A suppression subtractive hybridization cDNA library from bacterial-blight-resistant cotton

Library Description

Organism:	Gossypium hirsutum
Cultivar:	Im216
Developmental stage:	8, 14, 20, 30, 45 and 60 hours post inoculation
Tissue:	Foliar leaves inoculated with Xanthomonas campestris pv. malvacearum 3631

Equal quantities of RNA from all stages were combined prior to mRNA isolation. In the cDNA subtraction procedure, the reference cDNA was from non-inoculated leaves

Source: Margaret Essenberg, Oklahoma State University

Gene Content Analysis

723 ESTs from this library were grouped into 86 UniGene entries (putative genes) [UniGene build #10, 16-Oct-2008]. EST counts for each entry may be used to calculate an approximate expression level in transcripts per million (TPM).

ESTs	TPM	UniGene Entry
218	301521	Ghi.17304	Transcribed locus, weakly similar to NP_192902.1 ATOSM34 (OSMOTIN 34) [Arabidopsis thaliana].
114	157676	Ghi.17307	Transcribed locus, weakly similar to NP_179068.1 PR1 (PATHOGENESIS-RELATED GENE 1) [Arabidopsis thaliana].
47	65007	Ghi.17306	Transcribed locus, weakly similar to NP_179068.1 PR1 (PATHOGENESIS-RELATED GENE 1) [Arabidopsis thaliana].
42	58091	Ghi.16905	Acidic chitinase (achi).
23	31812	Ghi.1015	Transcribed locus, moderately similar to XP_001713861.1 PREDICTED: hypothetical protein [Homo sapiens].
22	30429	Ghi.17299	Transcribed locus, moderately similar to NP_197797.1 acidic endochitinase (CHIB1) [Arabidopsis thaliana].
21	29046	Ghi.17303	Transcribed locus, weakly similar to NP_191010.1 ATEP3 (Arabidopsis thaliana chitinase class IV); chitinase.
12	16598	Ghi.4	Transcribed locus, weakly similar to NP_001052173.1 Os04g0179100 [Oryza sativa (japonica cultivar-group)].
11	15214	Ghi.6434	Transcribed locus, weakly similar to NP_001058421.1 Os06g0691200 [Oryza sativa (japonica cultivar-group)].
9	12448	Ghi.6442	Transcribed locus.
9	12448	Ghi.17316	Transcribed locus, weakly similar to NP_177641.1 PR5 (PATHOGENESIS-RELATED GENE 5) [Arabidopsis thaliana].
9	12448	Ghi.16888	Proline-rich protein (PRPL).
8	11065	Ghi.8390	Clone pCPR10-12 PR protein class 10.
8	11065	Ghi.17310	Transcribed locus, moderately similar to NP_001053524.1 Os04g0556300 [Oryza sativa (japonica cultivar-group)].
8	11065	Ghi.17260	Transcribed locus, weakly similar to NP_192216.1 AOP1 (2-oxoglutarate?dependent dioxygenase 1.1); oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [Arabidopsis tha.
7	9682	Ghi.8394	Transcribed locus, weakly similar to NP_001053826.1 Os04g0610000 [Oryza sativa (japonica cultivar-group)].
6	8299	Ghi.705	Transcribed locus, moderately similar to NP_190383.1 ALDH2B4 (ALDEHYDE DEHYDROGENASE 2); 3-chloroallyl aldehyde dehydrogenase/ aldehyde dehydrogenase (NAD) [Arabidopsis thaliana].
6	8299	Ghi.17308	Transcribed locus, strongly similar to NP_054524.1 ribosomal protein L20 [Nicotiana tabacum].
5	6916	Ghi.9265	Transcribed locus, weakly similar to NP_190972.1 photoassimilate-responsive protein-related [Arabidopsis thaliana].
5	6916	Ghi.8397	Transcribed locus, moderately similar to NP_568975.2 oxidoreductase, zinc-binding dehydrogenase family protein [Arabidopsis thaliana].
5	6916	Ghi.6441	Transcribed locus, weakly similar to NP_001061422.1 Os08g0271300 [Oryza sativa (japonica cultivar-group)].
5	6916	Ghi.17305	Transcribed locus, moderately similar to NP_179896.1 NRAMP3 (NRAMP metal ion transporter 3); manganese ion transmembrane transporter/ metal ion transmembrane transporter [Arabidopsis thaliana].
