Home > Archive>Volume 24, Issue 2, 2016 >151-159. DOI:10.11926/j.issn.1005-3395.2016.02.004
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Molecular Evolutionary Patterns of the psbA Gene in Gymnosperms
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Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine,Pharmacy Faculty, Hubei University of Chinese Medicine

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    Abstract:

    To understand the molecular mechanisms of ecological responding to terrestrial habitat in gymnosperm species, 53 representative species, belonging to four subclasses of gymnosperms, were selected to molecular evolutionary analysis based on psbA gene coding sequences. Firstly, the phylogenetic tree under geological timescale was established based on relaxed molecular clock model. Secondly, the positive selection signal among PSBA were detected by the estimated ω values by using six models, including MEC/JTT, MEC/cpREV, M5, M7, M8 and M8a. Then, the co-evolutionary network of amino acid sites within the PSBA was investigated by Bootstrap method. The results indicated that the species differentiation process from phylogenetic tree of gymnosperms along the timescale supported to previous studies. The three amino acid sites (13, 19, 243) in PSBA protein endured positive selection during the evolutionary history of gymnosperm species. Certain pairs of site within PSBA protein evolved into a co-evolutionary network. Therefore, the psbA sequences have the potential to be DNA marker during the establishment of the phylogenetic relationship of gymnosperms. The modification of PSBA protein by the site adaptation and protein intra network might be an important factor benefits the adaptive evolution of gymnosperm species against the terrestrial habitat.

    Reference
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    [20] Darriba D, Taboada G L, Doallo R, et al. jModelTest 2: More models, new heuristics and parallel computing [J]. Nat Methods. 2012, 9(8): 772. doi: 10.1038/nmeth.2109.
    [21] Drummond A J, Suchard M A, Xie D, et al. Bayesian phylo-genetics with BEAUti and the BEAST 1.7 [J]. Mol Biol Evol, 2012, 29(8): 1969-1973. doi: 10.1093/molbev/mss075.
    [22] Andrew R M S, Drummond A. Tracer V 1.6.0 [CP]. 2013-12-11.
    [23] Fares M A, Mcnally D. CAPS: Coevolution analysis using protein sequences [J]. Bioinformatics, 2006, 22(22): 2821-2822. doi: 10.1093/ bioinformatics/btl493.
    [24] Lovell S C, Robertson D L. An integrated view of molecular coevolution in protein-protein interactions [J]. Mol Biol Evol, 2010, 27(11): 2567-2575. doi: 10.1093/molbev/msq144.
    [25] Fares M A. Natural Selection: Methods and Applications [M]. New York: Apple Academic Press Inc., 2014: 1-274.linear sequence of extant gymnosperms [J]. Phyto-taxa, 2011, 19(2): 55-70.
    5-8339.2009.01002.x.
    [2] Christenhusz M J M, Reveal J L, Farjon A, et al. A new classification and linear sequence of extant gymnosperms [J]. Phyto-taxa, 2011, 19(2): 55-70.
    [3] Chaw S M, Walters T W, Chang C C, et al. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region [J]. Mol Phylogenet Evol, 2005, 37(1): 214-234. doi: 10.1016/j.ympev.2005.01.006.
    [4] Mao K S, Milne R I, Zhang L B, et al. Distribution of living Cupressaceae reflects the breakup of Pangea [J]. Proc Natl Acad Sci USA, 2012, 109(20): 7793-7798. doi: 10.1073/pnas.1114319109.
    [5] Mattoo A K, Marder J B, Edelman M. Dynamics of the photosystem II reaction center [J]. Cell, 1989, 56(2): 241-246. doi: 10.1016/0092-8674(89)90897-0.
    [6] Rhee K H, Morris E P, Barber J, et al. Three-dimensional structure of the plant photosystem II reaction centre at 8 Å resolution [J]. Nature, 1998, 396(6708): 283-286. doi: 10.1038/24421.
    [7] Pakrasi H B. Genetic analysis of the form and function of photosystem I and photosystem II [J]. Annu Rev Genet, 1995, 29: 755-776. doi: 10.1146/annurev.ge.29.120195.003543.
    [8] Vogt L, Vinyard D J, Khan S, et al. Oxygen-evolving complex of photosystem II: An analysis of second-shell residues and hydrogen-bonding networks [J]. Curr Opin Chem Biol, 2015, 25: 152-158. doi: 10.1016/j.cbpa.2014.12.040.
    [9] Umena Y, Kawakami K, Shen J R, et al. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å [J]. Nature, 2011, 473(7345): 55-60. doi: 10.1038/nature09913.
