Plastid Phylogenomics Of Tilia L. (Malvaceae)

Tilia L. (basswood or lime-tree) is a genus of the family Malvaceae, which contains 23 species and 14 subspecies tree disjunctly distributed in the temperate area across Asia, Europe and North America. Most species are the dominant elements in the temperate forests, and many of which are ecologically and economically important. Tilia is a distinct genus characterized by paddle-shaped bracts of inflorenscences. However, the taxonomy of Tilia is difficult and controversial due to limited taxonomic characters, frequently occurred hybridization and polyploid species. Recent molecular phylogenetic studies based on molecular markers could not resolve interspecific relationships of Tilia, and species relationships within the genus are poorly known. Understanding the phylogenetic relationship between species is critical for elucidating the evolutionary history and current geological distribution patters of Tilia, as well for the evolutionary biology, conservation and genetic resources management of Tilia. In this study,50 completed plastid genomes representing the total 23 species of Tilia, according to the latest revision of this genus, were successfully sequenced by Illumina technology. The phylogeny of Tilia was reconstructed through phylogenetic analyses and species relationships among this genus also been inferred and discussed. Main conclusions are summarized as below:1. Comparative chloroplast genomics of Tilia and other Malvaceae taxaTilia plastid genome exhibits the general structure of published angiosperm plastid genomes, which is 162,250 bp to 163,001 bp in length. The genome size, GC content and the genome structure of Tilia is very similar to those of Gossypium and Theobroma. Four Tilia species all encode an identical set of 113 unique genes including 79 protein-coding genes,30 tRNA genes and 4 rRNA genes. They all share the same gene order and organization of plastid genome in angiosperm. In terms of genome size, the plastid genome of Tilia is slightly larger than those of Gossypium and Theobroma, which is mainly caused by the large (more than 100 bp) insertions in LSC region. Comparison of sequences divergence in four selected species(Tilia amurensis, T. mandshurica, T. oliveri and T. paucicostata) reveals extremely low divergence, and there were no mutational hotspots identified. Although there were limited informative sites found from the plastid genome, the resolution of phylogeny for the four Tilia species suggested that plastid phylogenomics was an efficient way to resolve the phylogenetic relationships of this genus.2. Plastid phylogenomics of TiliaPhylogeny of Tilia was reconstructed based on the plastid genome of 23 species and 2 outgroups. Phylogenetic trees based on datasets of LSC, SSC, IRs, coding region and noncoding region indicated similar topological structure of that based on analysis of whole genome through maximum likelihood (ML) and Bayesian Inference (BI) analysis, respectively. As expected, the analysis of whole genomes provided a better resolved phylogenetic tree. There are three main clades identified from the phylogenetic tree of Tilia with very high bootstrap support (BS) values and posterior probability (PP) values. Clade Ⅰ includes six individuals of four species exhibiting incongruence between molecular data and morphology or geological distribution, which could be the result of incomplete lineage sorting or hybridization amony taxa. In Clade Ⅱ, T. endochrysea from central China is sister to the subclade consisted of T. kiusiana from Japan and all the North American samples which clustered together. Clade Ⅱ demonstrate the ancestors of North American basswood had very close link with those of flourishing in East Asia, however, it need more evidences to explain the East Asia-North America disjunctly distribution of Tilia. Clade Ⅲ contains 10 subclades which were strongly supported as monophyletic, but the relationships among the Easten Asian species were poorly resolved. Incongruence between molecular evidence and morphological data were observed in Clades Ⅰ and most subclades of Clade Ⅲ from the reconstructed phylogenetic tree of Tilia based on plastid genomes, which could be very likely resulted from plastid capture and/or gene introgression through hybridization, as well as rapid radiation and incomplete lineage sorting. The plastid genome size of Tilia is ca.162 kb, but only few parsimony informative sites were identified due to the slow molecular evolution rate, which contribute to the difficulty in building the phylogenetic relationship of this genus.Although hybridization, polyploidization and rapid radiation posed challenges in resolving the phylogeny of Tilia, a phylogentic frame of this genus was established for further study. Nuclear data are necessary to comprehensively clarify the evolutionary history of Tilia in the future.