Evaluation of monocot and eudicot divergence using the sugarcane transcriptome

Plant Physiology

Volumn 134, Issue 3, 2004, Pages 951-959

  Vincentz, Michel ^a   Cara, Frank A A ^a   Okura, Vagner K ^a   Da Silva, Felipe R ^a   Pedrosa, Guilherme L ^a   Hemerly, Adriana S ^b   Capella, Adriana N ^a   Marins, Mozart ^c   Ferreira, Paulo C ^b   França, Suzelei C ^c   Grivet, Laurent ^a   Vettore, Andre L ^a   Kemper, Edson L ^a   Burnquist, Willian L ^d   Targon, Maria L P ^e   Siqueira, Walter J ^e   Kuramae, Eiko E ^f   Marino, Celso L ^f   Camargo, Luis E A ^g   Carrer, Helaine ^g   Coutinho, Luis L ^g   Furlan, Luiz R ^f   Lemos, Manoel V F ^f   Nunes, Luiz R ^h   Gomes, Suely L ^g   Santelli, Roberto V ^g   Goldman, Maria H ^g   Bacci Jr , Maurício ^f   Giglioti, Eder A ⁱ   Thiemann, Otávio H ^g   Silva, Flávio H ⁱ   Van Sluys, Marie Anne ^g   Nobrega, Francisco G ^j   Arruda, Paulo ^a   Menck, Carlos F M ^g   more..

^a UNIVERSITY OF CAMPINAS   (Brazil)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c UNIVERSITY OF RIBEIRÃO PRETO   (Brazil)

^d Centro de Tecnologia Copersucar   (Brazil)

^e INSTITUTO AGRONÔMICO   (Brazil)

^f SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^g UNIVERSITY OF SÃO PAULO   (Brazil)

^h UNIVERSIDADE DE MOGI DAS CRUZES   (Brazil)

ⁱ FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

^j INSTITUTO DE PESQUISA E DESENVOLVIMENTO   (Brazil)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENES; GENETIC ENGINEERING; PROTEINS;

GENOME ANALYSIS; MONOCOTS;

SUGAR CANE;

ARABIDOPSIS; ARUNDINARIA; EMBRYOPHYTA; LILIOPSIDA; MAGNOLIOPHYTA; ORYZA SATIVA; SACCHARUM; SACCHARUM HYBRID CULTIVAR; SACCHARUM OFFICINARUM;

EID: 12144291425     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.033878     Document Type: Article

References (51)

1. Allen KD (2002) Assaying gene content in Arabidopsis. Proc Natl Acad Sci USA 99: 9568-9572
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Aravind L, Watanabe H, Lipman DJ, Koonin EV (2000) Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci USA 97: 11319-11324
5. Bergelson J, Kreitman M, Stahl EA, Tian D (2001) Evolutionary dynamics of plant R-genes. Science 292: 2281-2285
6. Braun EL, Halpern AL, Nelson MA, Natvig DO (2000) Large-scale comparison of fungal sequence information: mechanisms of innovation in Neurospora crassa and gene loss in Saccharomyces cerevisiae. Genome Res 10: 416-430
7. Brendel V, Kurtz S, Walbot V (2002) Comparative genomics of Arabidopsis and maize: prospects and limitations. Genome Biol 3: REVIEWS1005
8. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94
9. Copley R, Letunic I, Bork P (2001) Genome and protein evolution in eukaryotes. Curr Opin Chem Biol 6: 39-15
10. Cronk QC (2001) Plant evolution and development in a post-genomic context. Nat Rev Genet 2: 607-619
11. Doebley J, Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10: 1075-1082
12. Emanuelsson O, Nielsen H, von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci 8: 978-984
13. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) Version 3.5c. Department of Genetics, University of Washington, Seattle
14. Felsenstein J (1997) An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol 46: 101-111
15. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X et al. (2002) Sequence and analysis of rice chromosome 4. Nature 420: 316-320
16. Fulton TM, Van der Hoeven R, Eannetta NT, Tanksley SD (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467
17. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
18. Grivet L, Arruda P (2002) Sugarcane genomics: depicting the complex genome of an important tropical crop. Curr Opin Plant Biol 5: 122-127
19. Henikoff S, Greene E, Pietrokovski S, Bork P, Attwood T, Hood L (1997) Gene families: the taxonomy of protein paralogs and chimeras. Science 278: 609-614
20. Kellog E (2001) Evolutionary history of the grasses. Plant Physiol 125: 1198-1205
21. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379
22. Kondrashov F, Rogozin I, Wolf Y, Koonin E (2002) Selection in the evolution of gene duplication. Genome Biol 3: 1-9
23. Koonin EV, Aravind L, Kondrashov AS (2000) The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576
24. Ku HM, Vision T, Liu J, Tanksley SD (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97: 9121-9126
25. Lander E, Linton L, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
26. Liu H, Sachidanandam R, Stein L (2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res 11: 2020-2026
27. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26: 1107-1115
28. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155
29. Poethig RS (2001) Life with 25,000 genes. Genome Res 11: 313-316
30. Quackenbush J, Cho J, Lee D, Llang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29: 159-164
31. Rubin G, Yandell M, Wortman J (2000) Comparative genomics of the eukaryotes. Science 287: 2204-2215
32. Rujan T, Martin W (2001) How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet 17: 113-120
33. Salzberg SL, White O, Peterson J, Eisen JA (2001) Microbial genes in the human genome: lateral transfer or gene loss? Science 292: 1903-1906
34. Sankoff D (2001) Gene and genome duplication. Curr Opin Genet Dev 11: 681-684
35. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y et al. (2002) The genome sequence and structure of rice chromosome 1. Nature 420: 312-316
36. Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res 30: 91-93
37. Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296: 141-145
38. Somerville C, Somerville S (1999) Plant functional genomics. Science 285: 380-383
39. Souza GM, Simoes ACQ, Oliveira KC, Garay HM, Fiorini LC, Gomes FdS, Nishiyama-Junior MY, Silva AM (2001) The sugarcane signal transduction (SUCAST) catalogue: prospecting signal transduction in sugarcane. Genet Mol Biol 24: 25-34
40. Stanhope MJ, Lupas A, Italia MJ, Koretke KK, Volker C, Brown JR (2001) Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411: 940-944
41. Telles GP, Braga MVD, Dias Z, Quitzau JAA, da Silva FR, Meidanis J (2001) Bioinformatics of the sugarcane EST project. Genet Mol Biol 24: 8-15
42. Telles GP, da Silva FR (2001) Trimming and clustering sugarcane ESTs. Genet Mol Biol 1 24: 17-23
43. Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456
44. Vettore AL, da Silva FR, Kemper EL, Arruda P (2001) The libraries that made SUCEST. Genet Mol Biol 24: 1-7
45. Vettore AL, da Silva FR, Kemper EL, Souza GM, Silva AM, Ferro MIT, Henrique-Silva F, Giglioti EA, Lemos MV, Coutinho LL et al. (2003) Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane. Genome Res 13: 2725-2735
46. Vision T, Brown D, Tanksley S (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117
47. Wendel J (2000) Genome evolution in polyploids. Plant Mol Biol 42: 225-249
48. Wikstrom N, Savolainen V, Chase MW (2001) Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B Biol Sci 268: 2211-2220
49. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86: 6201-6205
50. Yang Y, Lai K, Tai P, Li W (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol 48: 597-604
51. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92