Shedding light on an extremophile lifestyle through transcriptomics

New Phytologist

Volumn 183, Issue 3, 2009, Pages 764-775

  Dassanayake, M ^a   Haas, J S ^a   Bohnert, H J ^a   Cheeseman, J M ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

454 pyrosequencing; Convergent evolution; Ecogenomics; Extremophiles; Functional genomics; Mangrove; Transcriptome profiling

Indexed keywords

MESSENGER RNA;

CONVERGENT EVOLUTION; DICOTYLEDON; ECOPHYSIOLOGY; EXTREMOPHILE; GENE EXPRESSION; GENETIC ANALYSIS; INTERTIDAL COMMUNITY; LIFE HISTORY TRAIT; MANGROVE; PHYLOGENETICS; RNA; SURVIVAL;

ARTICLE; CONTIG MAPPING; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLANT GENE; RHIZOPHORACEAE;

CONTIG MAPPING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; RHIZOPHORACEAE; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA;

ARABIDOPSIS; HERITIERA LITTORALIS; MAGNOLIOPHYTA; MALVACEAE; POPULUS; RHIZOPHORA MANGLE; RHIZOPHORACEAE;

EID: 67650915750     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2009.02913.x     Document Type: Article

References (53)

1. Agaton C, Unneberg P, Sievertzon M, Holmberg A, Ehn M, Larsson M, Odeberg J, Uhlén M, Lundeberg J. 2002. Gene expression analysis by signature pyrosequencing. Gene 289 : 31 39.
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 Research 25 : 3389 3402.
3. Banzai T, Hershkovits G, Katcoff DJ, Hanagata N, Dubinsky Z, Karube I. 2002. Identification and characterization of mRNA transcripts differentially expressed in response to high salinity by means of differential display in the mangrove, Bruguiera gymnorrhiza. Plant Science 162 : 499 505.
4. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS. 2007. SNP discovery via 454 transcriptome sequencing. Plant Journal 51 : 910 918.
5. Bogdanovaa EA, Shaginab DA, Lukyanov SA. 2008. Normalization of full-length enriched cDNA. Molecular BioSystems 4 : 205 212.
6. Bräutigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber APM. 2008. Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in nonmodel species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. Journal of Biotechnology 136 : 44 53.
7. Chase M. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141 : 399 436.
8. Cheung F, Haas B, Goldberg S, May G, Xiao Y, Town C. 2006. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. BMC Genomics 7 : 272.
9. Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Levesque CA, Tisserat N, Buell CR. 2008. Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics 9 : 542.
10. Conant GC, Wagner A. 2003. Convergent evolution of gene circuits. Nature Genetics 34 : 264 266.
11. Crooks JA. 2002. Characterizing ecosystem-level consequences of biological invasions: the role of ecosystem engineers. Oikos 97 : 153 166.
12. Doolittle RF. 1994. Convergent evolution: the need to be explicit. Trends in Biochemical Sciences 19 : 15 18.
13. Droege M, Hill B. 2008. The Genome Sequencer FLX(TM) System - longer reads, more applications, straight forward bioinformatics and more complete data sets. Journal of Biotechnology 136 : 3 10.
14. Duke NC, Ball MC, Ellison JC. 1998. Factors influencing biodivesity and distributional gradients in mangroves Global Ecology and Biogeography Letters 7 : 27 47.
15. Eddy J, Faud T. 1996. Global climate change impacts on habitats: assessing ecological implications of changes in climate. Bulletin of the Ecological Society of America 77 : 109 122.
16. Ellison AM, Farnsworth EJ, Merkt RE. 1999. Origins of mangrove ecosystems and the mangrove biodiversity anomaly. Global Ecology and Biogeography 8 : 95 115.
17. Emrich SJ, Barbazuk WB, Li L, Schnable PS. 2007. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Research 17 : 69 73.
18. Feller IC, McKee KL, Whigham DF, O'Neill JP. 2003. Nitrogen vs. phosphorus limitation across an ecotonal gradient in a mangrove forest. Biogeochemistry 62 : 145 175.
19. Flowers TJ, Troke PF, Yeo AR. 1977. The mechanism of salt tolerance in halophytes. Annual Review of Plant Physiology 28 : 89 121.
20. Garcia-Reyero N, Griffitt RJ, Liu L, Kroll KJ, Farmerie WG, Barber DS, Denslow ND. 2008. Construction of a robust microarray from a nonmodel species largemouth bass, Micropterus salmoides (Lacepède), using pyrosequencing technology. Journal of Fish Biology 72 : 2354 2376.
21. Gharizadeh B, Herman ZS, Eason RG, Jejelowo O, Pourmand N. 2006. Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing. Electrophoresis 27 : 3042 3047.
22. Huse S, Huber J, Morrison H, Sogin M, Welch D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8 : R143.
