Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences

Yahui Xuan; Yue Wu; Peng Li; Ruiling Liu; Yiwei Luo; Jianglian Yuan; Zhonghuai Xiang; Ningjia He

doi:10.7717/peerj.8158

Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences

PeerJ. 2019 Dec 12:7:e8158. doi: 10.7717/peerj.8158. eCollection 2019.

Authors

Yahui Xuan¹, Yue Wu¹, Peng Li¹, Ruiling Liu¹, Yiwei Luo¹, Jianglian Yuan¹, Zhonghuai Xiang¹, Ningjia He¹

Affiliation

¹ State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.

Abstract

Background: Species in the genus Morus (Moraceae) are deciduous woody plants of great economic importance. The classification and phylogenetic relationships of Morus, especially the abundant mulberry resources in China, is still undetermined. Internal transcribed spacer (ITS) regions are among the most widely used molecular markers in phylogenetic analyses of angiosperms. However, according to the previous phylogenetic analyses of ITS sequences, most of the mulberry accessions collected in China were grouped into the largest clade lacking for phylogenetic resolution. Compared with functional ITS sequences, ITS pseudogenes show higher sequence diversity, so they can provide useful phylogenetic information.

Methods: We sequenced the ITS regions and the chloroplast DNA regions TrnL-TrnF and TrnT-TrnL from 33 mulberry accessions, and performed phylogenetic analyses to explore the evolution of mulberry.

Results: We found ITS pseudogenes in 11 mulberry accessions. In the phylogenetic tree constructed from ITS sequences, clade B was separated into short-type sequence clades (clades 1 and 2), and a long-type sequence clade (clade 3). Pseudogene sequences were separately clustered into two pseudogroups, designated as pseudogroup 1 and pseudogroup 2. The phylogenetic tree generated from cpDNA sequences also separated clade B into two clades.

Conclusions: Two species were separated in clade B. The existence of three connection patterns and incongruent distribution patterns between the phylogenetic trees generated from cpDNA and ITS sequences suggested that the ITS pseudogene sequences connect with genetic information from the female progenitor. Hybridization has played important roles in the evolution of mulberry, resulting in low resolution of the phylogenetic analysis based on ITS sequences. An evolutionary pattern illustrating the evolution history of mulberry is proposed. These findings have significance for the conservation of local mulberry resources. Polyploidy, hybridization, and concerted evolution have all played the roles in the evolution of ITS sequences in mulberry. This study will expand our understanding of mulberry evolution.

Keywords: Concerted evolution; Internal transcribed spacer; Morus; Phylogenetic analyses; Pseudogenes.

Grants and funding

This project was funded by the National Key Research and Development Program (No. 2018YFD1000602), the Natural Science Foundation of China (No. 31572323), the special fund for Agro-scientific research in the public interest of China (No. 201403064), the “111” Project (B12006), the Chongqing Research Program of Basic Research and Frontier Technology (cstc2018jcyjAX0407), and the Fundamental Research Funds for the Central Universities (SWU118040). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.