Phylogenomics and phylogeography of Menispermum (Menispermaceae)

Shiqiang Song; Kenneth M Cameron; Yuguo Wang; Shenyi Wang; Xinjie Jin; Faiza Hina; Zhaoping Yang; Pan Li

doi:10.3389/fpls.2023.1116300

Phylogenomics and phylogeography of Menispermum (Menispermaceae)

Front Plant Sci. 2023 Feb 22:14:1116300. doi: 10.3389/fpls.2023.1116300. eCollection 2023.

Authors

Shiqiang Song^{1

2}, Kenneth M Cameron³, Yuguo Wang⁴, Shenyi Wang³, Xinjie Jin⁵, Faiza Hina², Zhaoping Yang¹, Pan Li²

Affiliations

¹ College of Life Sciences and Technologies, Tarim University, Alar, China.
² Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China.
³ Department of Botany, University of Wisconsin, Madison, WI, United States.
⁴ Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China.
⁵ College of Life and Environmental Science, Wenzhou University, Wenzhou, China.

Abstract

Introduction: Phylogenomics have been widely used to resolve ambiguous and controversial evolutionary relationships among plant species and genera, and the identification of unique indels in plastomes may even help to understand the evolution of some plant families. Menispermum L. (Menispermaceae) consists of three species, M. dauricum DC., M. canadense L., and M. mexicanum Rose, which are disjuncly distributed among East Asia, Eastern North America and Mexico. Taxonomists continue to debate whether M. mexicanum is a distinct species, a variety of M. dauricum, or simply a synonym of M. canadense. To date, no molecular systematics studies have included this doubtful species in phylogenetic analyses.

Methods: In this study, we examined phylogenomics and phylogeography of Menispermum across its entire range using 29 whole plastomes of Menispermaceae and 18 ITS1&ITS2 sequences of Menispermeae. We reconstructed interspecific relationships of Menispermum and explored plastome evolution in Menispermaceae, revealing several genomic hotspot regions for the family.

Results and discussion: Phylogenetic and network analyses based on whole plastome and ITS1&ITS2 sequences show that Menispermum clusters into two clades with high support values, Clade A (M. dauricum) and Clade B (M. canadense + M. mexicanum). However, M. mexicanum is nested within M. canadense and, as a result, we support that M. mexicanum is a synonym of M. canadense. We also identified important molecular variations in the plastomes of Menispermaceae. Several indels and consequently premature terminations of genes occur in Menispermaceae. A total of 54 regions were identified as the most highly variable plastome regions, with nucleotide diversity (Pi) values > 0.05, including two coding genes (matK, ycf1), four introns (trnK intron, rpl16 intron, rps16 intron, ndhA intron), and 48 intergenic spacer (IGS) regions. Of these, four informative hotspot regions (trnH-psbA, ndhF-rpl32, trnK-rps16, and trnP-psaJ) should be especially useful for future studies of phylogeny, phylogeography and conservation genetics of Menispermaceae.

Keywords: Menispermaceae; disjunct distribution; phylogeny; plastome evolution; systematic.

Grants and funding

This research was supported by the National Natural Science Foundation of China (Grant Nos. 31970225 & 32060053), and the NSFC-NSF Dimensions of Biodiversity Program (Grant No. 31461123001).