title: Comparative Analysis of the Chloroplast Genomic Information of Cunninghamia lanceolata (Lamb.) Hook with Sibling Species from the Genera Cryptomeria D. Don, Taiwania Hayata, and Calocedrus Kurz.
abstract: Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an important coniferous tree species for timber production, which accounts for ~40% of log supply from plantations in southern China. Chloroplast genetic engineering is an exciting field to engineer several valuable tree traits. In this study, we revisited the published complete Chinese fir (NC_021437) and four other coniferous species chloroplast genome sequence in Taxodiaceae. Comparison of their chloroplast genomes revealed three unique inversions found in the downstream of the gene clusters and evolutionary divergence were found, although overall the chloroplast genomic structure of the Cupressaceae linage was conserved. We also investigated the phylogenetic position of Chinese fir among conifers by examining gene functions, selection forces, substitution rates, and the full chloroplast genome sequence. Consistent with previous molecular systematics analysis, the results provided a well-supported phylogeny framework for the Cupressaceae that strongly confirms the "basal" position of Cunninghamia lanceolata. The structure of the Cunninghamia lanceolata chloroplast genome showed a partial lack of one IR copy, rearrangements clearly occurred and slight evolutionary divergence appeared among the cp genome of C. lanceolata, Taiwania cryptomerioides, Taiwania flousiana, Calocedrus formosana and Cryptomeria japonica. The information from sequence divergence and length variation of genes could be further considered for bioengineering research.
authors.affiliation: Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China. karrie.zheng@gmail.com.|College of Electronics and Information Science, Fujian Jiangxia University, Fuzhou 350108, China. karrie.zheng@gmail.com.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China. chenjh@njfu.edu.cn.
authors.forename: Jinhui
authors.initials: J
authors.lastname: Chen
authors.affiliation: Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China. haozd1992@163.com.
authors.forename: Zhaodong
authors.initials: Z
authors.lastname: Hao
authors.affiliation: Collaborative Innovation Center of Sustainable Forestry in Southern China; Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China. jshi@njfu.edu.cn.
authors.forename: Jisen
authors.initials: J
authors.lastname: Shi
mesh_terms: D002736:Chloroplasts / Q000235:genetics; D055028:Comparative Genomic Hybridization; D032485:Cryptomeria / Q000145:classification / Q000235:genetics*; D032486:Cunninghamia / Q000145:classification / Q000235:genetics*; D029779:Cupressaceae / Q000145:classification / Q000235:genetics*; D054628:Genome, Chloroplast / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity
keywords: Cunninghamia lanceolata (Lamb.) Hook; chloroplast; coniferous species; phylogeny