Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Li, Xinguo ^a   Wu, Harry X ^a   Dillon, Shannon K ^a   Southerton, Simon G ^a  

^a CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; CELLULASE; CHITINASE; COMPLEMENTARY DNA; LACCASE; PATULIN; PECTATE LYASE; TRANSCRIPTION FACTOR; TRANSCRIPTOME; TUBULIN; URIDINE DIPHOSPHATE GLUCOSE DEHYDROGENASE; PLANT RNA;

ARTICLE; CELL WALL; CLONE; COMPARATIVE GENOMIC HYBRIDIZATION; DATA BASE; DEVELOPMENTAL STAGE; DNA LIBRARY; EXPRESSED SEQUENCE TAG; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PINE; PLANT DEVELOPMENT; PLANT GENETICS; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; XYLEM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GENOMICS; PLANT GENE; PLANT GENOME;

PINUS RADIATA; RADIATA;

CELL WALL; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENES, PLANT; GENOME, PLANT; GENOMICS; PINUS; RNA, PLANT; TRANSCRIPTION FACTORS; XYLEM;

EID: 60549112895     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-41     Document Type: Article

References (87)

1. Wu HX Eldridge KG Matheson AC Powell MP McRae TA Achievement in forest tree improvement in Australia and New Zealand 8. Successful introduction and breeding of radiata pine to Australia Australian Forestry 2007, 70:215-225.
2. Powell MB McRae TA Wu HX Dutkowski GW Pilbeam DJ Breeding Strategy for Pinus radiata in Australia Proceedings of Forest Genetics and Tree Breeding in the Age of Genomics: Progress and Future. 2004 IUFRO Joint Conference of Division 2: 1-5 November; Charleston, South Carolina, USA 308-318.
3. Gapare WJ Wu HX Abarquez A Genetic control of the time of transition from juvenile to mature wood in Pinus radiata D. Don Annals of Forest Science 2006, 63(8):871-878. 10.1051/forest:2006070
4. Allona I Quinn M Shoop E Swope K St Cyr S Carlis J Riedl J Retzel E Campbell MM Sederoff R Whetten RW Analysis of xylem formation in pine by cDNA sequencing Proc Natl Acad Sci USA 1998, 95(16):9693-9698. 21401 9689143 10.1073/pnas.95.16.9693
5. Hertzberg M Aspeborg H Schrader J Andersson A Erlandsson R Blomqvist K Bhalerao R Uhlen M Teeri TT Lundeberg J Sundberg B Nilsson P Sandberg G A transcriptional roadmap to wood formation Proc Natl Acad Sci USA 2001, 98(25):14732-14737. 64750 11724959 10.1073/pnas.261293398
6. Kirst M Johnson AF Baucom C Ulrich E Hubbard K Staggs R Paule C Retzel E Whetten R Sederoff R Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana Proc Natl Acad Sci USA 2003, 100(12):7383-7388. 165884 12771380 10.1073/pnas.1132171100
7. Schrader J Nilsson J Mellerowicz E Berglund A Nilsson P Hertzberg M Sandberg G A high-resolution transcript profile across the wood-forming meristem of poplar identifies potential regulators of cambial stem cell identity Plant Cell 2004, 16(9):2278-2292. 520933 15316113 10.1105/ tpc.104.024190
8. Sterky F Bhalerao RR Unneberg P Segerman B Nilsson P Brunner AM Charbonnel-Campaa L Lindvall JJ Tandre K Strauss SH Sundberg B Gustafsson P Uhlen M Bhalerao RP Nilsson O Sandberg G Karlsson J Lundeberg J Jansson S A Populus EST resource for plant functional genomics Proc Natl Acad Sci USA 2004, 101(38):13951-13956. 518859 15353603 10.1073/pnas.0401641101