5	6916	Ghi.10717	Transcribed locus, moderately similar to NP_568052.1 RD19 (RESPONSIVE TO DEHYDRATION 19); cysteine-type peptidase [Arabidopsis thaliana].
4	5533	Ghi.8398	Transcribed locus.
4	5533	Ghi.8385	Transcribed locus, moderately similar to NP_195899.1 In2-1 protein, putative [Arabidopsis thaliana].
4	5533	Ghi.6523	Clone pCPR10-5 PR protein class 10.
4	5533	Ghi.6472	Transcribed locus, weakly similar to NP_566036.1 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein [Arabidopsis thaliana].
4	5533	Ghi.6444	Transcribed locus.
4	5533	Ghi.6429	Transcribed locus.
4	5533	Ghi.1309	Transcribed locus, moderately similar to NP_195131.1 caffeoyl-CoA 3-O-methyltransferase, putative [Arabidopsis thaliana].
4	5533	Ghi.10821	Glutathione S-transferase (GST).
3	4149	Ghi.8395	Transcribed locus, moderately similar to NP_051048.1 ribosomal protein S2 [Arabidopsis thaliana].
3	4149	Ghi.8393	Transcribed locus.
3	4149	Ghi.8392	Transcribed locus, moderately similar to NP_564761.1 ATB2; oxidoreductase [Arabidopsis thaliana].
3	4149	Ghi.8391	Transcribed locus, weakly similar to NP_563731.1 unknown protein [Arabidopsis thaliana].
3	4149	Ghi.8360	Transcribed locus, weakly similar to NP_001053720.1 Os04g0593400 [Oryza sativa (japonica cultivar-group)].
3	4149	Ghi.779	Transcribed locus, weakly similar to NP_172507.1 ATGSTU18 (GLUTATHIONE S-TRANSFERASE 29); glutathione transferase [Arabidopsis thaliana].
3	4149	Ghi.760	Transcribed locus, weakly similar to NP_192216.1 AOP1 (2-oxoglutarate?dependent dioxygenase 1.1); oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [Arabidopsis tha.
3	4149	Ghi.6586	Transcribed locus, moderately similar to NP_190470.1 ATBBC1 (breast basic conserved 1); structural constituent of ribosome [Arabidopsis thaliana].
3	4149	Ghi.6443	Transcribed locus, moderately similar to NP_187123.1 PR4 (PATHOGENESIS-RELATED 4) [Arabidopsis thaliana].
3	4149	Ghi.17309	Transcribed locus, weakly similar to NP_190480.1 ATPCA/ATPRX33/PRX33/PRXCA (PEROXIDASE 33); peroxidase [Arabidopsis thaliana].
3	4149	Ghi.17092	Transcribed locus, moderately similar to XP_001785944.1 predicted protein [Physcomitrella patens subsp. patens].
3	4149	Ghi.1451	Ubiquitin (UBI1).
2	2766	Ghi.8399	Transcribed locus, strongly similar to NP_001078309.1 ketol-acid reductoisomerase [Arabidopsis thaliana].
2	2766	Ghi.8139	1,3-beta-glucanase.
2	2766	Ghi.7199	Transcribed locus, moderately similar to NP_566588.1 unknown protein [Arabidopsis thaliana].
2	2766	Ghi.6032	Transcribed locus, moderately similar to NP_180747.1 leucine-rich repeat transmembrane protein kinase, putative [Arabidopsis thaliana].
2	2766	Ghi.16387	Transcribed locus, weakly similar to NP_191285.1 BGL2 (PATHOGENESIS-RELATED PROTEIN 2); glucan 1,3-beta-glucosidase/ hydrolase, hydrolyzing O-glycosyl compounds [Arabidopsis thaliana].
2	2766	Ghi.1502	Transcribed locus.
2	2766	Ghi.14345	Transcribed locus, weakly similar to NP_200052.1 photoassimilate-responsive protein, putative [Arabidopsis thaliana].
1	1383	Ghi.9818	Transcribed locus, strongly similar to NP_194858.1 PBA1 (20S proteasome beta subunit A 1); peptidase [Arabidopsis thaliana].
1	1383	Ghi.9761	Transcribed locus, weakly similar to XP_001779402.1 predicted protein [Physcomitrella patens subsp. patens].
1	1383	Ghi.9226	Transcribed locus, strongly similar to NP_001078076.1 small nuclear ribonucleoprotein D2, putative / snRNP core protein D2, putative / Sm protein D2, putative [Arabidopsis thaliana].
1	1383	Ghi.9142	Transcribed locus, moderately similar to NP_565369.1 secretory protein, putative [Arabidopsis thaliana].
