Complete Chloroplast Genome of Gladiolus gandavensis (Gladiolus) and Genetic Evolutionary Analysis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequencing, Assembly, and Annotation
2.2. Sequence Analysis
2.3. Phylogenetic Analysis with Other Species
2.4. Genetic Evolutionary Analysis
3. Results
3.1. Characteristics of Chloroplast Genomes
3.2. Bias of Codon Usage
3.3. Microsatellite Polymorphisms
3.4. IR Expansion and Contraction
3.5. Phylogenetic Analysis
3.6. Genetic Relationship Analysis of Gladiolus
4. Discussion
4.1. The Chloroplast Genome of G. gandavensis
4.2. The Evolutionary Genetics of G. gandavensis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Myouga, F. A Heterocomplex of Iron Superoxide Dismutases Defends Chloroplast Nucleoids against Oxidative Stress and is Essential for Chloroplast Development in Arabidopsis. Plant. Cell. 2008, 20, 11. [Google Scholar] [CrossRef] [PubMed]
- Kumar, P.N.; Raju, D.V.S. Dormancy in Gladiolus: The Cause and Remedy—A Review. Agric. Rev. 2007, 28, 309–312. [Google Scholar]
- Wang, D.; Qi, Y.; Li, B.; Zhang, G. A New Anthraquinone from Gladiolus Gandavensis. Nat. Prod. Res. 2003, 17, 365–368. [Google Scholar] [CrossRef]
- Tai, Z.; Yang, X.; Le, C.; Sun, W.; Yang, Y. Studies on the Chemical Constituents from The Aerial Parts of Gladiolus gandavensis. J. Chin. Med. Mater. 2010, 33, 1257–1259. [Google Scholar]
- Yamagami, T.; Mine, Y.; Ishiguro, M. Complete Amino Acid Sequence of Chitinase-a from Bulbs of Gladiolus (Gladiolus gandavensis). Biosci. Biotech. Bioch. 2014, 62, 386–389. [Google Scholar] [CrossRef]
- Zhao, L.; Jiang, X.W.; Zuo, Y.J.; Liu, X.L.; Chin, S.W.; Haberle, R.; Wen, J. Multiple Events of Allopolyploidy in The Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data. PLoS ONE 2016, 11, e0157123. [Google Scholar] [CrossRef] [PubMed]
- Schubert, M.; Petersson, U.; Haas, B. Proteome Map of the Chloroplast Lumen of Arabidopsis thaliana. J. Biol. Chem. 2002, 277, 8354–8365. [Google Scholar] [CrossRef]
- Ohyama, K. Chloroplast and Mitochondrial Genomes from A Liverwort, Marchantia polymorpha--Gene Organization and molecular evolution. J. Agric. Chem. Soc. Jpn. 1996, 60, 16–24. [Google Scholar] [CrossRef] [PubMed]
- Ferris, C.; Oliver, R.; Davy, A.; Hewitt, G. Using Chloroplast DNA to Trace Postglacial Migration Routes of Oaks into Britain. Mol. Ecol. 2010, 4, 731–738. [Google Scholar] [CrossRef]
- James, C.; Gibby, M.; Barrett, J. Molecular Studies in Pelargonium (Geraniaceae). A Taxonomic Appraisal of Section Ciconium and the Origin of the ‘Zonal’ and ‘Ivy-leaved’ cultivars. Plant Syst. Evol. 2004, 243, 131–146. [Google Scholar] [CrossRef]
- Heath, R.; Packer, L. Photoperoxidation in Isolated Chloroplast I. Kinetics and Stoichiometry ofFatty Acid Peroxidation. Arch. Biochem. Biophys. 1968, 125, 189–198. [Google Scholar] [CrossRef]
- Kasahara, M.; Swartz, T.E.; Olney, M.A.; Onodera, A.; Mochizuki, N.; Fukuzawa, H.; Briggs, W.R. Photochemical Properties of the Flavin Mononucleotide-Binding Domains of the Phototropins from Arabidopsis, rice, and Chlamydomonas reinhardtii. Plant. phys. 2002, 129, 762–773. [Google Scholar] [CrossRef] [Green Version]
