Phylogenetic analyses and evolutionary relationships of Saraca asoca with their allied taxa (Tribe-Detarieae) based on the chloroplast matK gene

Journal of Plant Biochemistry and Biotechnology

Volumn 24, Issue 1, 2015, Pages 65-74

  Saha, Jayita ^a   Gupta, Kamala ^a   Gupta, Bhaskar ^a  

^a PRESIDENCY UNIVERSITY   (India)

Author keywords

Detarieae; Disparity index; Maturase K; Maximum likelihood; MEGA; Saraca asoca

Indexed keywords

CAESALPINIOIDEAE; DETARIEAE; ENDERTIA SPECTABILIS; EURYPETALUM TESSMANNII; FABACEAE; LYSIDICE RHODOSTEGIA; SARACA ASOCA; SARACA DECLINATA; SARACA PALEMBANICA;

EID: 84887265834     PISSN: 09717811     EISSN: 09741275     Source Type: Journal    
DOI: 10.1007/s13562-013-0237-3     Document Type: Article

References (52)

1. Asahina H, Shinozaki J, Masuda K, Morimitsu Y, Satake M (2010) Identification of medicinal Dendrobium species by phylogenetic analyses using matK and rbcL sequences. J Nat Med 64:133–138
2. Bruneau A, Breteler FJ, Wieringa JJ, Gervais GYF, Forest F (2000) Phylogenetic relationships in tribes Macrolobieae and Detarieae as inferred from chloroplast trnL intron sequences. In: Herendeen P, Bruneau A (eds) Advances in legume systematic Part 9. Royal Botanic gardens, Kew, pp 121–149
3. Bruneau A, Forest F, Herendeen P, Klitgaard BB, Lewis GP (2001) Phylogenetic relationship in the caesalpnioideae (Leguminosae) as inferred from the chloroplast trnL intron sequences. Syst Bot 26:487–514
4. Bruni I, Mattia FD, Galimberti A, Galasso G, Banfi E, Casiraghi M, Labra M (2010) Identification of poisonous plants by DNA barcoding approach. Int J Leg Med 124(6):595–603. doi:10.1007/s00414-010-0447-3
5. Clark LG, Zhang W, Wendel JF (1995) A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst Bot 20:436–460
6. Clegg MT, Gaut BS, Learn GH, Morton BR (1994) Rates and patterns of chloroplast DNA evolution. Proc Natl Acad Sci U S A 91:6795–6801
7. Ems SC, Morden CW, Dixon CK, Wolfe KH, Depamphilis CW, Palmer JD (1995) Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. Plant Mol Biol 29:721–733
8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
10. Fougere-Danezan M, Herendeen PS, Maumont S, Bruneau A (2010) Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal? Ann Bot 105:311–325
11. Gao T, Sun Z, Yao H, Song J, Zhu Y, Ma X, Chen S (2011) Identification of Fabaceae plants using the DNA barcode matK. Planta Med 77:92–94
12. Guo HY, Wang WW, Yang N, Guo BL, Zhang S, Yang RJ, Yuan Y, Yu JL, Hu SN, Sun Q, Yu J (2010) DNA barcoding provides distinction between Radix Astragali and its adulterants. Sci China Life Sci 53:992–999
13. Herendeen P, Lewis GP, Bruneau A (2003) Floral morphology in caesalpinioid legumes: testing the monophyly of the ‘Umtiza clade’. Int J Plant Sci 164:393–407
14. Hilu KW, Liang H (1997) The matK gene: sequence variation and application in plant systematics. Am J Bot 84:830–839
15. Holmquist R (1983) Transitions and transversion in evolutionary descent: an approach to understanding. J Mol Evol 19:134–144
16. Howe CJ, Barbrook AC, Koumandou VL, Nisbet RER, Symington HA, Wightman TF (2003) Evolution of the chloroplast genome. Phil Trans R Soc Lond B 358:99–107
17. Ito M, Kawamoto A, Kita Y, Yukawa T, Kurita S (1999) Phylogenetic relationships of Amaryllidaceae based on matK sequence data. J Plant Res 112:207–216
18. Johnson LS, Soltis DE (1995) Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann Mo Bot Gard 82:149–175
19. Kelchner SA (2000) The evolution of noncoding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard 87:482–498
20. Khidir WH, Hongping L (1997) The matK gene: sequence variation and application in plant systematics. Am J Bot 19:830–839
21. Kim DK, Kim JH (2011) Molecular phylogeny of tribe Forsythieae (Oleaceae) based on nuclear ribosomal DNA internal transcribed spacers and plastid DNA trnL-F and matK gene sequences. J Plant Res 124:339–347. doi:10.1007/s10265-010-0383-9
22. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
23. Kosakovsky P, Sergei L, Frost SDW (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 22:1208–1222
24. Kumar S, Gadagkar SR (2001) Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158:1321–1327
25. Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci U S A 105:2923–2928
26. Lake JA (1987) A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol 4:167–191
27. Lee J, Hymowitz T (2001) A molecular phylogenetic study of the subtribe Glycininae (Leguminosae) derived from the chloroplast DNA Rps16 Intron Sequences. Am J Bot 88(11):2064–2073
28. Lu JM, Wen J, Lutz S, Wang YP, Li DZ (2012) Phylogenetic relationships of Chinese Adiantum based on five plastid markers. J Plant Res 125:237–249. doi:10.1007/s10265-011-0441-y
29. Mercure M, Lewis GP, Bruneau A, Herendeen PS (2008) Phylogenetic patterns and diversification in the caesalpinioid legumes. 86(7):697–718
30. Moritz C, Schneider CJ, Wake DB (1992) Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst Biol 41:273–291
31. Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715–724
32. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426
33. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
34. Potter D, Gao F, Bortiri PE, Oh SH, Baggett S (2002) Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data. Plant Systemat Evol 231:77–89
35. Quicke DLJ (1993) Principle and techniques of contemporary taxonomy. Chapman & Hall, Glasgow
36. Redden KM, Herendeen PS, Wurdack KJ (2010) Phylogenetic relationships of the Northeastern South American Brownea Clade of tribe Detarieae (Leguminosae: Caesalpinioideae) based on morphology and molecular data. Syst Bot 35(3):524–533
37. Reddy BU (2009) A phylogenetic analysis of the Cucurbitaceae: evidences from matK nucleotide sequences. Int J Bioinformatics Res 1(2):47–53
38. Saha J, Gupta K, Gupta B (2013) A new insight into the phylogeny of vascular cryptogams with special reference to Lycophytes inferred from nuclear ITS/5.8S rDNA sequences. J Plant Biochem Biotechnol [In-Press] dx.doi.org/10.1007/s13562-013-0198-6
39. Saha J, Mitra T, Gupta K, Mukherjee S (2012) Phytoconstituents and HPTLC analysis in saraca asoca (roxb.)Wilde. Int J Pharm Sci 4(l):96–99
40. Salazar GA, Chase MW, Soto Arenas MA, Ingrouille MJ (2003) Phylogenetics of Cranichdeae with emphasis on Spiranthinae (Orchidaceae, Orchidoideae): evidence from plastid and nuclear DNA sequences. Am J Bot 90:777–795
41. Selvaraj D, Sarma RK, Sathishkumar R (2008) Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding. Bioinformation 3(1):24–27
42. Sergei L, Kosakovsky P, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676–679
43. Soltis DE, Soltis PS (1998) Choosing an approach and an appropriate gene for phylogenetic analysis. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Dordrecht, pp 21–24
44. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035
45. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
46. Tucker SC (2000a) Evolutionary loss of sepals and/or petals in Detarioid legume taxa Aphanocalyx, Brachystegia, and Monopetalanthus (Leguminosae: Caesalpinioideae). Am J Bot 87:608–624
47. Tucker SC (2000b) Floral development and homeosis in Saraca (Leguminosae: Caesalpinioideae: Detarieae). Int J Plant Sci 161:537–549
48. Tucker SC (2001) The ontogenetic basis for missing petals in Crudia (Leguminosae: Caesalpinioideae: Detarieae). Int J Plant Sci 162:83–89
49. Vijayan K, Tsou CH (2010) DNA barcoding in plants: taxonomy in a new perspective. Curr Sci 99(11):1530–1541
50. Whitfeld PR, Bottemley W (1983) Organization and structure of chloroplast genes. Annu Rev Plant Physiol 34:279–310
51. Wojciechowski MF, Lavin M, Sanderson MJ (2004) A phylogeny of legumes (leguminosae) based on analysis of the plastid matk gene resolves many well-supported subclades within the family. Am J Bot 91(11):1846–1862
52. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic, New York, pp 97–166