Comparative Study on Phylogenetics and Sequences Composition of Bamboos and Cereals

FAN Long-jiang; GUO Xing-yi; MA Nai-xun

Volume 19 Issue 2

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Comparative Study on Phylogenetics and Sequences Composition of Bamboos and Cereals

1.
Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, Zhejiang, China
2.
Research Institute of Subtropical Forestry, CAF, Fuyang 311400, Zhejiang, China

Received Date: 2005-03-30

Abstract

Phylogenetics and Sequence composition of bamboos and cereals were analyzed based on current 8 full-length mRNA sequences in the public nucleotides databases.The results indicated that bamboos had more shorter phylogenetic distance and similar sequence composition(GC content and codon usage)with rice than other cereals.The results suggested that rice,as model plant for Poaceae,should have significant genomic synteny with bamboos,and its genomic sequences are important resource for bamboo genome research.
- bamboo,
- rice,
- phylogenetics,
- GC content,
- codon usage

References

[1]	傅懋毅,杨校生. 我国竹类研究展望与竹林生境利用[J]. 竹类研究汇刊, 2003, 22 (2) : 1～8
[l8] Rice P, Longden I, Bleasby A. EMBOSS. The European MolecularBiology Open Softwar Suite [J /OL]. Trends in Genetics, 2000, 16(6) : 276～277. http: / /www. uk. embnet. org/Software EMBOSS/
[3]	马乃训. 中国竹类植物生物多样性及其开发利用[A] ,见:竺肇华. 中国热带地区竹藤发展[M] 1北京:中国林业出版社, 2001:36～46
[4]	Benson D A, Karsch-Mizrachi I, Lipman D J, et al. GenBank: update1Nucleic Acids. Res. 2004, 32 (Database issue) : D23-6. www[J /OL]. ncbi. nlm. nih. org
[5]	Guo Z H, Chen Y Y,LiD Z, et al. Genetic Variation and Evolution ofthe Alp ine Bamboos (Poaceae: Bambusoideae) using DNA SequenceData[J]. Plant Res, 2001, 114: 315～322
[6]	Guo Z H, Chen Y Y,LiD Z. Phylogenetic Studies on the Tham nocalam us Group and ltsAllies(Gramineae: Bambusoideae) Based on ITSSequence Data[J]. Mol Phylogenet Evol, 2002, 22 (l) : 20～30
[7]	Guo Z H,Li D Z. Phylogenetics of the Tham nocalam us group and itsallies (Gramineae: Bambusoideae) : inference from the seqdences ofGBSSI gene and ITS spacer[J]. Mol Phylogenet Evol, 2004, 30: 1～12
[8]	Mason-Gamer R J, Weil C F, Kellogg E A.Granule-bound starchSynthase: Structure, function, and phylogenetid utility [J]. Mol BiolEvol, 1998, 15 (12) : 1658～1673
[9]	Nadot S,Bittar G, CarterL, et al. A phylogenetic analysis ofmonocotyledons based on the chlorop last gene rp s4, using parsimony and anew numerical phenetics method [J]. Mol Phylogenet Evol, 1995, 4(3) : 257～282
[10]	ZhangW. Phylogeny of the grass family (Poaceae) from rp116 intronSequence data[J]. Mol Phylogenet Evol, 2000, 15 (1) : 135～146
[11]	Clark L G, ZhangW,Wendel J F. A Phylogeny of the Grass Family(Poaceae) Based on ndhF Sequence Data [J]. Syst Bot, 1995, 20(4) : 436～460
[12]	Mathews S, Tsai R C, Kellogg E A. Phylogenetic Structure in thegrass family(Poaceae) : evidene from the nuclear gene phytochromeB [J]. Am J Bot, 2000, 87 (1) : 96～107
[13]	GautB S, Peek A S,Morton B R, et al. Patterns of genetic diversiffication within the Adh gene family in the grasses (Poaceae) [J].Mol Biol Evol, 1999, 16 (8) : 1086～1097
[14]	Hilu KW,Alice L A, Liang H. Phylogeny of Poaceae inferred frommatK Sequences[J]. AnnMo Bot Gard, 1999, 86 (4) : 835～851
[15]	Kap linsky N J,Braun D M, Penterman J, et al. Utility and distribution of conserved noncoding sequences in the grasses[J]. Proc NatlAcad Sci USA, 2002, 99: 617～651
[16]	Baner P, LubkowitzM, Tyers R, et al. Regulation and a conservedintron sequence of liguleless3 /4knox class-I homeobox genes ingrasses[J]. Planta, 2004, 219: 359～368
[17]	Matsui T, Hatase Y, Ohobayashi K. A wound-induced ACC oxidasegene ofMoso Bamboo Shoot[J]. Pak J Biol Sci, 2001, 4: 228～232
[18]	Matsui T, Yokozeki Y, Inoue H. A wound-induced ACC SynthaseGene ofMoso Bamboo Shoot[J]. Asian J Plant Sci, 2003, 2: 205～211
[19]	Yany Z. Phylogenetic Analysis by Maximum Likelihood (PAML)Version 2 [M]. London: University College, 1999
[20]	Goldman N, Yang Z. A codon - based model of nucleotide substitution for p rotein - coding DNA sequences[J]. Mol Biol Evol, 1994,11: 725～736
[21]	Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from theinternational DNA sequence databases: status for the year 2000. Nucl. Acids Res. [J /OL] , 2000, 28: 292. http: / /www. kazusa. or. jpcodon
[22]	Gaut B S,Morton B R,MccaigBM, et al. Substitution rate comparisons between grasses and palms: synonymous rate differences at thenuclear gene Adh parallel rate differences at the p lastid gene rbeL[J]. Proc Natl Acad Sci USA, l996, 93: 10274～10279
[23]	Wong G K,Wang J, Tao L, et al. Compositional gradents in Gramineae genes[J]. Genome Res, 2002, 12: 851～856
[24]	Tian Y, Fan L, Thurau T, et al. The absene of TIR2type resistancegene analogues in sugar beet (B eta vulgaris L.) genome [J]. J MolEvol, 2004, 58 (1) : 40～53
[25]	GPWG(Grass PhylogenyWorking Group) . Phylogeny and subfamilial classification of the grasses (Poaceae) [J]. Annals of MissouriBotanical Garden, 2001, 88: 373～457
[26]	查普曼G P,皮特W E1禾本科植物导论(包括竹子及禾谷类作物) [M]. 王彦荣译. 北京:科学出版社, 1996: 30～49
[27]	Gielis J. Up stream Fundamental Research in Bamboo: Possibilitiesand Directions [A]. In: Proceedings of Vth International BambooCongres, Costa Rica, 1999
[28]	GaleM P,Devos KM. Comparative genetics in the grasses[J]. ProcNatl Acad Sci USA, 1998, 95: 1971～1974
[29]	The rice chromosome 10 sequencing consortium. In-dep th view ofstructur, activity, and evolution of rice chromosome 10 [J]. Science,2003, 300: 1566～1569
[30]	Paterson A H, Bowers J E, Chapman B A. Ancient polyp loidizationp redating divergence of the cereals and its consequences for comparative genomics [J]. Proc Natl Acad Sci USA, 2004, 101: 9903 ～9908
[31]	Zhang Y, Xu G, Guo X, et al. Two ancient rounds of polyp loidy inrice genome[J]. J Zhejiang Univ(SCIENCE) , 2005, 6B: 87～90