- Kagawa, T. Arabidopsis NPL1: A Phototropin Homolog Controlling the Chloroplast High-Light Avoidance Response. Science 2001, 291, 2138–2141. [Google Scholar] [CrossRef]
- Heckathorn, S.A. The Small, Methionine-Rich Chloroplast Heat-Shock Protein Protects Photosystem II Electron Transport during Heat Stress. Plant Phys. 1998, 116, 439–444. [Google Scholar] [CrossRef] [PubMed]
- Boyer, J.; Potter, J. Chloroplast Response to Low Leaf Water Potentials: IV. Quantum Yield is Reduced. Plant Physiol. 1973, 51, 989–1092. [Google Scholar] [CrossRef] [PubMed]
- Tamburino, R.; Vitale, M.; Ruggiero, A. Chloroplast Proteome Response to Drought Stress and Recovery in Tomato (Solanum lycopersicum L.). BMC Plant Biol. 2017, 17, 40. [Google Scholar] [CrossRef]
- Mittova, V.; Tal, M.; Volokita, M. Salt Stress Induces Up-Regulation of an Efficient Chloroplast Antioxidant System in the Salt-tolerant Wild tomato Species Lycopersicon pennellii but not in theCultivated Species. Physiol. Plant. 2010, 115, 3. [Google Scholar] [CrossRef] [PubMed]
- Siddhartha, D. Role of Temperature Stress on Chloroplast Biogenesis andProtein Import in Pea. Plant Physiol. 2009, 150, 1050–1061. [Google Scholar]
- Shinozaki, K.; Ohme, M.; Tanaka, M.; Wakasugi, T.; Hayashida, N.; Matsubayashi, T. The Complete Nucleotide Sequence of the Tobacco Chloroplast Genome: Its Gene Organization and Expression. EMBO J. 1986, 5, 2043–2049. [Google Scholar] [CrossRef] [PubMed]
- Hiratsuka, J.; Shimada, H.; Whittier, R.; Ishibashi, T.; Sakamoto, M.; Mori, M. The Complete Sequence of the rice (Oryza sativa) Chloroplast Genome: Intermolecular Recombination between Distinct tRNA Genes Accounts for a Major Plastid DNA Inversion during the Evolution of the Cereals. Mol. Gen. Genet. 1989, 217, 185–194. [Google Scholar] [CrossRef] [PubMed]
- Maier, R.; Kai, N.; Igloi, G. Complete Sequence of the Maize Chloroplast Genome: Gene Content, Hotspots of Divergence and Fine Tuning of Genetic Information by Transcript Editing. J. Mol. Biol. 1995, 251, 614. [Google Scholar] [CrossRef] [PubMed]
- Ni, Z.; Zhou, P.; Xin, Y.; Xu, M.; Xu, L.A. Parent–offspring variation transmission in full-sib families revealed predominantly paternal inheritance of chloroplast DNA in Pinus massoniana (Pinaceae). Tree Genet. Genomes 2021, 17, 36. [Google Scholar] [CrossRef]
- Palmer, J.; Stein, D. Conservation of chloroplast genome structure among vascular plants. Curr. Genet. 1986, 10, 823–833. [Google Scholar] [CrossRef]
- Zhang, X.; Gu, C.; Zhang, T.; Tong, B.; Zhang, H.; Wu, Y.; Yang, C. Chloroplast (Cp) Transcriptome of P. davidiana Dode× P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny. BMC Evol. Biol. 2020, 20, 51. [Google Scholar] [CrossRef]
- McPherson, H.; Merwe, M.; Delaney, S.; Edwards, M.; Henry, R.; McIntosh, E. Capturing Chloroplast Variation for Molecular Ecology Studies: A Simple Next Generation Sequencing Approach Applied to a Rainforest Tree. BMC Ecol. 2013, 13, 8. [Google Scholar] [CrossRef]
- Bruce, B.D. Chloroplast Transit Peptides: Structure, Function and Evolution. Trends Cell. Biol. 2000, 10, 440–447. [Google Scholar] [CrossRef]
