title: Complete Plastid Genome Sequencing of Four Tilia Species (Malvaceae): A Comparative Analysis and Phylogenetic Implications.
abstract: Tilia is an ecologically and economically important genus in the family Malvaceae. However, there is no complete plastid genome of Tilia sequenced to date, and the taxonomy of Tilia is difficult owing to frequent hybridization and polyploidization. A well-supported interspecific relationships of this genus is not available due to limited informative sites from the commonly used molecular markers. We report here the complete plastid genome sequences of four Tilia species determined by the Illumina technology. The Tilia plastid genome is 162,653 bp to 162,796 bp in length, encoding 113 unique genes and a total number of 130 genes. The gene order and organization of the Tilia plastid genome exhibits the general structure of angiosperms and is very similar to other published plastid genomes of Malvaceae. As other long-lived tree genera, the sequence divergence among the four Tilia plastid genomes is very low. And we analyzed the nucleotide substitution patterns and the evolution of insertions and deletions in the Tilia plastid genomes. Finally, we build a phylogeny of the four sampled Tilia species with high supports using plastid phylogenomics, suggesting that it is an efficient way to resolve the phylogenetic relationships of this genus.
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.|School of Life Science, Yunnan University, Kunming 650091, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Cai
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
authors.forename: Peng-Fei
authors.initials: PF
authors.lastname: Ma
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
authors.forename: Hong-Tao
authors.initials: HT
authors.lastname: Li
authors.affiliation: Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.
authors.forename: De-Zhu
authors.initials: DZ
authors.lastname: Li
mesh_terms: D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D017343:Genes, Plant; D018745:Genome, Plant; D054627:Genome, Plastid; D023281:Genomics; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D032384:Tilia / Q000235:genetics*
chemical_list: D018744:DNA, Plant