9. 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 TT Boerjan W Gustafsson P Uhlen M Sundberg B Lundeberg J Gene discovery in the wood-forming tissues of poplar: Analysis of 5,692 expressed sequence tags Proc Natl Acad Sci USA 1998, 95:13330-13335. 23802 9789088 10.1073/pnas.95.22.13330
10. Whetten R Sun YH Zhang Y Sederoff R Functional genomics and cell wall biosynthesis in loblolly pine Plant Mol Biol 2001, 47(1-2):275-291. 10.1023/A:1010652003395 11554476
11. Andersson-Gunneras S Mellerowicz EJ Love J Segerman B Ohmiya Y Coutinho PM Nilsson P Henrissat B Moritz T Sundberg B Biosynthesis of cellulose-enriched tension wood in Populus: Global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis Plant J 2006, 45(2):144-165. 10.1111/j.1365-313X.2005.02584.x 16367961
12. Moreau C Aksenov N Lorenzo MG Segerman B Funk C Nilsson P Jansson S Tuominen H A genomic approach to investigate developmental cell death in woody tissues of Populus trees Genome Biol 2005, 6(4):R34. 1088962 15833121 10.1186/gb-2005-6-4-r34
13. Pavy N Johnson JJ Crow JA Paule C Kunau T MacKay J Retzel EF ForestTreeDB: A database dedicated to the mining of tree transcriptomes Nucleic Acids Res 2007, 35:D888-D894. 1716727 17130142 10.1093/nar/gkl882
14. Pavy N Paule C Parsons L Crow JA Morency MJ Cooke J Johnson JE 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 MacKay J Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters BMC Genomics 2005, 6:144. 1277824 16236172 10.1186/1471-2164-6-144
15. Qiu D Wilson IW Gan S Washusen R Moran GF Southerton SG Gene expression in Eucalyptus branch wood with marked variation in cellulose microfibril orientation and lacking G-layers New Phytologist 2008, 179(1):94-103. 10.1111/j.1469-8137.2008.02439.x 18422902
16. The Picea sitchensis Unigene Library Browser http://www.ncbi.nlm.nih.gov/ UniGene/lbrowse2.cgi?TAXID=3332
17. Tuskan GA DiFazio S Jansson S Bohlmann J Grigoriev I Hellsten U Putnam N Ralph S Rombauts S Salamov A Schein J Sterck L Aerts A Bhalerao RR Bhalerao RP Blaudez D Boerjan W Brun A Brunner A Busov V Campbell M Carlson J Chalot M Chapman J Chen GL Cooper D Coutinho PM Couturier J Covert S Cronk Q Cunningham R Davis J Degroeve S Dejardin A Depamphilis C Detter J Dirks B Dubchak I Duplessis S Ehlting J Ellis B Gendler K Goodstein D Gribskov M Grimwood J Groover A Gunter L Hamberger B Heinze B Helariutta Y Henrissat B Holligan D Holt R Huang W Islam-Faridi N Jones S Jones-Rhoades M Jorgensen R Joshi C Kangasjarvi J Karlsson J Kelleher C Kirkpatrick R Kirst M Kohler A Kalluri U Larimer F Leebens-Mack J Leple JC Locascio P Lou Y Lucas S Martin F Montanini B Napoli C Nelson DR Nelson C Nieminen K Nilsson O Pereda V Peter G Philippe R Pilate G Poliakov A Razumovskaya J Richardson P Rinaldi C Ritland K Rouze P Ryaboy D Schmutz J Schrader J Segerman B Shin H Siddiqui A Sterky F Terry A Tsai CJ Uberbacher E Unneberg P Vahala J Wall K Wessler S Yang G Yin T Douglas C Marra M Sandberg G Peer Van de Y Rokhsar D The genome of black cottonwood, Populus trichocarpa (Torr. & Gray) Science 2006, 313:1596-1604. 10.1126/science.1128691 16973872
