publication . Article . Other literature type . 2020

Phylogenetic relationships of Atractylodes lancea, A. chinensis and A. macrocephala, revealed by complete plastome and nuclear gene sequences.

Linfang Huang; Hui Zhang; Xi Wu; Chang Liu; Haimei Chen; Weiwei Fang; Ziyue Wang; Mei Jiang; Liqiang Wang;
Open Access English
  • Published: 28 Jan 2020 Journal: PLoS ONE, volume 15, issue 1 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Atractylodes lancea, A. chinensis, and A. macrocephala are the three most widely used medicinal species of the Atractylodes genus. Their similar morphological features cause disagreement as whether they are three unique species, leading to their frequent misuses in medical products. Our study aimed to understand their relationships through both the complete plastome sequences and nuclear sequences, to identify molecular markers for their differentiation and explore the evolutionary relationships among three species. We sequenced, annotated, and analyzed the plastomes of these three species. The plastomes are 153,201, 153,258, and 153,265 bps in length for A. lan...
Subjects
free text keywords: Research Article, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Sequence Alignment, Biology and Life Sciences, Evolutionary Biology, Evolutionary Systematics, Phylogenetics, Phylogenetic Analysis, Taxonomy, Computer and Information Sciences, Data Management, Molecular Biology, Molecular Biology Techniques, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Computational Techniques, Split-Decomposition Method, Multiple Alignment Calculation, Sequencing techniques, DNA sequencing, Dideoxy DNA sequencing, DNA sequence analysis, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Medicine, R, Science, Q, Atractylodes, biology.organism_classification, biology, Nuclear gene, Chloroplast DNA, Atractylodes lancea, Nucleotide diversity, Phylogenetic tree
45 references, page 1 of 3

1 Mizukami H, Shimizu R, Kohjyouma M, Kohda H, Kawanishi F, Hiraoka N. Phylogenetic analysis of Atractylodes plants based on chloroplast trn K sequence. Biol Pharm Bull. 1998;21(5):474–478. 10.1248/bpb.21.474 9635503 [OpenAIRE] [PubMed] [DOI]

2 Kim JH, Doh EJ, Lee G. Evaluation of medicinal categorization of Atractylodes japonica Koidz. by using internal transcribed spacer sequencing analysis and HPLC fingerprinting combined with statistical tools. Evid Based Complement Alternat Med. 2016;2016:2926819. 10.1155/2016/2926819 27190530 [OpenAIRE] [PubMed] [DOI]

3 Shiba M, Kondo K, Miki E, Yamaji H, Morota T, Terabayashi S, et al Identification of medicinal Atractylodes based on ITS sequences of nrDNA. Biol Pharm Bull. 2006;29(2):315–320. 10.1248/bpb.29.315 16462038 [OpenAIRE] [PubMed] [DOI]

4 Yuan JH, Sun S, Peng F, Feng X, Zheng YH, Xia B. Genetic variations in trn L-F sequence and phylogenetic clustering of Lycoris species. China J Chin Mater Med. 2008;33(13):1523–1527.

5 Shimato Y, Ota M, Asai K, Atsumi T, Tabuchi Y, Makino T. Comparison of byakujutsu (Atractylodes rhizome) and sojutsu (Atractylodes lancea rhizome) on anti-inflammatory and immunostimulative effects in vitro. J Nat Med. 2018;72(1):192–201. 10.1007/s11418-017-1131-4 28983786 [OpenAIRE] [PubMed] [DOI]

6 Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008;27(4):617–631. 10.1007/s00299-008-0507-z 18246355 [OpenAIRE] [PubMed] [DOI]

7 Kress WJ. Plant DNA barcodes: Applications today and in the future. J Syst Evol. 2017;55(4):291–307. 10.1111/jse.12254 [OpenAIRE] [DOI]

