Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

BMC Plant Biology

Volumn 10, Issue , 2010, Pages

  Abdurakhmonov, Ibrokhim Y ^a   Buriev, Zabardast T ^a   Logan Young, Carla J ^b   Abdukarimov, Abdusattor ^a   Pepper, Alan E ^b  

^a S YU YUNUSOV INSTITUTE OF THE CHEMISTRY OF PLANT SUBSTANCES   (Uzbekistan)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GOSSYPIUM; GOSSYPIUM BARBADENSE; GOSSYPIUM HERBACEUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII; MAGNOLIOPHYTA; MALVACEAE;

PHYTOCHROME; PLANT DNA; VISUAL PROTEINS AND PIGMENTS;

ARTICLE; COTTON; DNA SEQUENCE; GENE DUPLICATION; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PLANT GENE; PLANT GENOME; POLYPLOIDY;

DNA, PLANT; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; GENOME, PLANT; GOSSYPIUM; MULTIGENE FAMILY; PHOTORECEPTORS, PLANT; PHYTOCHROME; POLYPLOIDY; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 77953639715     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-10-119     Document Type: Article

References (106)

1. Kendrick RE, Kronenberg GHM. Photomorphogenesis in plants 1994, Kluwer Academic Publishers, Dordrecht, the Netherlands, 2.
2. Quail PH. Photosensory perception and signal transduction in plants. Curr Opin Gen Dev 1994, 4:652-661.
3. Smith H. Physiological and Ecological Function within the Phytochrome Family. Annu Rev Plant Phys 1995, 46:289-315.
4. Chun L, Kawakami A, Christopher DA. Phytochrome A Mediates Blue Light and UV-A-Dependent Chloroplast Gene Transcription in Green Leaves. Plant Physiol 2001, 125:1957-1966. 10.1104/pp.125.4.1957, 88851, 11299375.
5. Quail P. Phytochrome: a light-activated molecular switch that regulates plant gene expression. Annu Rev Genet 1991, 25:389-409. 10.1146/annurev.ge.25.120191.002133, 1812812.
6. Rockwell NC, Su YS, Lagarias JC. Phytochrome Structure And Signaling Mechanisms. Annu Rev Plant Phys 2006, 57:837-858.
7. Sharrock RA, Quail PH. Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev 1989, 3:1745-1757. 10.1101/gad.3.11.1745, 2606345.
8. Schneider-Poetsch HAW, Marx S, Kolukisaoglu HU, Hanelt S, Braun B. Phytochrome evolution: phytochrome genes in ferns and mosses. Physiol Plantarum 1994, 91:241-250.
9. Kolukisaoglu HU, Marx S, Wiegmann C, Hanelt S, Schneider-Poetsch HAW. Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum. J Mol Evol 1995, 41:329-337. 10.1007/BF01215179, 7563118.
10. Mathews S, Lavin M, Sharrock RA. Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Ann Mo Bot Gard 1995, 82:296-321.
11. Wada M, Kanegae T, Nozue K, Fukuda S. Cryptogam phytochromes. Plant Cell Environ 1997, 20:685-690.
12. Wu SH, J Lagarias JC. The phytochrome photoreceptor in the green alga Mesotaenium caldariorum: implication for a conserved mechanism of phytochrome action. Plant Cell Environ 1997, 20:691-699.
13. Mathews S. Phytochrome Evolution in Green and Nongreen Plants. J Hered 2005, 96:197-204. 10.1093/jhered/esi032, 15695552.
14. Clack T, Mathews S, Sharrock RA. The phytochrome family in Arabidopsis is encoded by five genes: the sequence and expression of PHYD and PHYE. Plant Mol Biol 1994, 25:413-27. 10.1007/BF00043870, 8049367.
15. Cowl JS, Hartley N, Xie DX, Whitelam GC, Murphy GP, Harberd NP. The PHYC gene of Arabidopsis: absence of the third intron found in PHYA and PHYB. Plant Physiol 1994, 106:813-814. 10.1104/pp.106.2.813, 159602, 7991704.
16. Mathews S, McBreen K. Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D. Mol Phylogenet Evol 2008, 49:411-23. 10.1016/j.ympev.2008.07.026, 18768161.
17. Pratt LH. Phytochromes: differential properties, expression patterns and molecular evolution. Photochem Photobiol 1995, 61:10-21.