23. Inan G, Zhang Q, Li P, Wang Z, Cao Z, Zhang H, Zhang C, Quist TM, Goodwin SM, Zhu J et al. 2004. Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development in extremophiles. Plant Physiology 135 : 1718 1737.
24. Kandil FE, Grace MH, Seigler DS, Cheeseman JM. 2004. Polyphenolics in Rhizophora mangle L. leaves and their changes during leaf development and senescence. Trees 18 : 518 528.
25. Karrenberg S, Widmer A. 2008. Ecologically relevant genetic variation from a non-Arabidopsis perspective. Current Opinion in Plant Biology 11 : 156 162.
26. Liang S, Zhou R, Dong S, Shi S. 2008. Adaptation to salinity in mangroves: implication on the evolution of salt-tolerance. Chinese Science Bulletin 53 : 1708 1715.
27. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M et al. 2007. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nature Methods 4 : 495 500.
28. Melzer S, Lens F, Gennen J, Vanneste S, Rohde A, Beeckman T. 2008. Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana. Nature Genetics 40 : 1489 1492.
29. Miyama M, Hanagata N. 2007. Microarray analysis of 7029 gene expression patterns in Burma mangrove under high-salinity stress. Plant Science 172 : 948 957.
30. Miyama M, Shimizu H, Sugiyama M, Hanagata N. 2006. Sequencing and analysis of 14 842 expressed sequence tags of burma mangrove, Bruguiera gymnorrhiza. Plant Science 171 : 234 241.
31. Novaes E, Drost D, Farmerie W, Pappas G, Grattapaglia D, Sederoff R, Kirst M. 2008. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9 : 312.
32. Paliyavuth C, Clough B, Patanaponpaiboon P. 2004. Salt uptake and shoot water relations in mangroves. Aquatic Botany 78 : 349 360.
33. Parani M, Lakshmi M, Senthikumar P, Ram N, Parida A. 1998. Molecular phylogeny of mangroves V. Analysis of genome relationships in mangrove species using RAPD and RFLP markers. Theoretical and Applied Genetics 97 : 617 625.
34. Phillippy A, Schatz M, Pop M. 2008. Genome assembly forensics: finding the elusive mis-assembly. Genome Biology 9 : R55.
35. Plaziat J-C, Cavagnetto C, Koeniguer J-C, Baltzer F. 2001. History and biogeography of the mangrove ecosystem, based on a critical reassessment of the paleontological record. Wetlands Ecology and Management 9 : 161 180.
36. Pop M, Salzberg SL. 2008. Bioinformatics challenges of new sequencing technology. Trends in Genetics 24 : 142 149.
37. Popp M. 1984. Chemical composition of Australian mangroves I. Inorganic ions and organic acids. Zeitschrift für Pflanzenphysiologie 113 : 395 409.
38. Poroyko V, Hejlek LG, Spollen WG, Springer GK, Nguyen HT, Sharp RE, Bohnert HJ. 2005. The maize root transcriptome by serial analysis of gene expression. Plant Physiology 138 : 1700 1710.
39. Proffitt CE, Travis SE. 2005. Albino mutation rates in red mangroves (Rhizophora mangle L.) as a bioassay of contamination history in Tampa Bay, Florida, USA. Wetlands 25 : 326 334.
40. Reusch T, Wood T. 2007. Molecular ecology of global change. Molecular Ecology 16 : 3973 3992.
41. Rieder MJ, Taylor SL, Tobe VO, Nickerson DA. 1998. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Research 26 : 967 973.
42. Saenger P. 2002. Mangrove ecology, silviculture and conservation. Berlin, Germany : Springer.
43. Scholander PF, Hammel HT, Hemmingsen E, Garey W. 1962. Salt balance in mangroves. Plant Physiology 37 : 722 729.
44. Soltis DE, Soltis PS, Chase MW, Mort ME, Albach DC, Zanis M, Savolainen V, Hahn WH, Hoop SB, Fay MF et al. 2000. Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequences. Botanical Journal of the Linnean Society 133 : 381 461.
45. Stiller JW, DeEtte C, Jeffrey R, Johnson C. 2003. A single origin of plastids revisited: convergent evolution in organellar genome content. Journal of Phycology 39 : 95 105.
46. Swaminathan K, Varala K, Hudson M. 2007. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 8 : 132.
47. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The clustal-x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25 : 4876 4882.
48. Tomlinson PB. 1986. The botany of mangroves. Cambridge, UK : Cambridge University Press.
49. Torres T, Metta M, Ottenwälder B, Schlötterer C. 2008. Gene expression profiling by massively parallel sequencing. Genome Research 18 : 172 177.
50. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 17 : 1636 1647.
51. Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. 2007. Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiology 144 : 32 42.
52. Wicker T, Schlagenhauf E, Graner A, Close T, Keller B, Stein N. 2006. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7 : 275.
53. Wooller MJ, Behling H, Smallwood B, Fogel M. 2004. Mangrove ecosystem dynamics and elemental cycling at Twin Cays, Belize, during the Holocene. Journal Of Quaternary Science 19 : 1 9.