Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

BMC Genomics

Table 1 Protein-encoding genes with the highest numbers of reads per ORF in the pyruvate (P _exp ) and sulfur (S _exp ) cDNA libraries

	¹TK#	P_explibrary	TK#	S_explibrary
1	108²	Tko-sR04 + hypothetical protein	1311	50S ribosomal protein L7 Ae
2	1311	50S ribosomal protein L7 Ae	560	DNA/RNA-binding protein A1bA
3	560	DNA/RNA-binding protein A1bA	1694	ferrodoxin 1
4	1694	ferredoxin 1	108²	Tko-sR04 + hypothetical protein
5	1067	hypothetical protein	2289	histone B
6	2289	histone B	1417	50S ribosomal protein L1P
7	1431	glutamate dehydrogenase	1411	hypothetical protein
8	1331	Lrp/AsnC family transcriptional regulator	1431	glutamate dehydrogenase
9	1484	hypothetical protein	895	S-layer protein
10	895	S-layer protein	1331	Lrp-AsnC family transcriptional regulator
11	1411	hypothetical protein	1416	Acidic ribosomal protein P0
12	2284²	Tko-sR67 + 7, 8-dihydro-8-oxoguanine-triphosphatase	2286	H/ACA RNA protein complex Garl
13	537	peroxiredoxin	1067	hypothetical protein
14	1417	50S ribosomal protein L1P	1484	hypothetical protein
15	2065	RNA-binding protein	594	hypothetical protein
16	1245	hypothetical protein	1251	30S ribosomal protein S15
17	1416	acidic ribosomal protein P0	2065	RNA-binding protein
18	1565²	Tko-sR50 + hypothetical protein	1245	hypothetical protein
19	36	hypothetical protein	2284²	Tko-sR67 + 7, 8-dihydro-8-oxoguanine-triphosphatase
20	38	flagellin	615	50S ribosomal protein L37 Ae
21	2006	hypothetical protein	904	hypothetical protein
22	594	hypothetical protein	738	hypothetical protein
23	1651	hypothetical protein	1016	hypothetical protein
24	1842	Transposase	537	peroxiredoxin
25	1004	UDP-glucose 4-epimerase	1543	hypothetical protein

¹The TKxxxx numerical gene designation for the promoter proximal gene in the transcription units that had ≥4,000 reads (Additional file 10: Table S7). The genes are listed in decreasing order of cDNA reads, with shading identifying genes present in both lists.
²The automated analysis assigned the cDNA reads to genes TK0108, TK2284 and TK1565. Manual inspection revealed the presence of Tko-sR04, Tko-sR67 and Tko-sR50, respectively, within the 5′-terminal region of each transcript.

ISSN: 1471-2164