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通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Comparative Study on Phylogenetics and Sequences Composition of Bamboos and Cereals

1. Institute of Crop Science/Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, Zhejiang, China

2. Research Institute of Subtropical Forestry, CAF, Fuyang 311400, Zhejiang, China

Received Date: 2005-03-30

Abstract: Phylogenetics and Sequence composition of bamboos and cereals were analyzed based on current 8 full-length mRNA sequences in the public nucleotides databases.The results indicated that bamboos had more shorter phylogenetic distance and similar sequence composition(GC content and codon usage)with rice than other cereals.The results suggested that rice,as model plant for Poaceae,should have significant genomic synteny with bamboos,and its genomic sequences are important resource for bamboo genome research.

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Reference (31)

[1]	傅懋毅,杨校生. 我国竹类研究展望与竹林生境利用[J]. 竹类研究汇刊, 2003, 22 (2) : 1～8
[2]	[l8] Rice P, Longden I, Bleasby A. EMBOSS. The European MolecularBiology Open Softwar Suite [J /OL]. Trends in Genetics, 2000, 16(6) : 276～277. http: / /www. uk. embnet. org/Software EMBOSS/
[3]	马乃训. 中国竹类植物生物多样性及其开发利用[A] ,见:竺肇华. 中国热带地区竹藤发展[M] 1北京:中国林业出版社, 2001:36～46
[4]	Benson D A, Karsch-Mizrachi I, Lipman D J, et al. GenBank: update1Nucleic Acids. Res. 2004, 32 (Database issue) : D23-6. www[J /OL]. ncbi. nlm. nih. org
[5]	Guo Z H, Chen Y Y,LiD Z, et al. Genetic Variation and Evolution ofthe Alp ine Bamboos (Poaceae: Bambusoideae) using DNA SequenceData[J]. Plant Res, 2001, 114: 315～322
[6]	Guo Z H, Chen Y Y,LiD Z. Phylogenetic Studies on the Tham nocalam us Group and ltsAllies(Gramineae: Bambusoideae) Based on ITSSequence Data[J]. Mol Phylogenet Evol, 2002, 22 (l) : 20～30
[7]	Guo Z H,Li D Z. Phylogenetics of the Tham nocalam us group and itsallies (Gramineae: Bambusoideae) : inference from the seqdences ofGBSSI gene and ITS spacer[J]. Mol Phylogenet Evol, 2004, 30: 1～12
[8]	Mason-Gamer R J, Weil C F, Kellogg E A.Granule-bound starchSynthase: Structure, function, and phylogenetid utility [J]. Mol BiolEvol, 1998, 15 (12) : 1658～1673
[9]	Nadot S,Bittar G, CarterL, et al. A phylogenetic analysis ofmonocotyledons based on the chlorop last gene rp s4, using parsimony and anew numerical phenetics method [J]. Mol Phylogenet Evol, 1995, 4(3) : 257～282
[10]	ZhangW. Phylogeny of the grass family (Poaceae) from rp116 intronSequence data[J]. Mol Phylogenet Evol, 2000, 15 (1) : 135～146
[11]	Clark L G, ZhangW,Wendel J F. A Phylogeny of the Grass Family(Poaceae) Based on ndhF Sequence Data [J]. Syst Bot, 1995, 20(4) : 436～460
[12]	Mathews S, Tsai R C, Kellogg E A. Phylogenetic Structure in thegrass family(Poaceae) : evidene from the nuclear gene phytochromeB [J]. Am J Bot, 2000, 87 (1) : 96～107
[13]	GautB S, Peek A S,Morton B R, et al. Patterns of genetic diversiffication within the Adh gene family in the grasses (Poaceae) [J].Mol Biol Evol, 1999, 16 (8) : 1086～1097