    [10] Kupitz C, Basu S, Grotjohann I, et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser [J]. Nature, 2014, 513(7517): 261-265. doi:10.1038/nature13453.
    [11] Ran J H, Shen T T, Liu W J, et al. Evolution of the bHLH genes involved in stomatal development: Implications for the expansion of developmental complexity of stomata in land plants [J]. PLoS ONE, 2013, 8(11): e78997. doi: 10.1371/journal.pone.0078997.
    [12] Yang Z H. Computational Molecular Evolution [M]. Oxford: Oxford University ress, 2006: 1-376 .
    [13] Schuettpelz E, Pryer K M. Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy [J]. Proc Natl Acad Sci USA, 2009, 106(27): 11200-11205. doi: 10.1073/pnas.0811136106.
    [14] Wang H C, Moore M J, Soltis P S, et al. Rosid radiation and the rapid rise of angiosperm-dominated forests [J]. Proc Natl Acad Sci USA, 2009, 106(10): 3853-3858. doi: 10.1073/pnas.0813376106.
    [15] Sen L, Su Y J, Zhang B, et al. Adaptive evolution of the rbcL gene in Pteridaceous ferns [J]. J Trop Subtrop Bot, 2010, 18(1): 1-8. doi: 10.3969/j.issn.1005-3395.2010.01.001. 森林, 苏应娟, 张冰, 等. 凤尾蕨科植物rbcL基因的适应性进化分析 [J]. 热带亚热带植物学报, 2010, 18(1): 1-8. doi: 10.3969/j.issn. 1005-3395.2010.01.001.
    [16] Sen L, Fares M A, Liang B, et al. Molecular evolution of rbcL in three gymnosperm families: Identifying adaptive and coevolu­tionary patterns [J]. Biol Direct, 2011, 6: 29. doi: 10.1186/1745-6150-6-29.
    [17] Sen L, Fares M, Su Y J, et al. Molecular evolution of psbA gene in ferns: Unraveling selective pressure and co-evolutionary pattern [J]. BMC Evol Biol, 2012, 12: 145. doi: 10.1186/1471-2148-12-145.
    [18] Katoh K, Standley D M. MAFFT: Iterative refinement and additional methods [M]// Russell D J. Multiple Sequence Alignment Methods: Methods in Molecular Biology, Vol. 1079. New York: Humana Press, 2014: 131-146. doi: 10.1007/978-1-62703-646-7_8.
    [19] Yi X, Gao L, Wang B, et al. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms [J]. Gen Biol Evol, 2013, 5(4): 688-698. doi: 10.1093/gbe/evt042.
    [20] Darriba D, Taboada G L, Doallo R, et al. jModelTest 2: More models, new heuristics and parallel computing [J]. Nat Methods. 2012, 9(8): 772. doi: 10.1038/nmeth.2109.
    [21] Drummond A J, Suchard M A, Xie D, et al. Bayesian phylo-genetics with BEAUti and the BEAST 1.7 [J]. Mol Biol Evol, 2012, 29(8): 1969-1973. doi: 10.1093/molbev/mss075.
    [22] Andrew R M S, Drummond A. Tracer V 1.6.0 [CP]. 2013-12-11.
    [23] Fares M A, Mcnally D. CAPS: Coevolution analysis using protein sequences [J]. Bioinformatics, 2006, 22(22): 2821-2822. doi: 10.1093/ bioinformatics/btl493.
    [24] Lovell S C, Robertson D L. An integrated view of molecular coevolution in protein-protein interactions [J]. Mol Biol Evol, 2010, 27(11): 2567-2575. doi: 10.1093/molbev/msq144.
    [25] Fares M A. Natural Selection: Methods and Applications [M]. New York: Apple Academic Press Inc., 2014: 1-274.linear sequence of extant gymnosperms [J]. Phyto-taxa, 2011, 19(2): 55-70.
    , Farjon A, erative refinement and additional methods [M]// Russell D J. Multiple Sequence Alignment Methods: Methods in Molecular Biology, Vol. 1079. New York: Humana Press, 2014: 131-146. doi: 10.1007/978-1-62703-646-7_8.
    [19] Yi X, Gao L, Wang B, et al. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms [J]. Gen Biol Evol, 2013, 5(4): 688-698. doi: 10.1093/gbe/evt042.
    [20] Darriba D, Taboada G L, Doallo R, et al. jModelTest 2: More models, new heuristics and parallel computing [J]. Nat Methods. 2012, 9(8): 772. doi: 10.1038/nmeth.2109.
