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

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.

Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming

“…The incongruence detected between our plastid result and these two nuclear topologies may be due to the hybridization events during the diversification of the Yulania and Michelia clades and their close relatives. Hybridizations have played an important role in the evolution of Magnoliaceae (Kim et al, 2019) and many other lineages of angiosperms (Wen et al, 2018(Wen et al, , 2020Liu et al, 2019Liu et al, , 2020aLiu et al, , 2020b.…”

“…Recent advances in nextgeneration sequencing (NGS) technologies have facilitated the utility of genomic data to resolve difficult phylogenetic problems . Genome skimming has been widely used in the last several years to generate sequences of whole plastomes, entire nuclear ribosomal DNA repeats, and mitochondrial genes, and it has been successfully employed in many plant lineages, for example, Araliaceae (Valcárcel & Wen, 2019), Bignoniaceae (Mabry & Simpson, 2018), Rosaceae (Liu et al, 2019(Liu et al, , 2020a(Liu et al, , 2020b, Taxaceae (Zhang et al, 2019), Vitaceae (Zhang et al, 2015(Zhang et al, , 2016Wen et al, 2018), and Wightiaceae (Xia et al, 2019).…”

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

“…Some regions of the nrDNA repeat, especially the internal transcribed spacer (ITS) and sometimes also the external transcribed spacer (ETS) have been widely used for lower-level phylogenetic reconstruction in flowering plants (Baldwin et al, 1995;Álvarez & Wendel, 2003;Soltis et al, 2008). Recently, the entire nrDNA repeats including ETS, 18S, ITS1, 5.8S, ITS2, and 26S regions have been assembled from genome skimming data, and depending on the region of the repeat that has been utilized, has also been effective in providing phylogenetic resolution at shallow evolutionary levels (for example, in the Rosaceae: Liu et al, 2019Liu et al, , 2020aLiu et al, , 2020b. Hence, genome skimming has been a valuable approach for providing genomic data for phylogenetic inferences.…”

Typification of 23 names in Eriobotrya (Maleae, Rosaceae)

“…The generic delimitation among the members of Maleae has been notoriously controversial for a long time, and efforts to resolve the intergeneric relationships have not been successful (Phipps et al 1991;Campbell et al 2007;Li et al 2012;Lo and Donoghue 2012;Verbylaitė et al 2006;Sun et al 2018). As part of our integrative systematic studies of Eriobotrya and close relatives (Wen et al 2017;Liu et al 2020), it will be necessary to typify the taxa described under Eriobotrya.…”