Free Access
Issue
Ann. For. Sci.
Volume 66, Number 5, July-August 2009
Article Number 509
Number of page(s) 21
DOI https://doi.org/10.1051/forest/2009037
Published online 09 July 2009
References of  Ann. For. Sci. 66 (2009) 509
  1. Allona I., Quinn M., Shoop E., Swope K., St Cyr S., Carlis J., Riedl J., Retzel E., Campbell M.M., Sederoff R., and Whetten R.W., 1998. Analysis of xylem formation in pine by cDNA sequencing. Proc. Natl. Acad. Sci. USA 95: 9693–9698 [PubMed] [CrossRef].
  2. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J., 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410 [PubMed] [CrossRef].
  3. Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., and Yeh L.S., 2004. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32: D115–D119 [PubMed] [CrossRef].
  4. Bhalerao R., Keskitalo J., Sterky F., Erlandsson R., Bjorkbacka H., Birve S.J., Karlsson J., Gardestrom P., Gustafsson P., Lundeberg J., and Jansson S., 2003. Gene expression in autumn leaves. Plant Physiol. 131: 430–442 [PubMed] [CrossRef].
  5. Bommer U.A. and Thiele B.J., 2004. The translationally controlled tumour protein (TCTP). Int. J. Biochem. Cell Biol. 36: 379–385 [PubMed] [CrossRef].
  6. Cans C., Passer B.J., Shalak V., Nancy-Portebois V., Crible V., Amzallag N., Allanic D., Tufino R., Argentini M., Moras D., Fiucci G., Goud B., Mirande M., Amson R., and Telerman A., 2003. Translationally controlled tumor protein acts as a guanine nucleotide dissociation inhibitor on the translation elongation factor eEF1A. Proc. Natl. Acad. Sci. USA 100: 13892–13897 [PubMed] [CrossRef].
  7. Chagne D., Chaumeil P., Ramboer A., Collada C., Guevara A., Cervera M.T., Vendramin G.G., Garcia V., Frigerio J.M., Echt C., Richardson T., and Plomion C., 2004. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor. Appl. Genet. 109: 1204–1214 [PubMed] [CrossRef].
  8. Chang S., Puryear J., and Cairney J., 1993. A simple and efficient method for isolating RNA from pine trees. Plant Mol. Biol. Rep. 11: 113–116 [CrossRef].
  9. Cho C., Lee H., Chung E., Kim K., Heo J., Kim J., Chung J., Ma Y., Fukui K., Lee D., Kim D., Chung Y., and Lee J., 2007. Molecular characterization of the soybean L-asparaginase gene induced by low temperature stress. Mol. Cells 23: 280–286 [PubMed].
  10. Delectis florae reipublicae popularis sinicae agendae academiae sinicae edita, 1998. Flora : reipublicae popularis sinicae (in Chinese) Science Press, Beijing, Vol. 22, 66–67.
  11. Dieringer D. and Schlotterer C., 2003. Microsatellite analyzer (MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes 3: 167–169 [CrossRef].
  12. Eveno E., Collada C., Guevara M.A., Leger V., Soto A., Diaz L., Leger P., Gonzalez-Martinez S.C., Cervera M.T., Plomion C., and Garnier-Gere P.H., 2008. Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses. Mol. Biol. Evol. 25: 417–437.
  13. Ewing B. and Green P., 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186–194.
  14. Ewing B., Hillier L., Wendl M.C., and Green P., 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8: 175–185.
  15. Ewing R.M., Ben Kahla A., Poirot O., Lopez F., Audic S., and Claverie J.M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9: 950–959
  16. Finn R.D., Tate J., Mistry J., Coggill P.C., Sammut S.J., Hotz H.R., Ceric G., Forslund K., Eddy S.R., Sonnhammer E.L., and Bateman A., 2008. The Pfam protein families database. Nucleic Acids Res. 36: D281–D288 [PubMed] [CrossRef].
  17. Fukuoka H., Nunome T., Minamiyama Y., Kono I., Namiki N., and Kojima A., 2005. Read2Marker: a data processing tool for microsatellite marker development from a large data set. Biotechniques 39: 472 [PubMed] [CrossRef], 474, 476.
  18. Girke T., Lauricha J., Tran H., Keegstra K., and Raikhel N., 2004. The cell wall navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol. 136: 3003–3008; discussion 3001.
  19. Grant M. and Bevan M.W., 1994. Asparaginase gene expression is regulated in a complex spatial and temporal pattern in nitrogen-sink tissues. Plant J. 5: 695–704 [CrossRef].
  20. Green P., Documentation for phrap and cross_match. 1999. [online] Available from http://bozeman.mbt.washington.edu/phrap.docs/phrap.html [accessed 7 March 2007].