- Liu, B.; Xie, Y.; Li, Z.; Liu, Y. SOAPdenovo2: An Empirically Improved Memory-Efficient Short-Read de novo Assembler. GigaScience 2012, 1, 18. [Google Scholar]
- Xu, M.; Guo, L.; Gu, S. TGS-GapCloser: A Fast and Accurate Gap Closer for Large Genomes with Low Coverage of Error-Prone Long Reads. GigaScience 2020, 9, 9. [Google Scholar] [CrossRef]
- Kuravadi, N.; Tiwari, P.; Tanwar, U. Identification and Characterization of EST-SSR Markers in Cluster Bean (Cyamopsis spp.). Crop. Sci. 2013, 54, 3. [Google Scholar] [CrossRef]
- Standley, D. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol. Biol. Evol. 2013, 30, 772. [Google Scholar]
- Darling, A.; Mau, B.; Blattner, F. Mauve: Multiple Alignment of Conserved Genomic Sequence with Rearrangements. Genome Res. 2004, 14, 1394–1403. [Google Scholar] [CrossRef] [PubMed]
- Kurtz, S. The Vmatch Large Scale Sequence Analysis Software-a Manual. Center. Bioinform. 2010, 170, 391–392. [Google Scholar]
- Yu, Z.J. KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Genom. Proteom. Bioinform. 2010, 8, 77–80. [Google Scholar]
- Dempster, A. Maximum-Likelihood from Incomlete Data via the Em Algorithm. J. R. Stat. Soc. Ser. B 1977, 39, 1–38. [Google Scholar]
- Huang, B.; Wang, Z.; Huang, J.; Li, X.; Zhu, H.; Wen, Q.; Xu, L. Population Genetic Structure Analysis Reveals Significant Genetic Differentiation of the Endemic Species Camellia chekiangoleosa Hu. with a Narrow Geographic Range. Forests 2022, 13, 234. [Google Scholar] [CrossRef]
- Ni, Z.; Ye, Y.; Bai, T.; Xu, L. Complete Chloroplast Genome of Pinus massoniana (Pinaceae): Gene Rearrangements, Loss of ndh Genes, and Short Inverted Repeats Contraction, Expansion. Molecules 2017, 22, 1528. [Google Scholar] [CrossRef] [PubMed]
- Backeljau, T.; de Bruyn, L.; de Wolf, H.; Jordaens, K.; van Dongen, S.; Winnepennincks, B. Multiple UPGMA and Neighbor-Joining Trees, and the Performance of Some Computer Packages. Mol. Biol. Evol. 1966, 13, 2. [Google Scholar] [CrossRef]
- Lee, E.; Smith, D.; Fanwick, P.; Byrn, S. Characterization and Anisotropic Lattice Expansion/Contraction of Polymorphs of Tenofovir Disoproxil Fumarate. Cryst. Growth. Des. 2010, 10, 2314–2322. [Google Scholar] [CrossRef]
- Dong, W.; Chao, X.; Tao, C.; Zhou, S.; Nicolas, S. Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales. PLoS ONE 2013, 8, e77965. [Google Scholar]
- Wang, J.; Hartling, J.; Flanagan, J. The structure of ClpP at 2.3 AResolution Suggests a Model for ATP-Dependent Proteolysis. Cell 1997, 91, 447. [Google Scholar] [CrossRef]
- Hricová, A.; Quesada, V.; Micol, J.L. The SCABRA3 Nuclear Gene Encodes the Plastid RpoTp RNA Polymerase, which is Required for Chloroplast Biogenesis and Mesophyll Cell Proliferation in Arabidopsis. Plant Phys. 2006, 141, 942–956. [Google Scholar] [CrossRef] [PubMed]
- Haynes, C.; Petrova, K.; Benedetti, C.; Yun, Y.; Ron, D. ClpP Mediates Activation of a Mitochondrial Unfolded Protein Response in C. elegans. Dev. Cell 2007, 13, 467–480. [Google Scholar] [CrossRef]