18. DOE Joint Genome Institute Announces. 2008 Genome Sequencing Targets http://www.jgi.doe.gov/News/news_6_8_07.html
19. Wakamiya I Newton RJ Johnston JS Price HJ Genome Size and Environmental-Factors in the Genus Pinus Am J Bot 1993, 80(11):1235-1241. 10.2307/2445706
20. Cato S McMillan L Donaldson L Richardson T Echt C Gardner R Wood formation from the base to the crown in Pinus radiata: Gradients of tracheid wall thickness, wood density, radial growth rate and gene expression Plant Mol Biol 2006, 60(4):565-581. 10.1007/s11103-005-5022-9 16525892
21. Aquea F Arce-Johnson P Identification of genes expressed during early somatic embryogenesis in Pinus radiata Plant Physiology and Biochemistry 2008, 46(5-6):559-568. 10.1016/j.plaphy.2008.02.012
22. Aspeborg H Schrader J Coutinho PM Stam M Kallas A Djerbi S Nilsson P Denman S Amini B Sterky F Master E Sandberg G Mellerowicz E Sundberg B Henrissat B Teeri TT Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen Plant Physiol 2005, 137(3):983-997. 1065399 15734915 10.1104/pp.104.055087
23. Huang DW Sherman BT Tan Q Kir J Liu D Bryant D Guo Y Stephens R Baseler MW Lane HC Lempicki RA DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists Nucleic Acids Res 2007, 35:W169-W175. 1933169 17576678 10.1093/nar/gkm415
24. Huang DW Sherman BT Tan Q Collins JR Alvord WG Roayaei J Stephens R Baseler MW Lane HC Lempicki RA The DAVID Gene Functional Classification Tool: A novel biological module-centric algorithm to functionally analyze large gene lists Genome Biol 2007, 8(9):R183. 2375021 17784955 10.1186/gb-2007-8-9-r183
25. Girke T Lauricha J Tran H Keegstra K Raikhel N The cell wall navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism Plant Physiol 2004, 136(2):3003-3008. 523362 15489283 10.1104/pp.104.049965
26. Guillaumie S San-Clemente H Deswarte C Martinez Y Lapierre C Murigneux A Barriere Y Pichon M Goffner D MAIZEWALL. Database and developmental gene expression profiling of cell wall biosynthesis and assembly in maize Plant Physiol 2007, 143(1):339-363. 1761967 17098859 10.1104/ pp.106.086405
27. Reynard GJ Reynolds W Verma R Deshaies RJ Cks1 is required for G(1) cyclin-cyclin-dependent kinase activity in budding yeast Mol Cell Biol 2000, 20(16):5858-5864. 86063 10913169 10.1128/MCB.20.16.5858-5864.2000
28. Guo AY Chen X Gao G Zhang H Zhu QH Liu XC Zhong YF Gu XC He K Luo JC PlantTFDB: A comprehensive plant transcription factor database Nucleic Acids Res 2008, 36:D966-D969. 2238823 17933783 10.1093/nar/gkm841
29. Boerjan W Ralph J Baucher M Lignin biosynthesis Annual Review of Plant Biology 2003, 54:519-546. 10.1146/annurev.arplant.54.031902.134938 14503002
30. Ye ZH Kneusel RE Matern U Varner JE An alternative methylation pathway in lignin biosynthesis in Zinnia Plant Cell 1994, 6(10):1427-1439. 160531 7994176 10.1105/tpc.6.10.1427
31. Burlat V Kwon M Davin LB Lewis NG Dirigent proteins and dirigent sites in lignifying tissues Phytochemistry 2001, 57(6):883-897. 10.1016/ S0031-9422(01)00117-0 11423139
32. Krauskopf E Harris PJ Putterill J The cellulose synthase gene PrCESA10 is involved in cellulose biosynthesis in developing tracheids of the gymnosperm Pinus radiata Gene 2005, 350(2):107-116. 10.1016/ j.gene.2005.02.018 15823508
33. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004, 32(5):1792-1797. 390337 15034147 10.1093/nar/gkh340
34. Tamura K Dudley J Nei M Kumar S MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0 Mol Biol Evol 2007, 24(8):1596-1599. 10.1093/molbev/msm092 17488738
35. Richmond TA Somerville CR The cellulose synthase superfamily Plant Physiol 2000, 124(2):495-498. 1539280 11027699 10.1104/pp.124.2.495
36. Djerbi S Lindskog M Arvestad L Sterky F Teeri TT The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes Planta 2005, 221(5):739-746. 10.1007/ s00425-005-1498-4 15940463
37. Ohlsson AB Djerbi S Winzell A Bessueille L Staldal V Li XG Blomqvist K Bulone V Teeri TT Berglund T Cell suspension cultures of Populus tremula × P. tremuloides exhibit a high level of cellulose synthase gene expression that coincides with increased in vitro cellulose synthase activity Protoplasma 2006, 228(4):221-229. 10.1007/s00709-006-0156-4 16838081
38. Li X Tian J Differential expression on cell wall formative genes in cell suspension cultures of Populus tomentosa Carr Yi Chuan 2004, 26(5):676-682. 15640084
39. Nairn CJ Haselkorn T Three loblolly pine CesA genes expressed in developing xylem are: Orthologous to secondary cell wall CesA genes of angiosperms New Phytologist 2005, 166(3):907-915. 10.1111/ j.1469-8137.2005.01372.x 15869651
40. Nicol F His I Jauneau A Vernhettes S Canut H Hofte H A plasma membrane-bound putative endo-1,4-beta-D-glucanase is required for normal wall assembly and cell elongation in Arabidopsis EMBO J 1998, 17(19):5563-5576. 1170885 9755157 10.1093/emboj/17.19.5563
41. Uggla C Magel E Moritz T Sundberg B Function and dynamics of auxin and carbohydrates during earlywood/latewood transition in Scots pine Plant Physiol 2001, 125(4):2029-2039. 88858 11299382 10.1104/pp.125.4.2029
42. Witt HJ UDP-glucose metabolism during differentiation and dedifferentiation of Riella-Helicophylla Journal of Plant Physiology 1992, 140(3):276-281.
43. Darley CP Forrester AM McQueen-Mason SJ The molecular basis of plant cell wall extension Plant Mol Biol 2001, 47(2-2):179-195. 10.1023/ A:1010687600670 11554471
44. Bourquin V Nishikubo N Abe H Brumer H Denman S Eklund M Christiernin M Teeri TT Sundberg B Mellerowicz EJ Xyloglucan endotransglycosylases have a function during the formation of secondary cell walls of vascular tissues Plant Cell 2002, 14(12):3073-3088. 151203 12468728 10.1105/ tpc.007773
45. Yang SH Wang HY Sathyan P Stasolla C Loopstra CA Real-time RT-PCR analysis of loblolly pine (Pinus taeda) arabinogalactan-protein and arabinogalactan-protein-like genes Physiologia Plantarum 2005, 124(1):91-106. 10.1111/j.1399-3054.2005.00479.x
46. Zhang Y Brown G Whetten R Loopstra CA Neale D Kieliszewski MJ Sederoff RR An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine Plant Mol Biol 2003, 52(1):91-102. 10.1023/A:1023978210001 12825692
47. Lafarguette F Leple JC Dejardin A Laurans F Costa G Lesage-Descauses MC Pilate G Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood New Phytologist 2004, 164(1):107-121. 10.1111/j.1469-8137.2004.01175.x