8 Ma XQ, Duan JA, Zhu DY, Dong TT, Tsim KW. Species identification of Radix astragali (Huangqi) by DNA sequence of its 5S-rRNA spacer domain. Phytochemistry. 2000;54(4):363–368. 10.1016/s0031-9422(00)00111-4 10897476 [OpenAIRE] [PubMed] [DOI]

9 Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016;17(1):134 10.1186/s13059-016-1004-2 27339192 [OpenAIRE] [PubMed] [DOI]

10 He L, Qian J, Li X, Sun Z, Xu X, Chen S. Complete chloroplast genome of medicinal plant Lonicera japonica: genome rearrangement, intron gain and loss, and implications for phylogenetic studies. Molecules. 2017;22(2):pii: E249. 10.3390/molecules22020249 28178222 [OpenAIRE] [PubMed] [DOI]

11 Park I, Yang S, Choi G, Kim WJ, Moon BC. The complete chloroplast genome sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and development of molecular markers for distinguishing species in the Aconitum Subgenus Lycoctonum. Molecules. 2017;22(11):pii: E2012. 10.3390/molecules22112012 29160852 [OpenAIRE] [PubMed] [DOI]

12 Dong W, Xu C, Li W, Xie X, Lu Y, Liu Y, et al Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Front Plant Sci. 2017;8:1148 10.3389/fpls.2017.01148 28713409 [OpenAIRE] [PubMed] [DOI]

13 Huang Y, Li X, Yang Z, Yang C, Yang J, Ji Y. Analysis of complete chloroplast genome sequences improves phylogenetic resolution in Paris (Melanthiaceae). Front Plant Sci. 2016;7:1797 10.3389/fpls.2016.01797 27965698 [OpenAIRE] [PubMed] [DOI]

14 Mariotti R, Cultrera NG, Diez CM, Baldoni L, Rubini A. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biol. 2010;10:211 10.1186/1471-2229-10-211 20868482 [OpenAIRE] [PubMed] [DOI]

15 Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome. 2011;54(8):663–673. 10.1139/G11-026 21793699 [PubMed] [DOI]

45 references, page 1 of 3
Abstract
Atractylodes lancea, A. chinensis, and A. macrocephala are the three most widely used medicinal species of the Atractylodes genus. Their similar morphological features cause disagreement as whether they are three unique species, leading to their frequent misuses in medical products. Our study aimed to understand their relationships through both the complete plastome sequences and nuclear sequences, to identify molecular markers for their differentiation and explore the evolutionary relationships among three species. We sequenced, annotated, and analyzed the plastomes of these three species. The plastomes are 153,201, 153,258, and 153,265 bps in length for A. lan...
Subjects
free text keywords: Research Article, Research and Analysis Methods, Database and Informatics Methods, Bioinformatics, Sequence Analysis, Sequence Alignment, Biology and Life Sciences, Evolutionary Biology, Evolutionary Systematics, Phylogenetics, Phylogenetic Analysis, Taxonomy, Computer and Information Sciences, Data Management, Molecular Biology, Molecular Biology Techniques, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Computational Techniques, Split-Decomposition Method, Multiple Alignment Calculation, Sequencing techniques, DNA sequencing, Dideoxy DNA sequencing, DNA sequence analysis, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Medicine, R, Science, Q, Atractylodes, biology.organism_classification, biology, Nuclear gene, Chloroplast DNA, Atractylodes lancea, Nucleotide diversity, Phylogenetic tree
45 references, page 1 of 3

1 Mizukami H, Shimizu R, Kohjyouma M, Kohda H, Kawanishi F, Hiraoka N. Phylogenetic analysis of Atractylodes plants based on chloroplast trn K sequence. Biol Pharm Bull. 1998;21(5):474–478. 10.1248/bpb.21.474 9635503 [OpenAIRE] [PubMed] [DOI]

