title: Revisiting the Plastid Phylogenomics of Pinaceae with Two Complete Plastomes of Pseudolarix and Tsuga.
abstract: Phylogeny of the ten Pinaceous genera has long been contentious. Plastid genomes (plastomes) provide an opportunity to resolve this problem because they contain rich evolutionary information. To comprehend the plastid phylogenomics of all ten Pinaceous genera, we sequenced the plastomes of two previously unavailable genera, Pseudolarix amabilis (122,234 bp) and Tsuga chinensis (120,859 bp). Both plastomes share similar gene repertoire and order. Here for the first time we report a unique insertion of tandem repeats in accD of T. chinensis From the 65 plastid protein-coding genes common to all Pinaceous genera, we re-examined the phylogenetic relationship among all Pinaceous genera. Our two phylogenetic trees are congruent in an identical tree topology, with the five genera of the Abietoideae subfamily constituting a monophyletic clade separate from the other three subfamilies: Pinoideae, Piceoideae, and Laricoideae. The five genera of Abietoideae were grouped into two sister clades consisting of (1) Cedrus alone and (2) two sister subclades of Pseudolarix-Tsuga and Abies-Keteleeria, with the former uniquely losing the gene psaM and the latter specifically excluding the 3 psbA from the residual inverted repeat.
authors.affiliation: Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Nankang District, Taipei 11529, Taiwan Department of Life Science, National Taiwan Normal University, Wenshan District, Taipei 11677, Taiwan Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan.
authors.forename: Edi
authors.initials: E
authors.lastname: Sudianto
authors.affiliation: Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan.
authors.forename: Chung-Shien
authors.initials: CS
authors.lastname: Wu
authors.affiliation: Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan Present Address: Institute of Plant and Microbial Biology, Academia Sinica, Nankang District, Taipei 11529, Taiwan.
authors.forename: Ching-Ping
authors.initials: CP
authors.lastname: Lin
authors.affiliation: Biodiversity Program, Taiwan International Graduate Program, Biodiversity Research Center, Academia Sinica and National Taiwan Normal University, Nankang District, Taipei 11529, Taiwan Biodiversity Research Center, Academia Sinica, Nankang District, Taipei 11529, Taiwan smchaw@sinica.edu.tw.
authors.forename: Shu-Miaw
authors.initials: SM
authors.lastname: Chaw
mesh_terms: D054627:Genome, Plastid / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D055029:Inverted Repeat Sequences / Q000235:genetics; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D028201:Pinaceae / Q000235:genetics*; D018087:Plastids / Q000235:genetics; D028225:Tsuga / Q000254:growth & development*
keywords: Pinaceae; Pseudolarix; Tsuga; accD; plastid DNA; plastid phylogenomics