  21. Guillaumie S., San-Clemente H., Deswarte C., Martinez Y., Lapierre C., Murigneux A., Barriere Y., Pichon M., and Goffner D., 2007. MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize. Plant Physiol. 143: 339–363.
  22. Iseli C., Jongeneel C.V., and Bucher P., 1999. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 138–148.
  23. Kado T., Yoshimaru H., Tsumura Y., and Tachida H., 2003. DNA variation in a conifer, Cryptomeria japonica (Cupressaceae sensu lato). Genetics 164: 1547–1559 [PubMed].
  24. Kane N.C. and Rieseberg L.H., 2007. Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics 175: 1823–1834 [PubMed] [CrossRef].
  25. Kantety R.V., La Rota M., Matthews D.E., and Sorrells M.E., 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501–510 [PubMed] [CrossRef].
  26. Kobayashi S. and Hiroki S., 2003. Patterns of occurrence of hybrids of Castanopsis cuspidata and C. sieboldii in the IBP Minamata Special Research Area, Kumamoto Prefecture, Japan. J. Phytogeogr. Taxon. 51: 63–67.
  27. Kobayashi Y. and Sugawa T., 1959. Identification of wood of some Castanopsis species in Japan (in Japanese with English abstract). Bull. Gov. For. Exp. Stn. 118: 139–178.
  28. Kondo H., Tahira T., Hayashi H., Oshima K., and Hayashi K., 2000. Microsatellite genotyping of post-PCR fluorescently labeled markers. Biotechniques 29: 868–872 [PubMed].
  29. Kumpatla S.P. and Mukhopadhyay S., 2005. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48: 985–998 [PubMed] [CrossRef].
  30. Manos P.S. and Stanford A.M., 2001. The historical biogeography of Fagaceae: Tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. Int. J. Plant Sci. 162: S77–S93 [CrossRef].
  31. Metzgar D., Bytof J., and Wills C., 2000. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res. 10: 72–80 [PubMed].
  32. Moriguchi Y., Iwata H., Ujino-Ihara T., Yoshimura K., Taira H., and Tsumura Y., 2003. Development and characterization of microsatellite markers for Cryptomeria japonica D. Don. Theor. Appl. Genet. 106: 751–758.
  33. Murray M.G. and Thompson W.F., 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321–4325 [PubMed] [CrossRef].
  34. Nanjo T., Futamura N., Nishiguchi M., Igasaki T., Shinozaki K., and Shinohara K., 2004. Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol. 45: 1738–1748 [PubMed] [CrossRef].
  35. Navabpour S., Morris K., Allen R., Harrison E., S A.H.-M., and Buchanan-Wollaston V., 2003. Expression of senescence-enhanced genes in response to oxidative stress. J. Exp. Bot. 54: 2285–2292 [PubMed] [CrossRef].
  36. Nei M. and Kumar S., 2000. Molecular evolution and phylogenetics, Oxford University Press, New York, 333 p.
  37. Parkinson J., Anthony A., Wasmuth J., Schmid R., Hedley A., and Blaxter M., 2004. PartiGene–constructing partial genomes. Bioinformatics 20: 1398–1404 [PubMed] [CrossRef].
  38. Parkinson J., Guiliano D.B., and Blaxter M., 2002. Making sense of EST sequences by CLOBBing them. BMC Bioinformatics 3: 31 [PubMed] [CrossRef].
  39. Pashley C.H., Ellis J.R., McCauley D.E., and Burke J.M., 2006. EST databases as a source for molecular markers: lessons from Helianthus. J. Hered. 97: 381–388 [PubMed] [CrossRef].
  40. Pavy N., Paule C., Parsons L., Crow J.A., Morency M.J., Cooke J., Johnson J.E., Noumen E., Guillet-Claude C., Butterfield Y., Barber S., Yang G., Liu J., Stott J., Kirkpatrick R., Siddiqui A., Holt R., Marra M., Seguin A., Retzel E., Bousquet J., and MacKay J., 2005. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6: 144 [PubMed] [CrossRef].
  41. Petit R.J., El Mousadik A., and Pons O., 1998. Identifying populations for conservation on the basis of genetic markers. Conserv. Biol. 12: 844–855 [CrossRef].
  42. Raes J., Rohde A., Christensen J.H., Van de Peer Y., and Boerjan W., 2003. Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 133: 1051–1071 [PubMed] [CrossRef].
  43. Rozen S. and Skaletsky H.J., 2000. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S.A. and Misener S. (Eds.), Bioinformatics methods and protocols: Methods in molecular biology, Humana Press, Totowa, pp. 365–386.