48. Sardar HS Yang J Showalter AM Molecular interactions of arabinogalactan proteins with cortical microtubules and F-actin in bright yellow-2 tobacco cultured cells Plant Physiol 2006, 142(4):1469-1479. 1676048 17056757 10.1104/pp.106.088716
49. Mathur J Hulskamp M Microtubules and microfilaments in cell morphogenesis in higher plants Curr Biol 2002, 12(19):R669-R676. 10.1016/ S0960-9822(02)01164-8 12361589
50. Wasteneys GO Galway ME Remodelling the cytoskeleton for growth and form: An overview with some new views Annual Review of Plant Biology 2003, 54:691-722. 10.1146/annurev.arplant.54.031902.134818 14503008
51. Spokevicius AV Southerton SG MacMillan CP Qiu D Gan S Tibbits JFG Moran GF Bossinger G Beta-tubulin affects cellulose microfibril orientation in plant secondary fibre cell walls Plant J 2007, 51(4):717-726. 10.1111/ j.1365-313X.2007.03176.x 17605757
52. Oakley RV Wang YS Ramakrishna W Harding SA Tsai CJ Differential expansion and expression of alpha- and beta-tubulin gene families in Populus Plant Physiol 2007, 145:961-973. 2048781 17885081 10.1104/ pp.107.107086
53. McDowell JM Huang SR McKinney EC An YQ Meagher RB Structure and evolution of the actin gene family in Arabidopsis thaliana Genetics 1996, 142(2):587-602. 1206991 8852856
54. McKinney EC Kandasamy MK Meagher RB Arabidopsis contains ancient classes of differentially expressed actin-related protein genes Plant Physiol 2002, 128(3):997-1007. 152212 11891255 10.1104/pp.010906
55. Barrero RA Umeda M Yamamura S Uchimiya H Arabidopsis CAP regulates the actin cytoskeleton necessary for plant cell elongation and division Plant Cell 2002, 14(1):149-163. 150557 11826305 10.1105/tpc.010301
56. Kost B Chua NH The plant cytoskeleton: Vacuoles and cell walls make the difference Cell 2002, 108(1):9-12. 10.1016/S0092-8674(01)00634-1 11792316
57. Staiger CJ Signaling to the actin cytoskeleton in plants Annual Review of Plant Physiology and Plant Molecular Biology 2000, 51:257-288. 10.1146/annurev.arplant.51.1.257
58. Vale RD The molecular motor toolbox for intracellular transport Cell 2003, 112(4):467-480. 10.1016/S0092-8674(03)00111-9 12600311
59. Preuss ML Kovar DR Lee YRJ Staiger CJ Delmer DP Liu B A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibers Plant Physiol 2004, 136(4):3945-3955. 535827 15557092 10.1104/pp.104.052340
60. Groover A Robischon M Developmental mechanisms regulating secondary growth in woody plants Curr Opin Plant Biol 2006, 9(1):55-58. 10.1016/ j.pbi.2005.11.013 16337827
61. Kawaoka A Kaothien P Yoshida K Endo S Yamada K Ebinuma H Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis Plant J 2000, 22(4):289-301. 10.1046/j.1365-313x.2000.00737.x 10849346
62. Liljegren SJ Ditta GS Eshed HY Savidge B Bowman JL Yanofsky MF SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis Nature 2000, 404(6779):766-770. 10.1038/35008089 10783890
63. Oh S Park S Han KH Transcriptional regulation of secondary growth in Arabidopsis thaliana J Exp Bot 2003, 54(393):2709-2722. 10.1093/jxb/ erg304 14585825
64. Rogers LA Dubos C Surman C Willment J Cullis IF Mansfield SD Campbell MM Comparison of lignin deposition in three ectopic lignification mutants New Phytologist 2005, 168(1):123-140. 10.1111/j.1469-8137.2005.01496.x 16159327
