Plastome comparative genomics in maples resolves the infrageneric backbone relationships

Fabiola Areces-Berazain; Yixi Wang; Damien D Hinsinger; Joeri S Strijk

doi:10.7717/peerj.9483

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

PeerJ. 2020 Jul 13:8:e9483. doi: 10.7717/peerj.9483. eCollection 2020.

Authors

Fabiola Areces-Berazain^{1

2}, Yixi Wang¹, Damien D Hinsinger^{2

3}, Joeri S Strijk^{1

2

4}

Affiliations

¹ Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China.
² Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos.
³ Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commisariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France.
⁴ State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry, Guangxi University, Nanning, Guangxi, China.

Abstract

Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples.

Keywords: Acereae; Phylogenomics; Plastomes; Repeated sequences; SSRs.

Grants and funding

This work was supported by funding through the Bagui Scholarship team funding under Grant No. C33600992001 and the government of Guangxi Province (Provincial 100 Talent Program—recruitment of overseas talents for colleges and universities in Guangxi) to Joeri S. Strijk, and China Postdoctoral Science Foundation Grants (No. 2015M582481 and 2016T90822) to Damien D. Hinsinger. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.