  44. Rungis D., Berube Y., Zhang J., Ralph S., Ritland C.E., Ellis B.E., Douglas C., Bohlmann J., and Ritland K., 2004. Robust simple sequence repeat markers for spruce (Picea spp.) from expressed sequence tags. Theor. Appl. Genet. 109: 1283–1294 [PubMed] [CrossRef].
  45. Stephenson P., Collins B.A., Reid P.D., and Rubinstein B., 1996. Localization of ubiquitin to differentiating vascular tissues. Am. J. Bot. 83: 140–147 [CrossRef].
  46. Sterky F., Regan S., Karlsson J., Hertzberg M., Rohde A., Holmberg A., Amini B., Bhalerao R., Larsson M., Villarroel R., Van Montagu M., Sandberg G., Olsson O., Teeri T.T., Boerjan W., Gustafsson P., Uhlen M., Sundberg B., and Lundeberg J., 1998. Gene discovery in the wood-forming tissues of poplar: analysis of 5, 692 expressed sequence tags. Proc. Natl. Acad. Sci. USA 95: 13330–13335 [PubMed] [CrossRef].
  47. Sterky F., Bhalerao R.R., Unneberg P., Segerman B., Nilsson P., Brunner A.M., Charbonnel-Campaa L., Lindvall J.J., Tandre K., Strauss S.H., Sundberg B., Gustafsson P., Uhlen M., Bhalerao R.P., Nilsson O., Sandberg G., Karlsson J., Lundeberg J., and Jansson S., 2004. A Populus EST resource for plant functional genomics. Proc. Natl. Acad. Sci. USA 101: 13951–13956 [PubMed] [CrossRef].
  48. Tamura K., Dudley J., Nei M., and Kumar S., 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596–1599 [PubMed] [CrossRef].
  49. Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S., and McCouch S., 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441–1452 [PubMed] [CrossRef].
  50. Tsumura Y., Kado T., Takahashi T., Tani N., Ujino-Ihara T., and Iwata H., 2007. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 176: 2393–2403 [PubMed] [CrossRef].
  51. Ueno S., Taguchi Y., and Tsumura Y., 2008. Microsatellite markers derived from Quercus mongolica var. crispula (Fagaceae) inner bark expressed sequence tags. Genes Genet. Syst. 83: 179–187 [PubMed] [CrossRef].
  52. Ueno S., Yoshimaru H., Kawahara T., and Yamamoto S., 2000. Isolation of microsatellite markers in Castanopsis cuspidata var. sieboldii Nakai from an enriched library. Mol. Ecol. 9: 1188–1190 [PubMed].
  53. Ueno S., Yoshimaru H., Kawahara T., and Yamamoto S., 2003. A further six microsatellite markers for Castanopsis cuspidata var. sieboldii Nakai. Conserv. Genet. 4: 813–815 [CrossRef].
  54. Ujino-Ihara T., Yoshimura K., Ugawa Y., Yoshimaru H., Nagasaka K., and Tsumura Y., 2000. Expression analysis of ESTs derived from the inner bark of Cryptomeria japonica. Plant Mol. Biol. 43: 451–457 [PubMed] [CrossRef].
  55. Yamada H. and Miyaura T., 2003. Geographic occurrence of intermediate type between Castanopsis sieboldii and C. cuspidata (Fagaceae) based on the structure of leaf epidermis. J. Plant Res. 116: 477–482 [PubMed] [CrossRef].
  56. Yamaguchi-Shinozaki K. and Shinozaki K., 1993. The plant hormone abscisic acid mediates the drought-induced expression but not the seed-specific expression of rd22, a gene responsive to dehydration stress in Arabidopsis thaliana. Mol. Gen. Genet. 238: 17–25 [PubMed].
  57. Yamanaka T., 1966. Problems of Castanopsis cuspidata Schottky (in Japanese with English abstract). Bull. Fac. Educ., Kochi Univ. 18: 65–73.
  58. Yamazaki T. and Mashiba S., 1987a. A taxonomical revision of Castanopsis cuspidata (Thunb.) Schottky and the allies in Japan, Korea and Taiwan (1). J. Jap. Bot. 62: 289–298.
  59. Yamazaki T. and Mashiba S., 1987b. A taxonomical revision of Castanopsis cuspidata (Thunb.) Schottky and the allies in Japan, Korea and Taiwan (2). J. Jap. Bot. 62: 332–339.
  60. Yasodha R., Sumathi R., Chezhian P., Kavitha S., and Ghosh M., 2008. Eucalyptus microsatellites mined in silico: survey and evaluation. J. Genet. 87: 21–25 [PubMed] [CrossRef].
  61. Zhang L., Yu S., Cao Y., Wang J., Zuo K., Qin J., and Tang K., 2006. Distributional gradient of amino acid repeats in plant proteins. Genome 49: 900–905 [PubMed] [CrossRef].