Table 2: Localization of differentially expressed transcripts in the N. brasiliensis genome in vivo and in vitro, as identified by RNA-Seq. Most sequences were localized in intergenic regions (two were found in antisense gene regions, three corresponded to tRFs and one was overlapped between an IGR and the 5ยด end of the 23S rRNA).

ncRNA (RNA-Seq number) Assigned number in this work Position in genome Intergenic region (IGR) Antisense
PC-5p-1227_2433 Nbnc-3 431121-
431156
Putative hydrolase
< Nbnc-3 > hypothetical protein
PC-3p-38_178098 Nbnc-4 2052731-
2052756
FAD-dependent pyridine nucleotide-disulphide oxidoreductase
< Nbnc-4 > valyl-tRNA ligase
PC-5p-7930_296 Nbnc-5 7645558-
7645594
Hypothetical protein
< Nbnc-5 > hypothetical protein
PC-3p-79_77742 Nbnc-7 1392314-
1392294
Hypothetical protein
< Nbnc-7 > hypothetical protein
PC-5p-206_24405 Nbnc-8 2467033-
2467051
Hypothetical protein
< Nbnc-8 > pyruvate dehydrogenase subunit E1
PC-3p-27015_78 Nbnc-10 2510229-
2510251
Putative hydrolase
<Nbnc-10 > hypothetical protein
PC-3p-1044_3001 Nbnc-11 8615680-
8615702
Ferredoxin reductase
< Nbnc-11 > putative phosphohistidine phosphatase
PC-5p-1215_2462 Nbnc-12 9097543-
9097565
Hypothetical protein
< Nbnc-12 > 6-phosphogluconate dehydrogenase-like protein
PC-5p-36673_57 Nbnc-13 6046137-
6046162
Putative non-ribosomal peptide synthetase
PC-3p-12562_178 Nbnc-14 7645737-
7645773
Hypothetical protein
< Nbnc-14 > hypothetical protein
PC-5p-4197_599 Nbnc-15 2139099-
2139080
OmpR family two-component response regulator
PC-5p-5913_410 Nbnc-17 8421241-
8421211
Hypothetical protein
< Nbnc-17 > hypothetical protein
PC-3p-733_4626 Nbnc-18 2646061-
2646093
Cell division protein MraZ
< Nbnc-18 > 16S rRNA m(4)C1402 methyltransferase
PC-3p-238_20255 Nb-tRFthr 8659529-
8659494
atRNAthr
PC-5p-8894_263 Nb-tRFmet 1323299-
1323263
atRNAmet
PC-5p-26921_79 Nb-tRFcys 6642901-
6642936
atRNAcys
PC-3p-6945_343 Nb-rRF23S 1449884-
1449906
rRNA-16S ribosomal RNA
< Nb-rRF23S > rRNA-5S ribosomal RNA
23S ribosomal

aThese sequences represent tRNA-derived fragments.