2 Kim JH, Doh EJ, Lee G. Evaluation of medicinal categorization of Atractylodes japonica Koidz. by using internal transcribed spacer sequencing analysis and HPLC fingerprinting combined with statistical tools. Evid Based Complement Alternat Med. 2016;2016:2926819. 10.1155/2016/2926819 27190530 [OpenAIRE] [PubMed] [DOI]

3 Shiba M, Kondo K, Miki E, Yamaji H, Morota T, Terabayashi S, et al Identification of medicinal Atractylodes based on ITS sequences of nrDNA. Biol Pharm Bull. 2006;29(2):315–320. 10.1248/bpb.29.315 16462038 [OpenAIRE] [PubMed] [DOI]

4 Yuan JH, Sun S, Peng F, Feng X, Zheng YH, Xia B. Genetic variations in trn L-F sequence and phylogenetic clustering of Lycoris species. China J Chin Mater Med. 2008;33(13):1523–1527.

5 Shimato Y, Ota M, Asai K, Atsumi T, Tabuchi Y, Makino T. Comparison of byakujutsu (Atractylodes rhizome) and sojutsu (Atractylodes lancea rhizome) on anti-inflammatory and immunostimulative effects in vitro. J Nat Med. 2018;72(1):192–201. 10.1007/s11418-017-1131-4 28983786 [OpenAIRE] [PubMed] [DOI]

6 Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008;27(4):617–631. 10.1007/s00299-008-0507-z 18246355 [OpenAIRE] [PubMed] [DOI]

7 Kress WJ. Plant DNA barcodes: Applications today and in the future. J Syst Evol. 2017;55(4):291–307. 10.1111/jse.12254 [OpenAIRE] [DOI]

8 Ma XQ, Duan JA, Zhu DY, Dong TT, Tsim KW. Species identification of Radix astragali (Huangqi) by DNA sequence of its 5S-rRNA spacer domain. Phytochemistry. 2000;54(4):363–368. 10.1016/s0031-9422(00)00111-4 10897476 [OpenAIRE] [PubMed] [DOI]

9 Daniell H, Lin CS, Yu M, Chang WJ. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016;17(1):134 10.1186/s13059-016-1004-2 27339192 [OpenAIRE] [PubMed] [DOI]

10 He L, Qian J, Li X, Sun Z, Xu X, Chen S. Complete chloroplast genome of medicinal plant Lonicera japonica: genome rearrangement, intron gain and loss, and implications for phylogenetic studies. Molecules. 2017;22(2):pii: E249. 10.3390/molecules22020249 28178222 [OpenAIRE] [PubMed] [DOI]

11 Park I, Yang S, Choi G, Kim WJ, Moon BC. The complete chloroplast genome sequences of Aconitum pseudolaeve and Aconitum longecassidatum, and development of molecular markers for distinguishing species in the Aconitum Subgenus Lycoctonum. Molecules. 2017;22(11):pii: E2012. 10.3390/molecules22112012 29160852 [OpenAIRE] [PubMed] [DOI]

12 Dong W, Xu C, Li W, Xie X, Lu Y, Liu Y, et al Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Front Plant Sci. 2017;8:1148 10.3389/fpls.2017.01148 28713409 [OpenAIRE] [PubMed] [DOI]

13 Huang Y, Li X, Yang Z, Yang C, Yang J, Ji Y. Analysis of complete chloroplast genome sequences improves phylogenetic resolution in Paris (Melanthiaceae). Front Plant Sci. 2016;7:1797 10.3389/fpls.2016.01797 27965698 [OpenAIRE] [PubMed] [DOI]

14 Mariotti R, Cultrera NG, Diez CM, Baldoni L, Rubini A. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison. BMC Plant Biol. 2010;10:211 10.1186/1471-2229-10-211 20868482 [OpenAIRE] [PubMed] [DOI]

15 Kuang DY, Wu H, Wang YL, Gao LM, Zhang SZ, Lu L. Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics. Genome. 2011;54(8):663–673. 10.1139/G11-026 21793699 [PubMed] [DOI]

45 references, page 1 of 3
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