Home
LiteratureArticle Details
PMID: 15830128
Published · ppublish
English
Comparative Study
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies.
Abstract
A functional genomics project has been initiated to approach the molecular characterization of the main biological and agronomical traits of citrus. As a key part of this project, a citrus EST collection has been generated from 25 cDNA libraries covering different tissues, developmental stages and stress conditions. The collection includes a total of 22,635 high-quality ESTs, grouped in 11,836 putative unigenes, which represent at least one third of the estimated number of genes in the citrus genome. Functional annotation of unigenes which have Arabidopsis orthologues (68% of all unigenes) revealed gene representation in every major functional category, suggesting that a genome-wide EST collection was obtained. A Citrus clementina Hort. ex Tan. cv. Clemenules genomic library, that will contribute to further characterization of relevant genes, has also been constructed. To initiate the analysis of citrus transcriptome, we have developed a cDNA microarray containing 12,672 probes corresponding to 6875 putative unigenes of the collection. Technical characterization of the microarray showed high intra- and inter-array reproducibility, as well as a good range of sensitivity. We have also validated gene expression data achieved with this microarray through an independent technique such as RNA gel blot analysis.
MeSH Terms
Citrus/genetics
DNA, Complementary/chemistry,genetics
Expressed Sequence Tags
Gene Expression Profiling
Gene Library
Genome, Plant
Genomics/methods
Molecular Sequence Data
Oligonucleotide Array Sequence Analysis/methods
RNA, Plant/genetics,metabolism
Reproducibility of Results
Sequence Analysis, DNA
Chemicals
DNA, Complementary
RNA, Plant
References (33)
33 references, click to expand
-
Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.Genome Res. 2003 Dec;13(12):2736-46 PMID: 14656975
-
Rapid cDNA sequencing (expressed sequence tags) from a directionally cloned human infant brain cDNA library.Nat Genet. 1993 Aug;4(4):373-80 PMID: 8401585
-
The Rice PIPELINE: a unification tool for plant functional genomics.Nucleic Acids Res. 2004 Jan 1;32(Database issue):D383-7 PMID: 14681439
-
Microarray analysis of developing Arabidopsis seeds.Plant Physiol. 2000 Dec;124(4):1570-81 PMID: 11115875
-
Consed: a graphical tool for sequence finishing.Genome Res. 1998 Mar;8(3):195-202 PMID: 9521923
-
Functional annotation of a full-length mouse cDNA collection.Nature. 2001 Feb 8;409(6821):685-90 PMID: 11217851
-
Sequence-based identification of T-DNA insertion mutations in Arabidopsis: actin mutants act2-1 and act4-1.Plant J. 1995 Oct;8(4):613-22 PMID: 7496405
-
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.Science. 1995 Oct 20;270(5235):467-70 PMID: 7569999
-
Genomic sequencing.Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991-5 PMID: 6326095
-
Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species.Plant J. 2003 Apr;34(1):125-34 PMID: 12662315
-
Base-calling of automated sequencer traces using phred. II. Error probabilities.Genome Res. 1998 Mar;8(3):186-94 PMID: 9521922
