title: The Complete Chloroplast Genome Sequence of a Relict Conifer Glyptostrobus pensilis: Comparative Analysis and Insights into Dynamics of Chloroplast Genome Rearrangement in Cupressophytes and Pinaceae.
abstract: Glyptostrobus pensilis, belonging to the monotypic genus Glyptostrobus (Family: Cupressaceae), is an ancient conifer that is naturally distributed in low-lying wet areas. Here, we report the complete chloroplast (cp) genome sequence (132,239 bp) of G. pensilis. The G. pensilis cp genome is similar in gene content, organization and genome structure to the sequenced cp genomes from other cupressophytes, especially with respect to the loss of the inverted repeat region A (IRA). Through phylogenetic analysis, we demonstrated that the genus Glyptostrobus is closely related to the genus Cryptomeria, supporting previous findings based on physiological characteristics. Since IRs play an important role in stabilize cp genome and conifer cp genomes lost different IR regions after splitting in two clades (cupressophytes and Pinaceae), we performed cp genome rearrangement analysis and found more extensive cp genome rearrangements among the species of cupressophytes relative to Pinaceae. Additional repeat analysis indicated that cupressophytes cp genomes contained less potential functional repeats, especially in Cupressaceae, compared with Pinaceae. These results suggested that dynamics of cp genome rearrangement in conifers differed since the two clades, Pinaceae and cupressophytes, lost IR copies independently and developed different repeats to complement the residual IRs. In addition, we identified 170 perfect simple sequence repeats that will be useful in future research focusing on the evolution of genetic diversity and conservation of genetic variation for this endangered species in the wild.
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Zhaodong
authors: http://orcid.org/0000-0002-8466-0561
authors: Z
authors: Hao
authors: College of Biology and the Envirionment, Nanjing Forestry University, Nanjing, China.
authors: Tielong
authors: T
authors: Cheng
authors: Southern Mountain Timber Forest Cultivation Lab, Fujian Academy of Forestry, Ministry of Forestry, Fuzhou, China.
authors: Renhua
authors: R
authors: Zheng
authors: College of Biology and the Envirionment, Nanjing Forestry University, Nanjing, China.
authors: Haibin
authors: H
authors: Xu
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Yanwei
authors: Y
authors: Zhou
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Meiping
authors: M
authors: Li
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Fengjuan
authors: F
authors: Lu
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Yini
authors: Y
authors: Dong
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Xin
authors: X
authors: Liu
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Jinhui
authors: J
authors: Chen
authors: Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China.|Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China.
authors: Jisen
authors: J
authors: Shi
mesh_terms: D029779:Cupressaceae / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D061125:Genes, Chloroplast / Q000235:genetics*; D014644:Genetic Variation; D054628:Genome, Chloroplast / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics; D010802:Phylogeny; D028201:Pinaceae / Q000145:classification / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D064028:Tracheophyta / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant