Keywords
Chloroplast genome
Phylogeny
Submitted : 2024-05-19
Accepted : 2024-06-03
Published : 2024-06-18
Abstract
Globally, the genus Dendrobium (Family: Orchidaceae) exhibits widespread distribution, predominantly occupying the tropical and subtropical areas of Asia. Although the chloroplast genomes (cpDNAs) of certain Dendrobium species have been documented, the evolutionary relationships among these species remain largely unexplored. In this pioneering investigation, a comprehensive analysis of the complete cpDNAs from Dendrobium species is presented, including Dendrobium flexicaule along with three closely related taxa (D. nobile, D. officinale, and D. huoshanense). The size of the novel complete cpDNAs ranged from 150,529 to 152,588 bp, and their cpDNA structure exhibits a unique quadrifoliate structure reminiscent of female quadrivalents, including large single copy, small single copy (SSC), and inverted repeat regions. A total of 175 simple sequence repeats were identified in the D. flexicaule cpDNA. A few pseudogenes of the NA(D)H dehydrogenase-like (NDH) genes were found in the annotated cpDNAs of the four Dendrobium species. Within the shared pseudogenes ndhF and ndhG, ndhF frequently undergoes mutations. Additionally, the phylogenetic analysis showed that D. flexicaule and D. scoriarum were close sister species. The research findings provide crucial genetic information for the molecular phylogenetic system of D. flexicaule.
References
Yu X, Zuo L, Lu D, et al., 2019, Comparative Analysis of Chloroplast Genomes of Five Robinia Species: Genome Comparative and Evolution Analysis. Gene, 2019(689): 141–151. https://doi.org/10.1016/j.gene.2018.12.023
Konhar R, Debnath M, Vishwakarma S, et al., 2019, The Complete Chloroplast Genome of Dendrobium nobile, an Endangered Medicinal Orchid from North-east India and its Comparison with Related Dendrobium Species. PeerJ, 2019(7): e7756. https://doi.org/10.7717/peerj.7756
Liang H, Zhang Y, Deng J, et al., 2020, The Complete Chloroplast Genome Sequences of 14 Curcuma Species: Insights into Genome Evolution and Phylogenetic Relationships Within Zingiberales. Frontiers in Genetics, 2020(11): 802. https://doi.org/10.3389/fgene.2020.00802
Tian X, Li D, 2002, Application of DNA Sequences in Plant Phylogenetic Study. Acta Botanica Yunnanica, 24(2): 170–184.
Palmer JD, 1985, Comparative Organization of Chloroplast Genomes. Annual Review of Genetics, 19(1): 325–354. https://doi.org/10.1146/annurev.ge.19.120185.001545
Raubeson LA, Jansen RK, 2005, Chloroplast Genomes of Plants, in Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants. CABI Publishing, Wallingford, 45¬–68. http://doi/10.1079/9780851999043.0045
Bendich AJ, 2004, Circular Chloroplast Chromosomes: the Grand Illusion. Plant Cell, 16(7): 1661–1666. https://doi.org/10.1105/tpc.160771
Frailey DC, Chaluvadi SR, Vaughn JN, et al., 2018, Gene Loss and Genome Rearrangement in the Plastids of Five Hemiparasites in the Family Orobanchaceae. BMC Plant Biology, 18(1): 30. https://doi.org/10.1186/s12870-018-1249-x
Böhle UR, Hilger H, Cerff R, et al., 1994, Non-coding Chloroplast DNA for Plant Molecular Systematics at the Infrageneric Level, in Molecular Ecology and Evolution: Approaches and Applications. Birkhäuser, Basel, 391¬–403.
Small RL, Lickey EB, Shaw J, et al., 2005, Amplification of Noncoding Chloroplast DNA for Phylogenetic Studies in Lycophytes and Monilophytes with a Comparative Example of Relative Phylogenetic Utility from Ophioglossaceae. Molecular Phylogenetics and Evolution, 36(3): 509–522. https://doi.org/10.1016/j.ympev.2005.04.018
Blazier JC, Ruhlman TA, Weng ML, et al., 2016, Divergence of RNA Polymerase ? Subunits in Angiosperm Plastid Genomes is Mediated by Genomic Rearrangement. Scientific Reports, 6(1): 24595. https://doi.org/10.1038/srep24595
Chumley TW, Palmer JD, Mower JP, et al., 2006, The Complete Chloroplast Genome Sequence of Pelargonium hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants. Molecular Biology and Evolution, 23(11): 2175–2190. https://doi.org/10.1093/molbev/msl089
Gao L, Su YJ, Wang T, 2010, Plastid Genome Sequencing, Comparative Genomics, and Phylogenomics: Current Status and Prospects. Journal of Systematics and Evolution, 48(2): 77–93. https://doi.org/10.1111/j.1759-6831.2010.00071.x
Guisinger MM, Kuehl JV, Boore JL, et al., 2011, Extreme Reconfiguration of Plastid Genomes in the Angiosperm Family Geraniaceae: Rearrangements, Repeats, and Codon Usage. Molecular Biology and Evolution, 28(1): 583–600. https://doi.org/10.1093/molbev/msq229
Liu J, Hu Z, Cheng Z, et al., 2021, Study on Seed Germination of Endangered Plant Dendrobium flexicaule. Seed, 2021(40): 48–51 + 56.