1	1383	Ghi.8486	Transcribed locus, weakly similar to NP_001078555.1 SDH3-1 (succinate dehydrogenase 3-1) [Arabidopsis thaliana].
1	1383	Ghi.801	Transcribed locus, moderately similar to NP_568675.1 Lon protease homolog 1, mitochondrial (LON) [Arabidopsis thaliana].
1	1383	Ghi.7890	Transcribed locus, weakly similar to NP_001130720.1 hypothetical protein LOC100191824 [Zea mays].
1	1383	Ghi.7874	Cultivar Xinhai14 putative ethylene responsive element binding protein 3.
1	1383	Ghi.7100	Transcribed locus, strongly similar to NP_564806.1 NRS/ER (NUCLEOTIDE-RHAMNOSE SYNTHASE/EPIMERASE-REDUCTASE) [Arabidopsis thaliana].
1	1383	Ghi.6506	Transcribed locus, moderately similar to NP_181221.1 GAMMA-TIP (Tonoplast intrinsic protein (TIP) gamma); water channel [Arabidopsis thaliana].
1	1383	Ghi.6457	Transcribed locus.
1	1383	Ghi.6440	Transcribed locus.
1	1383	Ghi.6439	Transcribed locus.
1	1383	Ghi.6432	Transcribed locus, weakly similar to NP_196048.1 glycine-rich RNA-binding protein [Arabidopsis thaliana].
1	1383	Ghi.6431	Transcribed locus.
1	1383	Ghi.5805	Transcribed locus, moderately similar to NP_565851.1 RPL24A (RIBOSOMAL PROTEIN L24); structural constituent of ribosome [Arabidopsis thaliana].
1	1383	Ghi.4250	Transcribed locus, strongly similar to NP_191429.1 60S ribosomal protein L11 (RPL11B) [Arabidopsis thaliana].
1	1383	Ghi.2072	Transcribed locus, moderately similar to XP_001752539.1 predicted protein [Physcomitrella patens subsp. patens].
1	1383	Ghi.1968	Transcribed locus, moderately similar to NP_001067344.1 Os12g0632000 [Oryza sativa (japonica cultivar-group)].
1	1383	Ghi.19060	Transcribed locus, moderately similar to NP_680473.2 signal transducer [Arabidopsis thaliana].
1	1383	Ghi.1865	Transcribed locus, moderately similar to NP_001053524.1 Os04g0556300 [Oryza sativa (japonica cultivar-group)].
1	1383	Ghi.17315	Transcribed locus, weakly similar to NP_197797.1 acidic endochitinase (CHIB1) [Arabidopsis thaliana].
1	1383	Ghi.17314	Transcribed locus, weakly similar to NP_001130495.1 hypothetical protein LOC100191593 [Zea mays].
1	1383	Ghi.17281	Transcribed locus, moderately similar to NP_179760.1 ATGRP7 (COLD, CIRCADIAN RHYTHM, AND RNA BINDING 2); RNA binding / double-stranded DNA binding / single-stranded DNA binding [Arabidopsis thaliana].
1	1383	Ghi.17267	Transcribed locus.
1	1383	Ghi.17218	Transcribed locus, weakly similar to NP_565649.1 cysteine proteinase, putative [Arabidopsis thaliana].
1	1383	Ghi.17185	Transcribed locus, moderately similar to NP_195585.1 ROC1 (rotamase CyP 1); peptidyl-prolyl cis-trans isomerase [Arabidopsis thaliana].
1	1383	Ghi.17074	Transcribed locus, strongly similar to NP_174013.1 60S ribosomal protein L10 (RPL10B) [Arabidopsis thaliana].
1	1383	Ghi.17057	Transcribed locus, weakly similar to NP_563725.1 zinc finger (CCCH-type) family protein [Arabidopsis thaliana].
1	1383	Ghi.16974	Transcribed locus, moderately similar to NP_188120.1 malate dehydrogenase (NAD), mitochondrial, putative [Arabidopsis thaliana].
1	1383	Ghi.16416	Transcribed locus, weakly similar to NP_001043197.1 Os01g0516900 [Oryza sativa (japonica cultivar-group)].
1	1383	Ghi.16414	Transcribed locus, moderately similar to XP_001751961.1 predicted protein [Physcomitrella patens subsp. patens].
1	1383	Ghi.16413	Transcribed locus, weakly similar to NP_196290.1 peroxidase, putative [Arabidopsis thaliana].
1	1383	Ghi.16270	1-aminocyclopropane-1-carboxylate oxidase (ACO1).
1	1383	Ghi.1398	Transcribed locus.
1	1383	Ghi.10830	Transcribed locus, weakly similar to NP_849837.1 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein [Arabidopsis thaliana].