Plastome comparative genomics in maples resolves the infrageneric backbone relationships

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.

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

“…Most nodes of the reconstructed phylogenomic tree had 100% bootstrap support values, indicating a suitable evolutionary placement for Acer species (Figure 4). The results showed that Acer and Dipteronia are monophyly, which is consistent with previous studies (Renner et al, 2008;Gao et al, 2020;Wang et al, 2020;Areces-Berazain et al, 2021). Acer pictum subsp.…”

“…Although many studies have placed A. sino-oblongum in Section Palmata (van Gelderen et al, 1994;Xu et al, 2008), the taxonomic status of this species must be revisited. Acer yangbiense, a rare and critically endangered species, is herein shown to be genetically distant from the other species in Section Lithocarpa, as in previous studies Areces-Berazain et al, 2021). This species has pale white to pale gray leaf blade abaxially, entire leaf margin, and slender fruiting pedicels, which are pretty different from other species in the Section Lithocarpa (van Gelderen et al, 1994;Xu et al, 2008).…”

“…In Maples of the World, section Glabra comprises species from the Glabra and Arguta series (van Gelderen et al, 1994). However, many studies, including the present one, have shown a certain genetic distance between these two series Areces-Berazain et al, 2020;Gao et al, 2020;Areces-Berazain et al, 2021). Series Glabra is monotypic, containing only A. glabrum and its subspecies.…”

“…Therefore, dividing the two series into two sections is more appropriate, as de Jong (2004) proposed. Species of sections Trifoliata and Pentaphylla were mixed (Figure 4), suggesting their sister relationship Gao et al, 2020;Wang et al, 2020;Areces-Berazain et al, 2021). These two sections have compound leaves, distinguishing them from most other sections in Acer (Xu et al, 2008).…”

Phylogenomics resolves deep subfamilial relationships in Malvaceaes.l.

“…We used ModelTest-NG v0.1.5 ( Darriba et al 2019 ) to select the best-fitting nucleotide substitution model for the plastome dataset [with one inverted repeat (IR) removed]. No partition was defined because, in our experience with plastome data, we have not observed an effect of partitioning on tree inference (see Areces-Berazain et al 2020 ). A maximum likelihood (ML) tree was built with RAxML-NG v0.9.0 ( Kozlov et al 2019 ) using the GTR+I + G model.…”