    [21] Drummond A J, Suchard M A, Xie D, et al. Bayesian phylo-genetics with BEAUti and the BEAST 1.7 [J]. Mol Biol Evol, 2012, 29(8): 1969-1973. doi: 10.1093/molbev/mss075.
    [22] Andrew R M S, Drummond A. Tracer V 1.6.0 [CP]. 2013-12-11.
    [23] Fares M A, Mcnally D. CAPS: Coevolution analysis using protein sequences [J]. Bioinformatics, 2006, 22(22): 2821-2822. doi: 10.1093/ bioinformatics/btl493.
    [24] Lovell S C, Robertson D L. An integrated view of molecular coevolution in protein-protein interactions [J]. Mol Biol Evol, 2010, 27(11): 2567-2575. doi: 10.1093/molbev/msq144.
    [25] Fares M A. Natural Selection: Methods and Applications [M]. New York: Apple Academic Press Inc., 2014: 1-274.mplex of photosystem II: An analysis of second-shell residues and hydrogen-bonding networks [J]. Curr Opin Chem Biol, 2015, 25: 152-158. doi: 10.1016/j.cbpa.2014.12.040.
    [9] Umena Y, Kawakami K, Shen J R, et al. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å [J]. Nature, 2011, 473(7345): 55-60. doi: 10.1038/nature09913.
    [10] Kupitz C, Basu S, Grotjohann I, et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser [J]. Nature, 2014, 513(7517): 261-265. doi:10.1038/nature13453.
    [11] Ran J H, Shen T T, Liu W J, et al. Evolution of the bHLH genes involved in stomatal development: Implications for the expansion of developmental complexity of stomata in land plants [J]. PLoS ONE, 2013, 8(11): e78997. doi: 10.1371/journal.pone.0078997.
    [12] Yang Z H. Computational Molecular Evolution [M]. Oxford: Oxford University Press, 2006: 1-376 .
    [13] Schuettpelz E, Pryer K M. Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy [J]. Proc Natl Acad Sci USA, 2009, 106(27): 11200-11205. doi: 10.1073/pnas.0811136106.
    [14] Wang H C, Moore M J, Soltis P S, et al. Rosid radiation and the rapid rise of angiosperm-dominated forests [J]. Proc Natl Acad Sci USA, 2009, 106(10): 3853-3858. doi: 10.1073/pnas.0813376106.
    [15] Sen L, Su Y J, Zhang B, et al. Adaptive evolution of the rbcL gene in Pteridaceous ferns [J]. J Trop Subtrop Bot, 2010, 18(1): 1-8. doi: 10.3969/j.issn.1005-3395.2010.01.001. 森林, 苏应娟, 张冰, 等. 凤尾蕨科植物rbcL基因的适应性进化分析 [J]. 热带亚热带植物学报, 2010, 18(1): 1-8. doi: 10.3969/j.issn. 1005-3395.2010.01.001.
    [16] Sen L, Fares M A, Liang B, et al. Molecular evolution of rbcL in three gymnosperm families: Identifying adaptive and coevolu­tionary patterns [J]. Biol Direct, 2011, 6: 29. doi: 10.1186/1745-6150-6-29.
    [17] Sen L, Fares M, Su Y J, et al. Molecular evolution of psbA gene in ferns: Unraveling selective pressure and co-evolutionary pattern [J]. BMC Evol Biol, 2012, 12: 145. doi: 10.1186/1471-2148-12-145.
    [18] Katoh K, Standley D M. MAFFT: Iterative refinement and additional methods [M]// Russell D J. Multiple Sequence Alignment Methods: Methods in Molecular Biology, Vol. 1079. New York: Humana Press, 2014: 131-146. doi: 10.1007/978-1-62703-646-7_8.
    [19] Yi X, Gao L, Wang B, et al. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms [J]. Gen Biol Evol, 2013, 5(4): 688-698. doi: 10.1093/gbe/evt042.
    [20] Darriba D, Taboada G L, Doallo R, et al. jModelTest 2: More models, new heuristics and parallel computing [J]. Nat Methods. 2012, 9(8): 772. doi: 10.1038/nmeth.2109.
    [21] Drummond A J, Suchard M A, Xie D, et al. Bayesian phylo-genetics with BEAUti and the BEAST 1.7 [J]. Mol Biol Evol, 2012, 29(8): 1969-1973. doi: 10.1093/molbev/mss075.
    [22] Andrew R M S, Drummond A. Tracer V 1.6.0 [CP]. 2013-12-11.
    [23] Fares M A, Mcnally D. CAPS: Coevolution analysis using protein sequences [J]. Bioinformatics, 2006, 22(22): 2821-2822. doi: 10.1093/ bioinformatics/btl493.