- Liu, X.; Gillham, N.; Boynton, J. Chloroplast Ribosomal Protein Gene rps12 of Chlamydomonas Reinhardtii. Wild-Type Sequence, Mutation to Streptomycin Resistance and Dependence, and Function in Escherichia coli. J. Biol. Chem. 1989, 264, 16100. [Google Scholar] [CrossRef]
- Kawabe, A.; Miyashita, N. Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet. Syst. 2003, 78, 343–352. [Google Scholar] [CrossRef] [PubMed]
- Shackelton, L.; Parrish, C.; Holmes, E. Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses. J. Mol. Evol. 2006, 62, 551–563. [Google Scholar] [CrossRef]
- Dong, F.; Lin, Z.; Lin, J. Chloroplast Genome of Rambutan and Comparative Analyses in Sapindaceae. Plants 2021, 10, 283. [Google Scholar] [CrossRef]
- Li, J.; Jin, Z.; Tan, T. Genetic Diversity and Differentiation of Sinocalycanthus Chinensis Populations Revealed by Chloroplast Microsatellite (cpSSRs) Markers. Biochem. Syst. Ecol. 2012, 41, 48–54. [Google Scholar] [CrossRef]
- Cesare, M.; Hodkinson, T.; Barth, S. Chloroplast DNA Markers (cpSSRs, SNPs) for Miscanthus, Saccharum and Related grasses (Panicoideae, Poaceae). Mol. Breed. 2010, 26, 539–544. [Google Scholar] [CrossRef]
- Ranjan, P.; Bhat, K.V.; Misra, R.L.; Singh, S.K.; Ranjan, J.K. GeneticRelationships of Gladiolus Cultivars Inferred from Fluorescence based AFLP Markers. Sci. Hortic. 2010, 123, 562–567. [Google Scholar] [CrossRef]
Number | Specific Name | Latin Name | Origin |
---|---|---|---|
1 | 1 | Gladiolus abbreviatus | South Africa |
2 | 2 | Gladiolus alatus | South Africa |
3 | 3 | Gladiolus angustus | South Africa |
4 | 4 | Gladiolus brevifolius var brevifolius | South Africa |
5 | 5 | Gladiolus carinatus | South Africa |
6 | 6 | Gladiolus carmineus | South Africa |
7 | 7 | Gladiolus carneus | South Africa |
8 | 9 | Gladiolus carneus (macowanianus) | South Africa |
9 | 11 | Gladiolus ceresianus | South Africa |
10 | 12 | Gladiolus crassifolius | South Africa |
11 | 14 | Gladiolus dalenii | South Africa |
12 | 15 | Gladiolus densiflorus | South Africa |
13 | 18 | Gladiolus exiguus | South Africa |
14 | 19 | Gladiolus ferrugineus | South Africa |
15 | 21 | Gladiolus floribundus ssp floribundus | South Africa |
16 | 23 | Gladiolus griseus | South Africa |
17 | 25 | Gladiolus hirsutus | South Africa |
18 | 26 | Gladiolus hyalinus | South Africa |
19 | 29 | Gladiolus liliaceus | South Africa |
20 | 30 | Gladiolus longicollis | South Africa |
21 | 31 | Gladiolus macelatus | South Africa |
22 | 32 | Gladiolus martleyi | South Africa |
23 | 33 | Gladiolus meliusculus | South Africa |
24 | 35 | Gladiolus mostertiae | South Africa |
25 | 36 | Gladiolus ochroleucus | South Africa |
26 | 37 | Gladiolus oppositiflorus ssp salmoneus | South Africa |
27 | 38 | Gladiolus papilio | South Africa |
28 | 39 | Gladiolus pardalinus | South Africa |
29 | 41 | Gladiolus patersoniae | South Africa |
30 | 42 | Gladiolus permeabilis ssp permeabilis | South Africa |
31 | 43 | Gladiolus phoenix | South Africa |
32 | 44 | Gladiolus pole-evansii | South Africa |
33 | 45 | Gladiolus quadrangularis | South Africa |
34 | 46 | Gladiolus recurvus | South Africa |