-
Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.Genome Res. 2003 Dec;13(12):2725-35 PMID: 14613979
-
RNA isolation from plant tissues recalcitrant to extraction in guanidine.Biotechniques. 1995 Nov;19(5):734-7 PMID: 8588907
-
Recent highlights of the China Rice Functional Genomics Program.Trends Genet. 2003 Jul;19(7):390-4 PMID: 12850444
-
Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis.Plant Cell. 2001 Jan;13(1):113-23 PMID: 11158533
-
Fugu ESTs: new resources for transcription analysis and genome annotation.Genome Res. 2003 Dec;13(12):2747-53 PMID: 14613980
-
Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays.Plant J. 1998 Sep;15(6):821-33 PMID: 9807821
-
Expressed sequence tag analysis in Cycas, the most primitive living seed plant.Genome Biol. 2003;4(12):R78 PMID: 14659015
-
Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays.Biotechniques. 2001 Nov;31(5):1182, 1184, 1186 passim PMID: 11730025
-
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.Nucleic Acids Res. 2002 Feb 15;30(4):e15 PMID: 11842121
-
A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana.Science. 1994 Jun 3;264(5164):1452-5 PMID: 8197457
-
Basic local alignment search tool.J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
-
Annotated expressed sequence tags and cDNA microarrays for studies of brain and behavior in the honey bee.Genome Res. 2002 Apr;12(4):555-66 PMID: 11932240
-
Large-scale EST sequencing in rice.Plant Mol Biol. 1997 Sep;35(1-2):135-44 PMID: 9291967
-
Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.Genome Res. 2004 Mar;14(3):478-90 PMID: 14962987
-
A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil.Plant Physiol. 2000 Dec;124(4):1582-94 PMID: 11115876
-
Tomato mutants as tools for functional genomics.Curr Opin Plant Biol. 2002 Apr;5(2):112-7 PMID: 11856605
-
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
-
Functional genomics and cell wall biosynthesis in loblolly pine.Plant Mol Biol. 2001 Sep;47(1-2):275-91 PMID: 11554476
-
Significance analysis of microarrays applied to the ionizing radiation response.Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21 PMID: 11309499
-
MaizeGDB, the community database for maize genetics and genomics.Nucleic Acids Res. 2004 Jan 1;32(Database issue):D393-7 PMID: 14681441
-
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.Genome Res. 1998 Mar;8(3):175-85 PMID: 9521921
-
An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression.Nucleic Acids Res. 2001 Apr 15;29(8):E41-1 PMID: 11292855
Article Info
Journal
Plant molecular biology
Abbr.
Plant Mol Biol
ISSN
0167-4412
Published
2005-02-00
Pages
375-91
Language
English
Region
Netherlands
NLM ID
9106343
Subset
IM
Databases
GENBANK
CX286781,
CX286782,
CX286783,
CX286784,
CX286785,
CX286786,
CX286787,
CX286788,
CX286789,
CX286790,
CX286791,
CX286792,
CX286793,
CX286794,
CX286795,
CX286796,
CX286797,
CX286798,
CX286799,
CX286800,
CX286801,
CX286802,
CX286803,
CX286804,
CX286805,
CX286806,
CX286807,
CX286808,
CX286809,
CX286810,
CX286811,
CX286812,
CX286813,
CX286814,
CX286815,
CX286816,
CX286817,
CX286818,
CX286819,
CX286820,
CX286821,
CX286822,
CX286823,
CX286824,
CX286825,
CX286826,
CX286827,
CX286828,