    [24] Lovell S C, Robertson D L. An integrated view of molecular coevolution in protein-protein interactions [J]. Mol Biol Evol, 2010, 27(11): 2567-2575. doi: 10.1093/molbev/msq144.
    [25] Fares M A. Natural Selection: Methods and Applications [M]. New York: Apple Academic Press Inc., 2014: 1-274.
    linear sequence of extant gymnosperms [J]. Phyto-taxa, 2011, 19(2): 55-70.
    [3] Chaw S M, Walters T W, Chang C C, et al. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region [J]. Mol Phylogenet Evol, 2005, 37(1): 214-234. doi: 10.1016/j.ympev.2005.01.006.
    [4] Mao K S, Milne R I, Zhang L B, et al. Distribution of living Cupressaceae reflects the breakup of Pangea [J]. Proc Natl Acad Sci USA, 2012, 109(20): 7793-7798. doi: 10.1073/pnas.1114319109.
    [5] Mattoo A K, Marder J B, Edelman M. Dynamics of the photosystem II reaction center [J]. Cell, 1989, 56(2): 241-246. doi: 10.1016/0092-8674(89)90897-0.
    [6] Rhee K H, Morris E P, Barber J, et al. Three-dimensional structure of the plant photosystem II reaction centre at 8 Å resolution [J]. Nature, 1998, 396(6708): 283-286. doi: 10.1038/24421.
    [7] Pakrasi H B. Genetic analysis of the form and function of photosystem I and photosystem II [J]. Annu Rev Genet, 1995, 29: 755-776. doi: 10.1146/annurev.ge.29.120195.003543.
    [8] Vogt L, Vinyard D J, Khan S, et al. Oxygen-evolving complex of photosystem II: An analysis of second-shell residues and hydrogen-bonding networks [J]. Curr Opin Chem Biol, 2015, 25: 152-158. doi: 10.1016/j.cbpa.2014.12.040.
    [9] Umena Y, Kawakami K, Shen J R, et al. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å [J]. Nature, 2011, 473(7345): 55-60. doi: 10.1038/nature09913.
    [10] Kupitz C, Basu S, Grotjohann I, et al. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser [J]. Nature, 2014, 513(7517): 261-265. doi:10.1038/nature13453.
    [11] Ran J H, Shen T T, Liu W J, et al. Evolution of the bHLH genes involved in stomatal development: Implications for the expansion of developmental complexity of stomata in land plants [J]. PLoS ONE, 2013, 8(11): e78997. doi: 10.1371/journal.pone.0078997.
    [12] Yang Z H. Computational Molecular Evolution [M]. Oxford: Oxford University Press, 2006: 1-376 .
    [13] Schuettpelz E, Pryer K M. Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy [J]. Proc Natl Acad Sci USA, 2009, 106(27): 11200-11205. doi: 10.1073/pnas.0811136106.
    [14] Wang H C, Moore M J, Soltis P S, et al. Rosid radiation and the rapid rise of angiosperm-dominated forests [J]. Proc Natl Acad Sci USA, 2009, 106(10): 3853-3858. doi: 10.1073/pnas.0813376106.
    [15] Sen L, Su Y J, Zhang B, et al. Adaptive evolution of the rbcL gene in Pteridaceous ferns [J]. J Trop Subtrop Bot, 2010, 18(1): 1-8. doi: 10.3969/j.issn.1005-3395.2010.01.001. 森林, 苏应娟, 张冰, 等. 凤尾蕨科植物rbcL基因的适应性进化分析 [J]. 热带亚热带植物学报, 2010, 18(1): 1-8. doi: 10.3969/j.issn. 1005-3395.2010.01.001.
    [16] Sen L, Fares M A, Liang B, et al. Molecular evolution of rbcL in three gymnosperm families: Identifying adaptive and coevolu­tionary patterns [J]. Biol Direct, 2011, 6: 29. doi: 10.1186/1745-6150-6-29.
    [17] Sen L, Fares M, Su Y J, et al. Molecular evolution of psbA gene in ferns: Unraveling selective pressure and co-evolutionary pattern [J]. BMC Evol Biol, 2012, 12: 145. doi: 10.1186/1471-2148-12-145.
    [18] Katoh K, Standley D M. MAFFT: Ite?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
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森林,余坤,胡志刚,汪文杰,徐雷,刘合刚,潘宏林.裸子植物psbA基因分子进化式样的研究[J].热带亚热带植物学报,2016,24(2):151~159

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  • Received:May 12,2015
  • Revised:September 06,2015
  • Adopted:November 18,2015
  • Online: March 28,2016
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