Biodiversity Science ›› 2019, Vol. 27 ›› Issue (4): 366-372.doi: 10.17520/biods.2018332

• Original Papers • Previous Article     Next Article

Assembling and analysis of Sanicula orthacantha chloroplast genome

Chen Zhixiang1, Yao Xueying1, Stephen R. Downie2, Wang Qizhi1, *()   

  1. 1 Department of Horticulture, Huaqiao University, Xiamen, Fujian 361021, China
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • Received:2018-12-18 Accepted:2019-01-09 Online:2019-06-05
  • Wang Qizhi

Sanicula orthacantha is a perennial herb widely distributed in China and is a widely used for medicinal purposes. In this study, the whole chloroplast genome was sequenced and analyzed using bioinformatics methods. The results showed that it was a circular molecule 157,163 bp in length with a typical quadripartite structure including a pair of inverted repeats (IRa and IRb) of 26,247 bp that were separated by large and small single copy regions (LSC and SSC) of 87,547 bp and 17,122 bp, respectively. A total of 129 predicted genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes were identified. Compared with other Apiaeceae species, the S. orthacantha chloroplast genome had few differences in size, order and structure. The success of sequencing the S. orthacantha chloroplast genome provides a new method for the complete chloroplast genome assembly and characterization of Sanicula species, providing a methodological guide for the study of Sanicula plant evolution and phylogeny.

Key words: high-throughput sequencing, Sanicula L., gene assembly, phylogenetic analysis

Fig. 1

Sequence map of the Sanicula orthacantha chloroplast genome. Genes drawn outside of the circle are transcribed counter-clockwise, while genes shown on the inside of the circle are transcribed clockwise. Genes belonging to different functional groups are color-coded. The dark gray in the inner circle indicates GC content, while the light gray corresponds to AT content."

Table 1

List of genes found in Sanicula orthacantha chloroplast genome"

Category for genes
Group of genes
Name of genes
Self replication
核糖体RNA基因 Ribosomal RNAs rrn4.5(×2), rrn5(×2), rrn16(×2), rrn 23(×2)
转运RNA基因 Transfer RNAs trnA-UGC(×2), trnC-GCA, trnD-GUG, trnE-UCC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2), trnK- UUU, trnL-CAA(×2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU (×2) trnP-UGG, trnQ-UUC, trnR-ACG(×2) trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(×2), trnV-UAC, trnW-CCA, trnY-GUA
Ribosomal small subunit (SSU)
rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15
Ribosomal large subuni (LSU)
rpl33, rpl20, rpl36, rpl14, rpl16, rpl22, rpl2(×2), rpl23(×2), rpl32
RNA聚合酶亚基基因 RNA polymerase rpoA, rpoB, rpoC1, rpoC2
Genes for
光合系统I基因 Photosystem I psaA, psaB, psaC, psaI, psaJ
光合系统II基因 Photosystem II psbA, psbB, psbK, psbI, psbM, psbD, psbC, psbE, psbJ, psbL, psbT, psbH, psbN, psbF, psbZ, psbJ
细胞色素复合物基因 Cytochrome b/f complex petA, petD, petG, petL, petN
ATP合酶基因 ATP synthase atpA, atpF, atpH, atpI, atpE, atpB
ATP-dependent protease subunit p gene
RubiscoCO large subunit
NADH脱氢酶基因 NADH dehydrogenase ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH
Other genes
成熟酶基因 Maturase matK
包裹膜蛋白基因 Envelop membrane protein cemA
Subunit of acetyl-CoA-carboxylase
c-type cytochrome synthesis ccsA gene
Transcription initiation factor IF-1
Genes of unknown
Conserved open reading frames
ycf1, ycf2(×2), ycf3, ycf4

Fig. 2

Phylogenetic tree of 15 species based on chloroplast genome using Maximum Likelihood method"

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