Characterization of the complete chloroplast genome of Carpinus tientaiensis

被引:7
作者
Yang, Yongzhi [1 ]
Wang, Mingcheng [1 ]
Lu, Zhiqiang [1 ]
Xie, Xiuyue [1 ]
Feng, Shuo [1 ]
机构
[1] Lanzhou Univ, Coll Life Sci, State Key Lab Grassland Agroecosyst, Lanzhou, Peoples R China
基金
国家高技术研究发展计划(863计划);
关键词
Carpinus tientaiensis; Chloroplast genome; Phylogenetic analysis;
D O I
10.1007/s12686-016-0668-y
中图分类号
X176 [生物多样性保护];
学科分类号
090705 ;
摘要
The complete chloroplast (cp) genome sequence of a rare xylophyta species, Carpinus tientaiensis, was determined by Illumina pair-end sequencing in this study. The whole cp genome was 160,104 bp in length, containing a large single copy region (LSC) of 91,509 bp and small single copy region (SSC) of 18,974 bp, which were separated by a pair of 26,033 bp and 26,143 bp inverted repeat regions (IRs). The genome contained 114 genes, including 71 protein-coding genes, 36 tRNA genes and 6 ribosomal RNA genes. The majority of these gene species occurred as a single copy and 15 gene species occurred in two copies. The overall AT content of C. tientaiensis chloroplast genome was 63.6%, while the corresponding values of the LSC, SSC and IR regions were 60.7%, 69.8% and 57.5%, respectively. A phylogenetic analysis demonstrated a close relationship between C. tientaiensis and Ostrya rehderiana.
引用
收藏
页码:339 / 341
页数:3
相关论文
共 10 条
[1]  
Doyle JJ., 1987, PHYTOCHEMISTRY B, V19, P11
[2]   PLANN: A COMMAND-LINE APPLICATION FOR ANNOTATING PLASTOME SEQUENCES [J].
Huang, Daisie I. ;
Cronk, Quentin C. B. .
APPLICATIONS IN PLANT SCIENCES, 2015, 3 (08)
[3]   MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability [J].
Katoh, Kazutaka ;
Standley, Daron M. .
MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30 (04) :772-780
[4]   Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data [J].
Kearse, Matthew ;
Moir, Richard ;
Wilson, Amy ;
Stones-Havas, Steven ;
Cheung, Matthew ;
Sturrock, Shane ;
Buxton, Simon ;
Cooper, Alex ;
Markowitz, Sidney ;
Duran, Chris ;
Thierer, Tobias ;
Ashton, Bruce ;
Meintjes, Peter ;
Drummond, Alexei .
BIOINFORMATICS, 2012, 28 (12) :1647-1649
[5]  
Li PC., 1979, Flora Republicae Popularis Sinicae, V21, P44, DOI DOI 10.1371/journal.pone.0159430
[6]   OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets [J].
Lohse, Marc ;
Drechsel, Oliver ;
Kahlau, Sabine ;
Bock, Ralph .
NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W575-W581
[7]  
Peng S, 2015, MITOCHONDR DNA, P1
[8]  
Shaw K., 2014, RED LIST BETULACEAE
[9]   RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies [J].
Stamatakis, Alexandros .
BIOINFORMATICS, 2014, 30 (09) :1312-1313
[10]   Velvet: Algorithms for de novo short read assembly using de Bruijn graphs [J].
Zerbino, Daniel R. ;
Birney, Ewan .
GENOME RESEARCH, 2008, 18 (05) :821-829