclear and four chloroplast regions, and the results showed that Eriobotrya and Rhaphiolepis were sister groups (Li et al, 2012). Further studies in Maleae, showed this sister relationship was supported using chloroplast, nrITS, and even whole plastome sequences (Lo and Donoghue, 2012; Xiang et al, 2016; Zhang et al, 2017; Sun et al, 2018; Liu et al, 2019; Idrees et al, 2020b). To better estimate the phylogenetic relationship between Eriobotrya and Rhaphiolepis, it is necessary to sample more taxa to reliably reconstruct the phylogenetics of the Eriobotrya and Rhaphiolepis genera

DNA Extraction and Sequencing

Nuclear Ribosomal DNA Assembly and Annotation

Mutation Events Analysis

Phylogenetic Analyses

Size and Organization of the nrDNA Sequences

Numbers and Pattern of Indel and Single-Nucleotide Polymorphism Mutations in nrDNA Sequences

Deletion

Phylogenetic Analyses Based on nrDNA and ITS Region

Phylogenetic Analyses Based on Six Regions of nrDNA Sequences

DISCUSSION

Relationship of Eriobotrya and Rhaphiolepis

Morphological Difference Between Eriobotrya and Rhaphiolepis