Lu W, 2021, The New List of Wild Plants under Key State Protection was Officially Released. Land Green, 48–49.
Ding X, Xu L, Xu H, et al., 2001, Morphological and DNA Molecular Evidence for Authentication of Dendrobium flexicaule from its Allied Species of Dendrobium. Acta Pharmaceutica Sinica, 2001(36): 868–873.
Zhang S, 2016, Effect of Environmental Conditions on Growth and Propagation of Dendrobium flexicaule in Funiu Mountain Area. Xiandai Horticulture, 2016(21): 13–14. https://doi.org/10.14051/j.cnki.xdyy.2016.21.110
Hu ZF, 2021, Optimization of Rapid Propagation System of Dendrobium flexicaule, thesis, China Three Gorges University.
Sun T, Yang Y, Hu S, et al., 2022, Identification and Quality Evaluation of Dendrobium flexicaule and its Related Species. Chinese Journal of Experimental Traditional Medical Formulae, 2022(28): 128¬–134.
Wu T, Deng G, Yin Q, et al., 2023, Characterization and Molecular Evolution Analysis of Periploca forrestii Inferred from its Complete Chloroplast Genome Sequence. Genome, 66(2): 34–50. https://doi.org/10.1139/gen-2022-0050
Qu XJ, Moore MJ, Li DZ, et al., 2019, PGA: a Software Package for Rapid, Accurate, and Flexible Batch Annotation of Plastomes. Plant Methods, 15(1): 50. https://doi.org/10.1186/s13007-019-0435-7
Greiner S, Lehwark P, Bock R, 2019, OrganellarGenomeDRAW (OGDRAW) version 1.3.1: Expanded Toolkit for the Graphical Visualization of Organellar Genomes. Nucleic Acids Research, 47(W1): 59–64. https://doi.org/10.1093/nar/gkz238
Sharp PM, Li WH, 1986, Codon Usage in Regulatory Genes in Escherichia coli does not Reflect Selection for “Rare” Codons. Nucleic Acids Research, 14(19): 7737–7749. https://doi.org/10.1093/nar/14.19.7737
Sharp PM, Li WH, 1986, An Evolutionary Perspective on Synonymous Codon Usage in Unicellular Organisms. Journal of Molecular Evolution, 24(1–2): 28–38. https://doi.org/10.1007/BF02099948
Wright F, 1990, The Effective Number of Codons Used in a Gene. Gene, 87(1): 23–29. https://doi.org/10.1016/0378-1119(90)90491-9
Li H, Guo Q, Xu L, et al., 2023, CPJSdraw: Analysis and Visualization of Junction Sites of Chloroplast Genomes. PeerJ, 2023(11): e15326. https://doi.org/10.7717/peerj.15326
Kearse M, Moir R, Wilson A, et al., 2012, Geneious Basic: An Integrated and Extendable Desktop Software Platform for the Organization and Analysis of Sequence Data. Bioinformatics, 28(12): 1647–1649. https://doi.org/10.1093/bioinformatics/bts199
Li X, Yang JB, Wang H, et al., 2021, Plastid NDH Pseudogenization and Gene Loss in a Recently Derived Lineage from the Largest Hemiparasitic Plant Genus Pedicularis (Orobanchaceae). Plant and Cell Physiology, 62(6): 971–984. https://doi.org/10.1093/pcp/pcab074
Du Z, Yang L, Zhang Z, et al., 2021, Characteristics of the Complete Chloroplast Genome of Dendrobium ochreatum and its Comparative Analysis. Chinese Journal of Tropical Crops, 2021(42): 3111–3119. https://10.0.15.129/j.issn.1000-2561.2021.11.009
Beier S, Thiel T, Münch T, et al., 2017, MISA-web: a Web Server for Microsatellite Prediction. Bioinformatics, 33(16): 2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Benson G, 1999, Tandem Repeats Finder: a Program to Analyze DNA Sequences. Nucleic Acids Research, 27(2): 573–580. https://doi.org/10.1093/nar/27.2.573
Kurtz S, 2001, REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale. Nucleic Acids Research, 29(22): 4633–4642. https://doi.org/10.1093/nar/29.22.4633
Moberly JG, Bernards MT, Waynant KV, 2018, Key Features and Updates for Origin 2018. Journal of Cheminformatics, 10(1): 5. https://doi.org/10.1186/s13321-018-0259-x
Rozas J, Ferrer-mata A, Sánchez-delbarrio JC, et al., 2017, DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution, 34(12): 3299–3302. https://doi.org/10.1093/molbev/msx248
Zhang Z, Li J, Zhao XQ, et al., 2006, KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. Genomics, Proteomics & Bioinformatics, 4(4): 259–263. https://doi.org/10.1016/S1672-0229(07)60007-2