18. Devlin PF, Patel SR, Whitelam GC. Phytochrome E influences internode elongation and flowering time in Arabidopsis. Plant Cell 1998, 10:1479-1487. 10.1105/tpc.10.9.1479, 144080, 9724694.
19. Reed JW, Nagatani A, Elich TD, M Fagan M, Chory J. Phytochrome A and phytochrome B have overlapping but distinct functions in Arabidopsis development. Plant Physiol 1994, 104:1139-1149. 159274, 12232154.
20. Shinomura T, Nagatani A, Chory J, Furuya M. The induction of seed germination in Arabidopsis thaliana is regulated principally by phytochrome B and secondarily by phytochrome A. Plant Physiol 1994, 104:363-371. 159207, 12232088.
21. Botto F, Sanchez RA, Whitelam GC, Casal JJ. Phytochrome A Mediates the Promotion of Seed Germination by Very Low Fluences of Light and Canopy Shade Light in Arabidopsis. Plant Physiol 1996, 110:439-444. 157738, 12226195.
22. Furuya M, Schafer E. Photoperception and signaling of induction reactions by different phytochromes. Trends Plant Sci 1996, 1:301-307.
23. Casal JJ, Sanchez RA, Yanovsky MJ. The function of phytochrome A. Plant Cell Environ 1997, 20:813-819.
24. Smith H, Xy Y, Quail PH. Antagonistic but Complementary Actions of Phytochromes A and B Allow Optimum Seedling De-Etiolation. Plant Physiol 1997, 114:637-641. 10.1104/pp.114.2.637, 158347, 9193095.
25. Qin M, Kuhn R, Moran S, Quail PH. Overexpressed phytochrome C has similar photosensory specificity to phytochrome B but a distinctive capacity to enhance primary leaf expansion. Plant J 1997, 12:1163-1172. 10.1046/j.1365-313X.1997.12051163.x, 9418054.
26. Whitelam GC, Devlin PF. Roles of different phytochromes in Arabidopsis photomorphogenesis. Plant Cell Environ 1997, 20:752-758.
27. Neff MM, Chory J. Genetic Interactions between Phytochrome A, Phytochrome B, and Cryptochrome 1 during Arabidopsis Development. Plant Physiol 1998, 118:27-35. 10.1104/pp.118.1.27, 34865, 9733523.
28. Devlin PF, Robson PRH, Patel SR, Samita R, Goosey L, Sharrock RA, Whitelam CG. Phytochrome D acts in the shade-avoidance syndrome in Arabidopsis by controlling elongation growth and flowering time. Plant Physiol 1999, 119:909-915. 10.1104/pp.119.3.909, 32105, 10069829.
29. Smith HB. Photoreceptors in Signal Transduction: Pathways of Enlightenment. Plant Cell 2000, 12:1-4. 10.1105/tpc.12.1.1, 1464685, 10634903.
30. Franklin KA, Praekelt U, Stoddart WM, Billingham OE, Halliday KJ, Whitelam GC. Phytochromes B, D, and E Act Redundantly to Control Multiple Physiological Responses in Arabidopsis. Plant Physiol 2003, 131:1340-1346. 10.1104/pp.102.015487, 166893, 12644683.
31. Franklin KA, Davis SJ, Stoddart WM, Vierstra RD, Whitelam GC. Mutant Analyses Define Multiple Roles for Phytochrome C in Arabidopsis Photomorphogenesis. Plant Cell 2003, 15:1981-1989. 10.1105/tpc.015164, 181325, 12953105.
32. Franklin KA, Whitelam GC. Light signals, phytochromes and cross-talk with other environmental cues. J Exp Bot 2004, 55:271-276. 10.1093/jxb/erh026, 14673030.
33. Josse EM, Foreman J, Halliday KJ. Paths through the phytochrome network. Plant Cell Environ 2008, 31:667 -677. 10.1111/j.1365-3040.2008.01794.x, 18266901.
34. Heschel MS, Butler CM, Barua D, Chiang GCK, Wheeler A, Sharrock RA, Whitelam GC, Donohue K. New Roles of Phytochromes during Seed Germination. Int J Plant Sci 2008, 169:531-540.
35. Somers DE, Devlin PF, Kay SA. Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 1998, 282:1488-1490. 10.1126/science.282.5393.1488, 9822379.
36. Devlin PF, Kay SA. Cryptochromes are required for phytochrome signaling to the circadian clock but not for rhythmicity. The Plant Cell 2000, 12:2499-2509. 10.2307/3871244, 102233, 11148293.
37. Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G. CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 2001, 410:1116-1120. 10.1038/35074138, 11323677.
38. Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G. Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science 2004, 303:1003-1006. 10.1126/science.1091761, 14963328.
39. Halliday KJ, Salter MG, Thingnaes E, Whitelam GC. Phytochrome control of flowering is temperature sensitive and correlates with expression of the floral integrator FT. Plant J 2003, 33:875-885. 10.1046/j.1365-313X.2003.01674.x, 12609029.
40. Endo M, Nakamura S, Araki T, Mochizuki N, Nagatani A. Phytochrome B in the mesophyll delays flowering by suppressing FLOWERING LOCUS T expression in Arabidopsis vascular bundles. Plant Cell 2005, 17:1941-1952. 10.1105/tpc.105.032342, 1167543, 15965119.
41. Monte E, Alonso JM, Ecker JR, Zhang Y, Li X, Young J, Austin-Phillips S, Quail PH. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell 2003, 15:1962-1980. 10.1105/tpc.012971, 181324, 12953104.
42. Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, Maloof JN, Clark R, Warthmann N, Chory J, Weigel D. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 2006, 38:711-715. 10.1038/ng1818, 1592229, 16732287.
43. Samis KE, Heath KD, Stinchcombe JR. Discordant longitudinal clines in flowering time and phytochrome C in Arabidopsis thaliana. Evolution 2008, 62:2971-2983. 10.1111/j.1558-5646.2008.00484.x, 18752603.
44. Hauser BA, Cordonnier-Pratt MM, Daniel-Vedele F, Pratt LH. The phytochrome gene family in tomato includes a novel subfamily. Plant Mol Biol 1995, 29:1143-1155. 10.1007/BF00020458, 8616214.
45. Pratt LH, Cordonnier-Pratt MM, Hauser BA, Caboche M. Tomato contains two differentially expressed genes encoding B-type phytochromes neither of which can be considered an ortholog of Arabidopsis phytochrome B. Planta 1995, 197:203-206. 10.1007/BF00239958, 7580861.
46. Pratt LH, Cordonnier-Pratt MM, Kelmenson PM, Lazarova GI, Kubota T, Alba RM. The phytochrome gene family in tomato (Solanum lycopersicum L.). Plant Cell Environ 1997, 20:672-677.
47. Howe GT, Bucciaglia PA, Hackett WP, Furnier GR, Cordonnier-Pratt MM, Gardner G. Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies. Mol Biol Evol 1998, 15:160-175.
48. Ouedraogo M, Hubac C. Effect of Far Red Light on Drought Resistance of Cotton. Plant Cell Physiol 1982, 23:1297-1303.
49. Singh G, Garg OP. Effect of red, far-red radiations on germination of cotton seed. Plant Cell Physiol 1971, 12:411-415.
50. Kasperbauer MJ. Cotton plant size and fiber developmental responses to FR/R ratio reflected from the soil surface. Physiol Plantarum 1994, 91:317-321.
51. Kasperbauer MJ. Cotton Fiber Length Is Affected by Far-Red Light Impinging on Developing Bolls. Crop Sci 2000, 40:1673-1678.
52. McCarty JC, Jenkins JN, Wu J. Primitive Accession Derived Germplasm by Cultivar Crosses as Sources for Cotton Improvement II. Genetic Effects and Genotypic Values. Crop Sci 2004, 44:1231-1235.
53. McCarty JC, Wu J, Jenkins JN. Genetic diversity for agronomic and fiber traits in day-neutral accessions derived from primitive cotton germplasm. Euphytica 2006, 148:283-293.
54. Childs KL, Miller FR, Cordonnier-Pratt MM, Pratt LH, Morgan PW, Mullet JE. The Sorghum photoperiod sensitivity gene Ma3, encodes a phytochrome B. Plant Physiol 1997, 97:714-719.
55. Hanumappa M, Pratt LH, Cordonnier-Pratt MM, Deitzer GF. A Photoperiod-Insensitive Barley Line Contains a Light-Labile Phytochrome B1. Plant Physiol 1999, 119:1033-1040. 10.1104/pp.119.3.1033, 32084, 10069841.
56. Izawa T, Oikawa T, Tokutomi S, Okuno K, Shimamoto K. Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant). Plant J 2000, 22:391-399. 10.1046/j.1365-313X.2000.00753.x, 10849355.