65. Zhong RQ Ye ZH Regulation of cell wall biosynthesis Curr Opin Plant Biol 2007, 10:564-572. 10.1016/j.pbi.2007.09.001 17950657
66. Patzlaff A McInnis S Courtenay A Surman C Newman LJ Smith C Bevan MW Mansfield S Whetten RW Sederoff RR Campbell MM Characterisation of a pine MYB that regulates lignification Plant J 2003, 36(6):743-754. 10.1046/j.1365-313X.2003.01916.x 14675440
67. Patzlaff A Newman LJ Dubos C Whetten R Smith C McInnis S Bevan MW Sederoff RR Campbell MM Characterisation of PtMYB1, an R2R3-MYB from pine xylem Plant Mol Biol 2003, 53(4):597-608. 10.1023/ B:PLAN.0000019066.07933.d6 15010621
68. Bedon F Grima-Pettenati J Mackay J Conifer R2R3-MYB transcription factors: Sequence analyses and gene expression in wood-forming tissues of white spruce (Picea glauca) BMC Plant Biology 2007, 7:17. 1851958 17397551 10.1186/1471-2229-7-17
69. Goicoechea M Lacombe E Legay S Mihaljevic S Rech P Jauneau A Lapierre C Pollet B Verhaegen D Chaubet-Gigot N Grima-Pettenati J EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis Plant J 2005, 43(4):553-567. 10.1111/j.1365-313X.2005.02480.x 16098109
70. Worley CK Zenser N Ramos J Rouse D Leyser O Theologis A Callis J Degradation of Aux/IAA proteins is essential for normal auxin signalling Plant J 2000, 21(6):553-562. 10.1046/j.1365-313x.2000.00703.x 10758506
71. Moyle R Schrader J Stenberg A Olsson O Saxena S Sandberg G Bhalerao RP Environmental and auxin regulation of wood formation involves members of the Aux/IAA gene family in hybrid Aspen Plant J 2002, 31(6):675-685. 10.1046/j.1365-313X.2002.01386.x 12220260
72. Zhao CS Craig JC Petzold HE Dickerman AW Beers EP The xylem and phloem transcriptomes from secondary tissues of the Arabidopsis root-hypocotyl Plant Physiol 2005, 138(2):803-818. 1150398 15923329 10.1104/ pp.105.060202
73. Ko JH Prassinos C Han KH Developmental and seasonal expression of PtaHB1, a gene encoding a class III HD-Zip protein, is closely associated with secondary growth and inversely correlated with the level of microRNA (miR166) New Phytol 2006, 169(3):469-478. 16411950 10.1111/ j.1469-8137.2005.01623.x
74. Bertaud F Holmbom B Chemical composition of earlywood and latewood in Norway spruce heartwood, sapwood and transition zone wood Wood Science and Technology 2004, 38(4):245-256. 10.1007/s00226-004-0241-9
75. Anagnost SE Mark RE Hanna RB Variation of microfibril angle within individual tracheids Wood and Fiber Science 2002, 34(2):337-349.
76. Koubaa A Zhang SYT Makni S Defining the transition from earlywood to latewood in black spruce based on intra-ring wood density profiles from X-ray densitometry Annals of Forest Science 2002, 59(5-6):511-518. 10.1051/forest:2002035
77. Ivkovich M Namkoong G Koshy M Genetic variation in wood properties of interior spruce. II. Tracheid characteristics Canadian Journal of Forestry Research 2002, 32(12):2128-2139. 10.1139/x02-139
78. Evans R Stringer S Kibblewhite RP Variation of microfibril angle, density and fibre orientation in twenty-nine Eucalyptus nitens trees Appita Journal 2000, 53(6):450-457.