CX286829,
CX286830,
CX286831,
CX286832,
CX286833,
CX286834,
CX286835,
CX286836,
CX286837,
CX286838,
CX286839,
CX286840,
CX286841,
CX286842,
CX286843,
CX286844,
CX286845,
CX286846,
CX286847,
CX286848,
CX286849,
CX286850,
CX286851,
CX286852,
CX286853,
CX286854,
CX286855,
CX286856,
CX286857,
CX286858,
CX286859,
CX286860,
CX286861,
CX286862,
CX286863,
CX286864,
CX286865,
CX286866,
CX286867,
CX286868,
CX286869,
CX286870,
CX286871,
CX286872,
CX286873,
CX286874,
CX286875,
CX286876,
CX286877,
CX286878,
CX286879,
CX286880,
CX286881,
CX286882,
CX286883,
CX286884,
CX286885,
CX286886,
CX286887,
CX286888,
CX286889,
CX286890,
CX286891,
CX286892,
CX286893,
CX286894,
CX286895,
CX286896,
CX286897,
CX286898,
CX286899,
CX286900,
CX286901,
CX286902,
CX286903,
CX286904,
CX286905,
CX286906,
CX286907,
CX286908,
CX286909,
CX286910,
CX286911,
CX286912,
CX286913,
CX286914,
CX286915,
CX286916,
CX286917,
CX286918,
CX286919,
CX286920,
CX286921,
CX286922,
CX286923,
CX286924,
CX286925,
CX286926,
CX286927,
CX286928,
CX286929,
CX286930,
CX286931,
CX286932,
CX286933,
CX286934,
CX286935,
CX286936,
CX286937,
CX286938,
CX286939,
CX286940,
CX286941,
CX286942,
CX286943,
CX286944,
CX286945,
CX286946,
CX286947,
CX286948,
CX286949,
CX286950,
CX286951,
CX286952,
CX286953,
CX286954,
CX286955,
CX286956,
CX286957,
CX286958,
CX286959,
CX286960,
CX286961,
CX286962,
CX286963,
CX286964,
CX286965,
CX286966,
CX286967,
CX286968,
CX286969,
CX286970,
CX286971,
CX286972,
CX286973,
CX286974,
CX286975,
CX286976,
CX286977,
CX286978,
CX286979,
CX286980,
CX286981,
CX286982,
CX286983,
CX286984,
CX286985,
CX286986,
CX286987,
CX286988,
CX286989,
CX286990,
CX286991,
CX286992,
CX286993,
CX286994,
CX286995,
CX286996,
CX286997,
CX286998,
CX286999,
CX287000,
CX287001,
CX287002,
CX287003,
CX287004,
CX287005,
CX287006,
CX287007,
CX287008,
CX287009,
CX287010,
CX287011,
CX287012,
CX287013,
CX287014,
CX287015,
CX287016,
CX287017,
CX287018,
CX287019,
CX287020,
CX287021,
CX287022,
CX287023,
CX287024,
CX287025,
CX287026,
CX287027,
CX287028,
CX287029,
CX287030,
CX287031,
CX287032,
CX287033,
CX287034,
CX287035,
CX287036,
CX287037,
CX287038,
CX287039,
CX287040,
CX287041,
CX287042,
CX287043,
CX287044,
CX287045,
CX287046,
CX287047,
CX287048,
CX287049,
CX287050,
CX287051,
CX287052,
CX287053,
CX287054,
CX287055,
CX287056,
CX287057,
CX287058,
CX287059,
CX287060,
CX287061,
CX287062,
CX287063,
CX287064,
CX287065,
CX287066,
CX287067,
CX287068,
CX287069,
CX287070,
CX287071,
CX287072,
CX287073,
CX287074,
CX287075,
CX287076,
CX287077,
CX287078,
CX287079,
CX287080,
CX287081,
CX287082,
CX287083,
CX287084,
CX287085,
CX287086,
CX287087,
CX287088,
CX287089,
CX287090,
CX287091,
CX287092,
CX287093,
CX287094,
CX287095,
CX287096,
CX287097,
CX287098,
CX287099,
CX287100,
CX287101,
CX287102,
CX287103,
CX287104,
CX287105,
CX287106,
CX287107,
CX287108,
CX287109,
CX287110,
CX287111,
CX287112,
CX287113,
CX287114,
CX287115,
CX287116,
CX287117,
CX287118,
CX287119,
CX287120,
CX287121,
CX287122,
CX287123,
CX287124,
CX287125,
CX287126,
CX287127,
CX287128,
CX287129,
CX287130,
CX287131,
CX287132,
CX287133,
CX287134,
CX287135,
CX287136,
CX287137,
CX287138,
CX287139,
CX287140,
CX287141,
CX287142,
CX287143,
CX287144,
CX287145,
CX287146,
CX287147,
CX287148,
