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.

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

Figure 1. Schematic diagram of the boundaries between the four regions (LSC, large single copy; SSC, short single copy; IR, inverted repeat) in the 16 plastid genomes sequenced in this study.

See Table 1 for full species names.

Figure 2. mVISTA alignment comparing the plastomes of Acer species against A. acuminatum.

The vertical scale to the right shows the percent of identity (50–100%) between the species compared. The black arrows indicate the boundaries of the inverted repeats. Coding regions are indicated in blue and non-coding regions in pink.

Figure 3. Sliding window analysis of polymorphic sites (S) for plastomes of 16 species of Acer (window length: 600 bp, step size: 100 bp).

Regions with the highest number of S are indicated. 1: trnH-psbA, 2: atpH-atpI, 3: atpI-rps2+rps2+rps2-rpoC2, 4: petN-psbM, 5: trnT -psbD (see Table 3 for details). One inverted repeat not shown.

Figure 4. Number of repeats found in Acer. plastomes using REPuter.

Only repeats ≥25 bp were considered. F, forward; P, palindrome; R, reverse. See Table 1 for full species names.

Figure 5. Number of simple sequence repeats (SSRs) found in Acer plastomes using MISA-web.

See Table 1 for full species names.

Figure 6. Number of simple sequence repeats (SSRs) found in Acer plastomes according to their location.

IR, inverted repeat; LSC, large single copy, SSC, short single copy. See Table 1 for full species names.

Figure 7. Maximum likelihood tree for Acer. plastomes inferred with RaxML-NG.

The topology is identical to the Bayesian 50% majority rule consensus tree. Numbers above and below branches are bootstrap values and posterior probabilities, respectively. Names on the right are Acer sections.