79. Audic S Claverie JM The significance of digital gene expression profiles Genome Res 1997, 7(10):986-995. 9331369
80. Schouten JP McElgunn CJ Waaijer R Zwijnenburg D Diepvens F Pals G Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification Nucleic Acids Res 2002, 30(12):E57. 117299 12060695 10.1093/nar/gnf056
81. Chang SJ Puryear J Cairney J A simple and efficient method for isolating RNA from pine trees Plant Molecular Biology Reporter 1993, 11(2):113-116. 10.1007/BF02670468
82. Huang XQ Madan A CAP3: A DNA sequence assembly program Genome Res 1999, 9(9):868-877. 310812 10508846 10.1101/gr.9.9.868
83. BIO301 - An automated functional annotation system for ESTs http:// bc02.iis.sinica.edu.tw/bio301/index.php
84. Bairoch A Bougueleret L Altairac S Amendolia V Auchincloss A Puy GA Axelsen K Baratin D Blatter MC Boeckmann B Bollondi L Boutet E Quintaje SB Breuza L Bridge A Saux VBL deCastro E Ciampina L Coral D Coudert E Cusin I David F Delbard G Dornevil D Duek-Roggli P Duvaud S Estreicher A Famiglietti L Farriol-Mathis N Ferro S Feuermann M Gasteiger E Gateau A Gehant S Gerritsen V Gos A Gruaz-Gumowski N Hinz U Hulo C Hulo N Innocenti A James J Jain E Jimenez S Jungo F Junker V Keller G Lachaize C Lane-Guermonprez L Langendijk-Genevaux P Lara V Le Mercier P Lieberherr D Lima TD Mangold V Martin X Michoud K Moinat M Morgat A Nicolas M Paesano S Pedruzzi I Perret D Phan I Pilbout S Pillet V Poux S Pozzato M Redaschi N Reynaud S Rivoire C Roechert B Sapsezian C Schneider M Sigrist C Sonesson K Staehli S Stutz A Sundaram S Tognolli M Verbregue L Veuthey AL Vitorello C Yip L Zuletta LF Apweiler R Alam-Faruque Y Barrell D Bower L Browne P Chan WM Daugherty L Donate ES Eberhardt R Fedotov A Foulger R Frigerio G Garavelli J Golin R Horne A Jacobsen J Kleen M Kersey P Laiho K Legge D Magrane M Martin MJ Monteiro P O'Donovan C Orchard S O'Rourke J Patient S Pruess M Sitnov A Whitefield E Wieser D Lin Q Rynbeek M di Martino G Donnelly M van Rensburg P Wu C Arighi C Arminski L Barker W Chen YX Crooks D Hu ZZ Hua HK Huang HZ Kahsay R Mazumder R McGarvey P Natale D Nikolskaya AN Petrova N Suzek B Vasudevan S Vinayaka CR Yeh LS Zhang J UniProt C The Universal Protein Resource (UniProt) Nucleic Acids Res 2008, 36:D190-D195. 2238893 18045787 10.1093/nar/gkn141
85. Lee Y Tsai J Sunkara S Karamycheva S Pertea G Sultana R Antonescu V Chan A Cheung F Quackenbush J The TIGR Gene Indices: Clustering and assembling EST and known genes and integration with eukaryotic genomes Nucleic Acids Res 2005, 33:D71-D74. 540018 15608288 10.1093/nar/gki064
86. Harris MA Deegan JI Lomax J Ashburner M Tweedie S Carbon S Lewis S Mungall C Day-Richter J Eilbeck K Blake JA Bult C Diehl AD Dolan M Drabkin H Eppig JT Hill DP Ni L Ringwald M Balakrishnan R Binkley G Cherry JM Christie KR Costanzo MC Dong Q Engel SR Fisk DG Hirschman JE Hitz BC Hong EL Krieger CJ Miyasato SR Nash RS Park J Skrzypek MS Weng S Wong ED Zhu KK Botstein D Dolinski K Livstone MS Oughtred R Berardini T Li DH Rhee SY Apweiler R Barrell D Camon E Dimmer E Huntley R Mulder N Khodiyar VK Lovering RC Povey S Chisholm R Fey P Gaudet P Kibbe W Kishore R Schwarz EM Sternberg P Van Auken K Giglio MG Hannick L Wortman J Aslett M Berriman M Wood V Jacob H Laulederkind S Petri V Shimoyama M Smith J Twigger S Jaiswal P Seigfried T Howe D Westerfield M Collmer C Torto-Alalibo T Feltrin E Valle G Bromberg S Burgess S McCarthy F Gene Ontology C The Gene Ontology project in 2008 Nucleic Acids Res 2008, 36:D440-D444. 2238979 17984083
87. Finn RD Tate J Mistry J Coggill PC Sammut SJ Hotz HR Ceric G Forslund K Eddy SR Sonnhammer ELL Bateman A The Pfam protein families database Nucleic Acids Res 2008, 36:D281-D288. 2238907 18039703 10.1093/nar/gkm960