Plastome variation and phylogeny of Taxillus (Loranthaceae).

Huei-Jiun Su,Daniel L Nickrent,Shu-Ling Liang,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0256345

Abstract

Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35–40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90–93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.

Highlights

The family Loranthaceae is the largest in the sandalwood order Santalales with 76 genera and over 1000 species distributed worldwide [1]
Following the major gene losses that occurred along the branch leading to all these accessions of Loranthaceae, loss or pseudogenization has occurred independently in a few lineages (S1 Fig), such as the pseudogenization of trnA-UGC in T. matsudai and H. parasitica and the independent losses of infA in the Scurrula clade, T. nigrans and T. chinensis
ClpP was reported as a pseudogene in T. nigrans by Zhao et al (2019) [20], but an intact clpP sequence was recovered from the transcriptome data, this loss was not labeled on S1 Fig

Summary

Introduction

The family Loranthaceae is the largest in the sandalwood order Santalales with 76 genera and over 1000 species distributed worldwide [1]. Despite its ecological and ethnobotanical value, relatively little is known about species relationships within the larger genera. Most genera have been represented as placeholder species in broad-scale phylogenetic work within Santalales and Loranthaceae [1,2,3,4], relatively few studies have examined interspecific relationships within a genus. Of the 76 Loranthaceae genera, 28 have 10 or more species [5]. Very few published studies that included a robust sampling of species within the genus are of Tristerix [6], Loranthus [7] and Dendropemon [8].

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Discussion

Conclusion