35 | 47 | Gladiolus rudis | South Africa |
36 | 48 | Gladiolus saccatus | South Africa |
37 | 49 | Gladiolus saundersii | South Africa |
38 | 50 | Gladiolus scabridus | South Africa |
39 | 51 | Gladiolus sericeovillosus | South Africa |
40 | 52 | Gladiolus splendens | South Africa |
41 | 53 | Gladiolus stellatus | South Africa |
42 | 54 | Gladiolus sufflavus | South Africa |
43 | 55 | Gladiolus teretifolius | South Africa |
44 | 59 | Gladiolus venustus | South Africa |
45 | 60 | Gladiolus vernus | South Africa |
46 | 61 | Gladiolus virescens | South Africa |
47 | 64 | G. gandavensis | China/Beiguan Island |
48 | 65 | G.gandavensis | China/Mazhan |
49 | 66 | G.gandavensis | China/Pucheng |
Category | Gene Group | Gene Contents |
---|---|---|
Photosynthesis | Subunits of photosystem I | psaA,psaB,psaC,psaI,psaJ |
Subunits of photosystem II | psbA,psbB,psbC,psbD,psbE,psbF, psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ | |
Subunits of cytochrome b/f complex | petA,petB*,petD*,petG,petN | |
Subunits of ATP synthase | atpA,atpB,atpE,atpF*,atpH,atpI | |
Subunits of NADH-dehydrogenase | ndhA*,ndhB*(2),ndhC,ndhD,ndhE,ndhF,ndhG,ndhH, ndhI,ndhJ,ndhK | |
Subunit of rubisco rbcL | rbcL | |
Self-replication | Small subunit of ribosome | rps11,rps12**(2),rps14,rps15,rps16*,rps18,rps19(2), rps2,rps3,rps4,rps7(2),rps8 |
Large subunit of ribosome | rpl14,rpl16*,rpl2*(2),rpl20,rpl22,rpl23(2),rpl32,rpl33, rpl36 | |
DNA-dependent RNA polymerase | rpoA,rpoB,rpoC1*,rpoC2 | |
Protease clpP | clpP | |
Maturase | matK | |
Envelope membrane protein cemA | cemA | |
Translation initiation factor infA | infA | |
Cytochrome c biogenesis ccsA | ccsA | |
Subunit Acetyl-CoA-Carboxylate | accD | |
Ribosomal RNAs | rrn16(2), rrn23(2), rrn4.5(2), rrn5(2) | |
Transfer RNA | trnA-UGC*(2), trnC-GCA, trnD-GUC, trnE-UUC,trnF-GAA,trnG-GCC*,trnG-UCC, trnH-GUG(2),trnI-CAU(2),trnI-GAU*(2), trnK-UUU*,trnL-CAA(2),trnL-UAA*, trnL-UAG,trnM-CAU,trnN-GUU(2), trnP-UGG,trnQ-UUG,trnR-ACG(2), trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA, trnT-GGU,trnT-UGU,trnV-GAC(2),trnV-UAC*, trnW-CCA,trnY-GUA,trnfM-CAU | |
other genes | Maturase | matK |
Protease | clpP** | |
Envelope membrane protein | cemA | |
Acetyl-CoA carboxylase | accD | |
c-type cytochrome synthesis gene | ccsA | |
Translation initiation factor | infA | |
Genes of unknown function | Conserved open reading frames | ycf1, ycf2, ycf2-D2, ycf3, ycf4, |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Qian, R.; Ye, Y.; Hu, Q.; Ma, X.; Zheng, J. Complete Chloroplast Genome of Gladiolus gandavensis (Gladiolus) and Genetic Evolutionary Analysis. Genes 2022, 13, 1599. https://doi.org/10.3390/genes13091599
Qian R, Ye Y, Hu Q, Ma X, Zheng J. Complete Chloroplast Genome of Gladiolus gandavensis (Gladiolus) and Genetic Evolutionary Analysis. Genes. 2022; 13(9):1599. https://doi.org/10.3390/genes13091599
Chicago/Turabian StyleQian, Renjuan, Youju Ye, Qingdi Hu, Xiaohua Ma, and Jian Zheng. 2022. "Complete Chloroplast Genome of Gladiolus gandavensis (Gladiolus) and Genetic Evolutionary Analysis" Genes 13, no. 9: 1599. https://doi.org/10.3390/genes13091599