[14]	Hilu KW,Alice L A, Liang H. Phylogeny of Poaceae inferred frommatK Sequences[J]. AnnMo Bot Gard, 1999, 86 (4) : 835～851
[15]	Kap linsky N J,Braun D M, Penterman J, et al. Utility and distribution of conserved noncoding sequences in the grasses[J]. Proc NatlAcad Sci USA, 2002, 99: 617～651
[16]	Baner P, LubkowitzM, Tyers R, et al. Regulation and a conservedintron sequence of liguleless3 /4knox class-I homeobox genes ingrasses[J]. Planta, 2004, 219: 359～368
[17]	Matsui T, Hatase Y, Ohobayashi K. A wound-induced ACC oxidasegene ofMoso Bamboo Shoot[J]. Pak J Biol Sci, 2001, 4: 228～232
[18]	Matsui T, Yokozeki Y, Inoue H. A wound-induced ACC SynthaseGene ofMoso Bamboo Shoot[J]. Asian J Plant Sci, 2003, 2: 205～211
[19]	Yany Z. Phylogenetic Analysis by Maximum Likelihood (PAML)Version 2 [M]. London: University College, 1999
[20]	Goldman N, Yang Z. A codon - based model of nucleotide substitution for p rotein - coding DNA sequences[J]. Mol Biol Evol, 1994,11: 725～736
[21]	Nakamura Y, Gojobori T, Ikemura T. Codon usage tabulated from theinternational DNA sequence databases: status for the year 2000. Nucl. Acids Res. [J /OL] , 2000, 28: 292. http: / /www. kazusa. or. jpcodon
[22]	Gaut B S,Morton B R,MccaigBM, et al. Substitution rate comparisons between grasses and palms: synonymous rate differences at thenuclear gene Adh parallel rate differences at the p lastid gene rbeL[J]. Proc Natl Acad Sci USA, l996, 93: 10274～10279
[23]	Wong G K,Wang J, Tao L, et al. Compositional gradents in Gramineae genes[J]. Genome Res, 2002, 12: 851～856
[24]	Tian Y, Fan L, Thurau T, et al. The absene of TIR2type resistancegene analogues in sugar beet (B eta vulgaris L.) genome [J]. J MolEvol, 2004, 58 (1) : 40～53
[25]	GPWG(Grass PhylogenyWorking Group) . Phylogeny and subfamilial classification of the grasses (Poaceae) [J]. Annals of MissouriBotanical Garden, 2001, 88: 373～457
[26]	查普曼G P,皮特W E1禾本科植物导论(包括竹子及禾谷类作物) [M]. 王彦荣译. 北京:科学出版社, 1996: 30～49
[27]	Gielis J. Up stream Fundamental Research in Bamboo: Possibilitiesand Directions [A]. In: Proceedings of Vth International BambooCongres, Costa Rica, 1999
[28]	GaleM P,Devos KM. Comparative genetics in the grasses[J]. ProcNatl Acad Sci USA, 1998, 95: 1971～1974
[29]	The rice chromosome 10 sequencing consortium. In-dep th view ofstructur, activity, and evolution of rice chromosome 10 [J]. Science,2003, 300: 1566～1569
[30]	Paterson A H, Bowers J E, Chapman B A. Ancient polyp loidizationp redating divergence of the cereals and its consequences for comparative genomics [J]. Proc Natl Acad Sci USA, 2004, 101: 9903 ～9908
[31]	Zhang Y, Xu G, Guo X, et al. Two ancient rounds of polyp loidy inrice genome[J]. J Zhejiang Univ(SCIENCE) , 2005, 6B: 87～90

Comparative Study on Phylogenetics and Sequences Composition of Bamboos and Cereals

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通讯作者: 陈斌, bchen63@163.com

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Comparative Study on Phylogenetics and Sequences Composition of Bamboos and Cereals

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