Complete plastomes of 17 species of maples (Sapindaceae: Acer): comparative analyses and phylogenomic implications

The genus Acer, commonly known as maple, is a large plant lineage that comprises many economically and ecologically important species. However, because of low interspecific morphological variations and scarcity of molecular data, it is challenging to estimate the enigmatic phylogeny of Acer, limiting further utilization and conservation of maples. In this study, we generated complete plastomes of 17 species of maples representing 10 major sections of Acer and conducted comprehensively comparative genomic and phylogenomic analyses in Acer. The 17 plastomes are perfectly conserved in linear gene order and range narrowly in length of 155–157 kb with four constituent parts (LSC, SSC, IRa and IRb), whereas three IR types (amplum-, flabellatum- and yangbiense-like) are observed and the IR borders variation resulted in remarkable gene content divergence (132–134). In addition, there are apparently heterogeneous sequence divergences across the cp genome and 20 noncoding loci with fast evolutionary rates are further identified as potential molecular markers for subsequent studies on Acer. Furthermore, whole plastome sequences obtained the highest phylogenetic resolution and provided strong support for most backbone nodes of Acer among the seven analyzed data sets (LSC, SSC, IRs, coding, noncoding, 20-markers and whole-cp-genome), highlighting the significance of increasing informative sites in resolving intractable phylogenetic relationships of Acer. The section Negundo diverged firstly in Acer and close relationships among sects. Arguta, Ginnala, Macrantha, Oblonga, Pentaphylla, Platanoidea and Trifoliata were uncovered. Interspecific relationships within species-rich sects. Macrantha, Palmata and Platanoidea are also clearly resolved by plastid phylogenomics.