57. Liu Kanazawa A, Matsumura H, Takahashi R, Harada J, Abe J. Genetic Redundancy in Soybean Photoresponses Associated With Duplication of the Phytochrome A Gene. Genetics 2008, 180:995-1007. 10.1534/genetics.108.092742, 2567397, 18780733.
58. Endrizzi JE, Turcotte EL, Kohel RJ. Genetics, cytology and evolution of Gossypium. Adv Genet 1985, 23:271-375.
59. Wendel JF. New World tetraploid cottons contain Old World cytoplasm. P Natl Acad Sci USA 1989, 86:4132-4136.
60. Wendel JF, Albert VA. Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of Chloroplast-DNA Restriction Site Data and Its Systematic and Biogeographic Implications. Syst Bot 1992, 17:115-143.
61. Wendel JF, Brubaker CL, Percival AE. Genetic diversity in Gossypium hirsutum and the origin of upland cotton. Am J Bot 1992, 79:1291-1310.
62. Cronn RC, Small RL, Haselkorn, Wendel JF. Rapid Diversification of the Cotton Genus (Gossypium: Malvaceae) Revealed by Analysis of Sixteen Nuclear and Chloroplast Genes. Am J Bot 2002, 89:707-725.
63. Senchina DS, Alvarez, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF. Rate Variation Among Nuclear Genes and the Age of Polyploidy in Gossypium. Mol Biol Evol 2003, 20:633-643. 10.1093/molbev/msg065, 12679546.
64. Soltis PS, Soltis DE, Chase MW. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 1999, 402:402-404. 10.1038/46528, 10586878.
65. Wang H, Moore MJ, Soltis PS, Charles D, Bell CD, Brockington SF, Alexander R, Davis CC, Latvis MM, Manchester SR, Soltis DE. Rosid radiation and the rapid rise of angiosperm-dominated forests. P Natl Acad Sci USA 2009, 10:3853-3858.
66. Cronn R, Cedroni M, Haselkorn T, Grover C, Wendel JF. PCR-mediated recombination in amplification products derived from polyploid cotton. Theor Appl Genet 2002, 104:482-489. 10.1007/s001220100741, 12582722.
67. Martin DP, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21:260-262. 10.1093/bioinformatics/bth490, 15377507.
68. Udall JA, Swanson JM, Haller K, Rapp RA, . (36 authors) A global assembly of cotton ESTs. Genome Res 2006, 16:441-450. 10.1101/gr.4602906, 1415220, 16478941, (36 authors).
69. Ossowski S, Schwab R, Weigel D. Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 2008, 53:674-690. 10.1111/j.1365-313X.2007.03328.x, 18269576.
70. Moose SP, Mumm RH. Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement. Plant Physiol 2008, 147:969-977. 10.1104/pp.108.118232, 2442525, 18612074.
71. Konieczny A, Ausubel FM. A Procedure for mapping Arabidopsis mutations using co-dominant ecotype specific PCR-markers. Plant J 1993, 4:403-410. 10.1046/j.1365-313X.1993.04020403.x, 8106085.
72. Neff MM, Neff JD, Chory J, Pepper AE. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 1998, 14:387-392. 10.1046/j.1365-313X.1998.00124.x, 9628033.
73. Wikström N, Savolainen V, Chase MW. Evolution of the angiosperms: Calibrating the family tree. P Roy Soc London B 2001, 268:2211-2220.
74. Seelanan T, Schnabel A, Wendel JF. Congruence and consensus in the cotton tribe (Malvaceae). Syst Bot 1997, 22:259-290.
75. Ohno S. Evolution by gene duplication 1970, Springer-Verlag, New York, USA.
76. Force A, Lynch M, Pickett FB, Amores A, Yan Y, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151:1531-1545. 1460548, 10101175.
77. Lynch M, Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154:459-473. 1460895, 10629003.
78. Wagner A. Birth and death of duplicated genes in completely sequenced eukaryotes. Trends Genet 2001, 17:237-239. 10.1016/S0168-9525(01)02243-0, 11335019.
79. Lynch M, Conery JS. The Evolutionary Fate and Consequences of Duplicate Genes. Science 2000, 290:1151-1155. 10.1126/science.290.5494.1151, 11073452.