Kumar S, Stecher G, Li M, et al., 2018, MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6): 1547–1549. https://doi.org/10.1093/molbev/msy096
Nakamura T, Yamada KD, Tomii K, et al., 2018, Parallelization of MAFFT for Large-scale Multiple Sequence Alignments. Bioinformatics, 34(14): 2490–2492. https://doi.org/10.1093/bioinformatics/bty121
Letunic I, Bork P, 2019, Interactive Tree of Life (iTOL) v4: Recent Updates and New Developments. Nucleic Acids Research, 47(W1): 256–259. https://doi.org/10.1093/nar/gkz239
Verma D, Daniell H, 2007, Chloroplast Vector Systems for Biotechnology Applications. Plant Physiology, 145(4): 1129–1143. https://doi.org/10.1104/pp.107.106690
Shi N, Yang Z, Miao K, et al., 2023, Comparative Analysis of the Medicinal Plant Polygonatum kingianum (Asparagaceae) with Related Verticillate Leaf Types of the Polygonatum Species based on Chloroplast Genomes. Frontiers in Plant Science, 2023(14): 1202634. https://doi.org/10.3389/fpls.2023.1202634
Shahzadi I, Abdulla H, Mehmood F, et al., 2020, Chloroplast Genome Sequences of Artemisia maritima and Artemisia absinthium: Comparative Analyses, Mutational Hotspots in Genus Artemisia and Phylogeny in Family Asteraceae. Genomics, 112(2): 1454–1463. https://doi.org/10.1016/j.ygeno.2019.08.016
Feng R, Mei C, Wang H, et al., 2019, Analysis of Codon Usage in the Chloroplast Genome of Grain Amaranth (Amaranthus hypochondriacus L.). Chinese Journal of Grassland, 2019(41): 8–15. https//doi.org/10.16742/j.zgcdxb.20180227
Liu H, Wang M, Yue W, et al., 2017, Analysis of Codon Usage in the Chloroplast Genome of Broomcorn millet (Panicum miliaceum L.). Plant Science Journal, 35(3): 362–371. https://doi.org/10.11913/PSJ.2095-0837.2017.30362
Botzman M, Margalit H, 2011, Variation in Global Codon Usage Bias among Prokaryotic Organisms is Associated with their Lifestyles. Genome Biology, 12(10): R109. https://doi.org/10.1186/gb-2011-12-10-r109
Nie X, Deng P, Feng K, et al., 2014, Comparative Analysis of Codon Usage Patterns in Chloroplast Genomes of the Asteraceae Family. Plant Molecular Biology Reporter, 32(4): 828–840. https://doi.org/10.1007/s11105-013-0691-z
Sharp PM, Matassi G, 1994, Codon Usage and Genome Evolution. Current Opinion in Genetics & Development, 4(6): 851–860. https://doi.org/10.1016/0959-437X(94)90070-1
Ma M, Zhang W, Meng H, et al., 2021, Codon Bias Analysis of Chloroplast Genome in Medicinal Plants of Amomum Roxb. Chinese Traditional and Herbal Drugs, 52(12): 3661–3670. https://doi.org/10.7501/j.issn.0253-2670.2021.12.024
Angellotti MC, Bhuiyan SB, Chen G, et al., 2007, CodonO: Codon Usage Bias Analysis within and Across Genomes. Nucleic Acids Research, 35(2): 132–136. https://doi.org/10.1093/nar/gkm392
Mehrotra S, Goyal V, 2014, Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function. Genomics, Proteomics & Bioinformatics, 12(4): 164–171. https://doi.org/10.1016/j.gpb.2014.07.003
Varré JS, D’Agostino N, Touzet P, et al., 2019, Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. International Journal of Molecular Sciences, 20(19): 4788. https://doi.org/10.3390/ijms20194788
Gupta PK, Varshney RK, 2000, The Development and Use of Microsatellite Markers for Genetic Analysis and Plant Breeding with Emphasis on Bread Wheat. Euphytica, 113(3): 163–185. https://doi.org/10.1023/A:1003910819967
Kang J, Lu J, Qiu S, et al., 2015, Dendrobium SSR Markers Play a Good Role in Genetic Diversity and Phylogenetic Analysis of Orchidaceae Species. Scientia Horticulturae, 183(12): 160–166. https://doi.org/10.1016/j.scienta.2014.12.018
Song Y, Wang S, Ding Y, et al., 2017, Chloroplast Genomic Resource of Paris for Species Discrimination. Scientific Reports, 7(1): 3427. https://doi.org/10.1038/s41598-017-02083-7
Niu ZT, Zhu SY, Pan JJ, 2017, Comparative Analysis of Dendrobium plastomes and Utility of Plastomic Mutational Hotspots. Scientific Reports, 7(1): 2073. https://doi.org/10.1038/s41598-017-02252-8