CX287149,
CX287150,
CX287151,
CX287152,
CX287153,
CX287154,
CX287155,
CX287156,
CX287157,
CX287158,
CX287159,
CX287160,
CX287161,
CX287162,
CX287163,
CX287164,
CX287165,
CX287166,
CX287167,
CX287168,
CX287169,
CX287170,
CX287171,
CX287172,
CX287173,
CX287174,
CX287175,
CX287176,
CX287177,
CX287178,
CX287179,
CX287180,
CX287181,
CX287182,
CX287183,
CX287184,
CX287185,
CX287186,
CX287187,
CX287188,
CX287189,
CX287190,
CX287191,
CX287192,
CX287193,
CX287194,
CX287195,
CX287196,
CX287197,
CX287198,
CX287199,
CX287200,
CX287201,
CX287202,
CX287203,
CX287204,
CX287205,
CX287206,
CX287207,
CX287208,
CX287209,
CX287210,
CX287211,
CX287212,
CX287213,
CX287214,
CX287215,
CX287216,
CX287217,
CX287218,
CX287219,
CX287220,
CX287221,
CX287222,
CX287223,
CX287224,
CX287225,
CX287226,
CX287227,
CX287228,
CX287229,
CX287230,
CX287231,
CX287232,
CX287233,
CX287234,
CX287235,
CX287236,
CX287237,
CX287238,
CX287239,
CX287240,
CX287241,
CX287242,
CX287243,
CX287244,
CX287245,
CX287246,
CX287247,
CX287248,
CX287249,
CX287250,
CX287251,
CX287252,
CX287253,
CX287254,
CX287255,
CX287256,
CX287257,
CX287258,
CX287259,
CX287260,
CX287261,
CX287262,
CX287263,
CX287264,
CX287265,
CX287266,
CX287267,
CX287268,
CX287269,
CX287270,
CX287271,
CX287272,
CX287273,
CX287274,
CX287275,
CX287276,
CX287277,
CX287278,
CX287279,
CX287280,
CX287281,
CX287282,
CX287283,
CX287284,
CX287285,
CX287286,
CX287287,
CX287288,
CX287289,
CX287290,
CX287291,
CX287292,
CX287293,
CX287294,
CX287295,
CX287296,
CX287297,
CX287298,
CX287299,
CX287300,
CX287301,
CX287302,
CX287303,
CX287304,
CX287305,
CX287306,
CX287307,
CX287308,
CX287309,
CX287310,
CX287311,
CX287312,
CX287313,
CX287314,
CX287315,
CX287316,
CX287317,
CX287318,
CX287319,
CX287320,
CX287321,
CX287322,
CX287323,
CX287324,
CX287325,
CX287326,
CX287327,
CX287328,
CX287329,
CX287330,
CX287331,
CX287332,
CX287333,
CX287334,
CX287335,
CX287336,
CX287337,
CX287338,
CX287339,
CX287340,
CX287341,
CX287342,
CX287343,
CX287344,
CX287345,
CX287346,
CX287347,
CX287348,
CX287349,
CX287350,
CX287351,
CX287352,
CX287353,
CX287354,
CX287355,
CX287356,
CX287357,
CX287358,
CX287359,
CX287360,
CX287361,
CX287362,
CX287363,
CX287364,
CX287365,
CX287366,
CX287367,
CX287368,
CX287369,
CX287370,
CX287371,
CX287372,
CX287373,
CX287374,
CX287375,
CX287376,
CX287377,
CX287378,
CX287379,
CX287380,
CX287381,
CX287382,
CX287383,
CX287384,
CX287385,
CX287386,
CX287387,
CX287388,
CX287389,
CX287390,
CX287391,
CX287392,
CX287393,
CX287394,
CX287395,
CX287396,
CX287397,
CX287398,
CX287399,
CX287400,
CX287401,
CX287402,
CX287403,
CX287404,
CX287405,
CX287406,
CX287407,
CX287408,
CX287409,
CX287410,
CX287411,
CX287412,
CX287413,
CX287414,
CX287415,
CX287416,
CX287417,
CX287418,
CX287419,
CX287420,
CX287421,
CX287422,
CX287423,
CX287424,
CX287425,
CX287426,
CX287427,
CX287428,
CX287429,
CX287430,
CX287431,
CX287432,
CX287433,
CX287434,
CX287435,
CX287436,
CX287437,
CX287438,
CX287439,
CX287440,
CX287441,
CX287442,
CX287443,
CX287444,
CX287445,
CX287446,
CX287447,
CX287448,
CX287449,
CX287450,
CX287451,
CX287452,
CX287453,
CX287454,
CX287455,
CX287456,
CX287457,
CX287458,
CX287459,
CX287460,
CX287461,
CX287462,
CX287463,
CX287464,
CX287465,
CX287466,
CX287467,