80. Moore RC, Purugganan MD. The evolutionary dynamics of plant duplicate genes. Curr Op Plant Biol 2005, 8:122-128.
81. Alba R, Kelmenson PM, Cordonnier-Pratt MM, Pratt LH. The Phytochrome Gene Family in Tomato and the Rapid Differential Evolution of this Family in Angiosperms. Mol Biol Evol 2000, 17:362-373.
82. Park CM, Bhoo SH, Song PS. Inter-domain crosstalk in the phytochrome molecules. Semin Cell Dev Biol 2000, 11:449-456. 10.1006/scdb.2000.0200, 11145874.
83. Kim JI, Shen Y, Han YJ, Park JE, Kirchenbauer D, Soh MS, Nagy F, Schäfer E, Song PS. Phytochrome phosphorylation modulates light signaling by influencing the protein-protein interaction. Plant Cell 2004, 16:2629-2640. 10.1105/tpc.104.023879, 520960, 15377754.
84. Chen M, Schwab R, Chory J. Characterization of the requirements for localization of phytochrome B to nuclear bodies. P Natl Acad Sci USA 2003, 100:14493-14498.
85. Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S. Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 2008, 178:2217-2226. 10.1534/genetics.107.082354, 2323810, 18245834.
86. Nekrutenko A, Makova KD, Li WH. The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res 2002, 12:198-202. 10.1101/gr.200901, 155263, 11779845.
87. Cronn RC, Small RL, Wendel JF. Duplicated genes evolve independently after polyploidy formation in cotton. P Natl Acad Sci USA 1999, 96:14406-14411.
88. Fisher RA. On the interpretation of χ2 from contingency tables, and the calculation of P. J Roy Stat Soc 1922, 85:87-94.
89. Nei M, Rogozin IB, Piontkivska H. Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc Natl Acad Sci USA 2000, 97:10866-10871. 10.1073/pnas.97.20.10866, 27115, 11005860.
90. White GM, Hamblin MT, Kresovich S. Molecular Evolution of the Phytochrome Gene Family in Sorghum: Changing Rates of Synonymous and Replacement Evolution. Mol Biol Evol 2004, 21:716-723. 10.1093/molbev/msh067, 14963106.
91. Borevitz JO, Ecker JR. Plant Genomics: The Third Wave. Annu Rev Genom Hum G 2004, 5:443-477.
92. Kohel RJ, Richmond TR, Lewis CF. Texas Marker-1. A description of a genetic standard for Gossypium hirsutum L. Crop Sci 1970, 10:670-671.
93. Kohel RJ, Yu J, Park Y, Lazo GR. Molecular mapping and characterization of traits controlling fiber quality in cotton. Euphytica 2001, 121:163-172.
94. Dellaporta SL, Wood J, Hicks JP. A plant DNA minipreparation: Version II. Plant Mol Biol Rep 1983, 1:19-21.
95. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 24:4876-4882.
96. Reddy OUK, Pepper AE, Abdurakhmonov I, Saha S, Jenkins JN, Brooks T, Bolek Y, El-Zik K. New Dinucleotide and Trinucleotide Microsatellite Marker Resources for Cotton Genome Research. J Cotton Sci 2001, 5:103-113.
97. Eckert KA, Kunkel TA. High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucleic Acids Res 1990, 18:3739-3744. 10.1093/nar/18.13.3739, 331072, 2374708.
98. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
99. Ma B, Tromp J, Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 2002, 18:440-445. 10.1093/bioinformatics/18.3.440, 11934743.
100. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
101. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980, 16:111-120. 10.1007/BF01731581, 7463489.
102. Swofford D. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4.0 2002, Sinauer Associates, Sunderland, MA, USA.
103. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
104. Jukes TH, Cantor CR. Evolution of protein molecules. Mammalian protein metabolism 1969, 21-123. Academic Press, New York, USA, Munro HN.
105. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986, 3:418-426.
106. Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25:1451-1452. 10.1093/bioinformatics/btp187, 19346325.