CX287468,
CX287469,
CX287470,
CX287471,
CX287472,
CX287473,
CX287474,
CX287475,
CX287476,
CX287477,
CX287478,
CX287479,
CX287480,
CX287481,
CX287482,
CX287483,
CX287484,
CX287485,
CX287486,
CX287487,
CX287488,
CX287489,
CX287490,
CX287491,
CX287492,
CX287493,
CX287494,
CX287495,
CX287496,
CX287497,
CX287498,
CX287499,
CX287500,
CX287501,
CX287502,
CX287503,
CX287504,
CX287505,
CX287506,
CX287507,
CX287508,
CX287509,
CX287510,
CX287511,
CX287512,
CX287513,
CX287514,
CX287515,
CX287516,
CX287517,
CX287518,
CX287519,
CX287520,
CX287521,
CX287522,
CX287523,
CX287524,
CX287525,
CX287526,
CX287527,
CX287528,
CX287529,
CX287530,
CX287531,
CX287532,
CX287533,
CX287534,
CX287535,
CX287536,
CX287537,
CX287538,
CX287539,
CX287540,
CX287541,
CX287542,
CX287543,
CX287544,
CX287545,
CX287546,
CX287547,
CX287548,
CX287549,
CX287550,
CX287551,
CX287552,
CX287553,
CX287554,
CX287555,
CX287556,
CX287557,
CX287558,
CX287559,
CX287560,
CX287561,
CX287562,
CX287563,
CX287564,
CX287565,
CX287566,
CX287567,
CX287568,
CX287569,
CX287570,
CX287571,
CX287572,
CX287573,
CX287574,
CX287575,
CX287576,
CX287577,
CX287578,
CX287579,
CX287580,
CX287581,
CX287582,
CX287583,
CX287584,
CX287585,
CX287586,
CX287587,
CX287588,
CX287589,
CX287590,
CX287591,
CX287592,
CX287593,
CX287594,
CX287595,
CX287596,
CX287597,
CX287598,
CX287599,
CX287600,
CX287601,
CX287602,
CX287603,
CX287604,
CX287605,
CX287606,
CX287607,
CX287608,
CX287609,
CX287610,
CX287611,
CX287612,
CX287613,
CX287614,
CX287615,
CX287616,
CX287617,
CX287618,
CX287619,
CX287620,
CX287621,
CX287622,
CX287623,
CX287624,
CX287625,
CX287626,
CX287627,
CX287628,
CX287629,
CX287630,
CX287631,
CX287632,
CX287633,
CX287634,
CX287635,
CX287636,
CX287637,
CX287638,
CX287639,
CX287640,
CX287641,
CX287642,
CX287643,
CX287644,
CX287645,
CX287646,
CX287647,
CX287648,
CX287649,
CX287650,
CX287651,
CX287652,
CX287653,
CX287654,
CX287655,
CX287656,
CX287657,
CX287658,
CX287659,
CX287660,
CX287661,
CX287662,
CX287663,
CX287664,
CX287665,
CX287666,
CX287667,
CX287668,
CX287669,
CX287670,
CX287671,
CX287672,
CX287673,
CX287674,
CX287675,
CX287676,
CX287677,
CX287678,
CX287679,
CX287680,
CX287681,
CX287682,
CX287683,
CX287684,
CX287685,
CX287686,
CX287687,
CX287688,
CX287689,
CX287690,
CX287691,
CX287692,
CX287693,
CX287694,
CX287695,
CX287696,
CX287697,
CX287698,
CX287699,
CX287700,
CX287701,
CX287702,
CX287703,
CX287704,
CX287705,
CX287706,
CX287707,
CX287708,
CX287709,
CX287710,
CX287711,
CX287712,
CX287713,
CX287714,
CX287715,
CX287716,
CX287717,
CX287718,
CX287719,
CX287720,
CX287721,
CX287722,
CX287723,
CX287724,
CX287725,
CX287726,
CX287727,
CX287728,
CX287729,
CX287730,
CX287731,
CX287732,
CX287733,
CX287734,
CX287735,
CX287736,
CX287737,
CX287738,
CX287739,
CX287740,
CX287741,
CX287742,
CX287743,
CX287744,
CX287745,
CX287746,
CX287747,
CX287748,
CX287749,
CX287750,
CX287751,
CX287752,
CX287753,
CX287754,
CX287755,
CX287756,
CX287757,
CX287758,
CX287759,
CX287760,
CX287761,
CX287762,
CX287763,
CX287764,
CX287765,
CX287766,
CX287767,
CX287768,
CX287769,
CX287770,
CX287771,
CX287772,
CX287773,
CX287774,
CX287775,
CX287776,
CX287777,
CX287778,
CX287779,
CX287780
Analysis Services
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
