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Table 8 Selected differentially represented Gene Ontologies of CDS with specific mers in X. fastidiosa subspecies or subclades

From: Identification of genetic relationships and subspecies signatures in Xylella fastidiosa

GO term1 Description FDR/p-value Annot. test/ref2 Non annot. Test/ref3 Enrichment
Specific to subsp. pauca: associated with the bacterial cell wall/envelope/plasma membrane; nucleotide metabolic/biosynthetic process, especially for purine
 GO:0000270 peptidoglycan metabolic process 4.40e-36/5.38e-39 723/168 988/771 over
 GO:0000902 cell morphogenesis 4.21e-4/2.27e-5 25/0 1686/939 over
 GO:0005886 plasma membrane 0.0017/1.15e-4 96/23 1615/916 over
 GO:0009252 peptidoglycan biosynthetic process 0.0029/2.08e-4 20/0 1691/939 over
 GO:0009273 peptidoglycan-based cell wall biogenesis 0.0029/2.08e-4 20/0 1691/939 over
 GO:0009279 cell outer membrane 0.0346/0.0035 19/1 1692/938 over
 GO:0009653 anatomical structure morphogenesis 4.21e-4/2.272e-5 25/0 1686/939 over
 GO:0016021 integral component of membrane 0.0060/4.49e-4 292/112 1419/827 over
 GO:0019867 outer membrane 0.0458/0.0047 25/3 1686/936 over
 GO:0030312 external encapsulating structure 0.0088/7.40e-4 22/1 1689/938 over
 GO:0031224 intrinsic component of membrane 0.0049/3.68e-4 293/112 1418/827 over
 GO:0042546 cell wall biogenesis 0.0029/2.08e-4 20/0 1691/939 over
 GO:0044036 cell wall macromolecule metabolic process 0.0012/7.19e-5 23/0 1688/939 over
 GO:0044038 cell wall macromolecule biosynthetic process 0.0029/2.08e-4 20/0 1691/939 over
 GO:0044425 membrane part 0.0014/8.82eE-5 302/112 1409/827 over
 GO:0044462 external encapsulating structure part 0.0346/0.0035 19/1 1692/938 over
 GO:0045229 external encapsulating structure organization 0.0023/1.55e-4 26/1 1685/938 over
 GO:0048856 anatomical structure development 4.21e-4/2.27e-5 25/0 1686/939 over
 GO:0071554 cell wall organization or biogenesis 0.0094/7.93e-4 23/1 1688/938 over
 GO:0071555 cell wall organization 0.0346/0.0035 19/1 1692/938 over
 GO:0006164 purine nucleotide biosynthetic process 0.0079/6.34e-4 27/2 1684/937 over
 GO:0009127 purine nucleoside monophosphate biosynthetic process 0.0088/7.40e-4 22/1 1689/938 over
 GO:0009144 purine nucleoside triphosphate metabolic process 0.0035/2.62e-4 28/1 1686/938 over
 GO:0009152 purine ribonucleotide biosynthetic process 0.0122/0.0010 26/2 1685/937 over
 GO:0009168 purine ribonucleoside monophosphate biosynthetic process 0.0088/7.4042e-4 22/1 1689/938 over
 GO:0009205 purine ribonucleoside triphosphate metabolic process 0.0035/2.6218e-4 25/1 1686/938 over
 GO:0072522 purine-containing compound biosynthetic process 0.0346/0.0034 18/1 1693/938 over
 GO:0072528 pyrimidine-containing compound biosynthetic process 0.0034/2.457e-4 29/2 1682/937 over
 GO:0009117 nucleotide metabolic process 0.0012/7.00e-5 64/11 1647/928 over
 GO:0009123 nucleoside monophosphate metabolic process 1.59e-5/5.71e-7 49/3 1662/936 over
 GO:0009124 nucleoside monophosphate biosynthetic process 0.0014/8.89e-5 32/2 1679/937 over
 GO:0009141 nucleoside triphosphate metabolic process 0.0034/2.45e-4 29/2 1682/937 over
 GO:0009156 ribonucleoside monophosphate biosynthetic process 6.00e-4/3.25e-5 30/1 1681/938 over
 GO:0009165 nucleotide biosynthetic process 0.0106/8.96e-4 43/7 1668/932 over
 GO:0009199 ribonucleoside triphosphate metabolic process 0.0023/1.55e-4 26/1 1685/938 over
 GO:0009260 ribonucleotide biosynthetic process 6.15e-4/3.36e-5 35/2 1676/937 over
 GO:0016032 viral process 0.0213/0.0019 0/6 1711/933 under
 GO:0019058 viral life cycle 0.0213/0.0019 0/6 1711/933 under
 GO:0019068 virion assembly 0.0213/0.0019 0/6 1711/933 under
 GO:0044403 Symbiont process 0.0213/0.0019 0/6 1711/933 under
Specific to subsp. fastidiosa (without CFBP 8073; group FAS): associated with DNA modification; vitamin process
 GO:0006304 DNA modification 0.0030/5.64e-6 16/0 1126/1280 over
 GO:0006305 DNA alkylation 0.0469/5.31e-4 10/0 1132/1280 over
 GO:0006306 DNA methylation 0.0469/5.31e-4 10/0 1132/1280 over
 GO:0044728 DNA methylation or demethylation 0.0469/5.31e-4 10/0 1132/1280 over
 GO:0009110 vitamin biosynthetic process 0.0469/5.56e-4 18/3 1124/1277 over
 GO:0042364 water-soluble vitamin biosynthetic process 0.0469/5.56e-4 18/3 1124/1277 over
Specific to subsp. multiplex: associated with metabolic process, catalytic activity and conformation of DNA; organelle organization
 GO:0006259 DNA metabolic process 0.0021/2.52e-5 53/21 1066/1222 over
 GO:0071103 DNA conformation change 0.0324/5.80eE-4 13/1 1106/1242 over
 GO:0140097 catalytic activity, acting on DNA 0.0018/2.11eE-5 33/8 1086/1235 over
 GO:0006996 organelle organization 0.0256/4.47e-4 162 1103/1241 over
Specific to subsp. morus: associated with DNA replication
 GO:0006260 DNA replication 0.0485/1.99e-5 31/10 1084/1491 over
Specific to the combination of subsp. morus and multiplex: associated with amino acid biosynthetic processes; ion binding
 GO:1901607 alpha-amino acid biosynthetic process 0.0390/2.30e-4 26/35 546/2009 over
Specific to the combination of subsp. morus, fastidiosa (including CFBP 8073), sandyi, sandyi-like (=clade III): associated with cellular component or protein complex disassembly; signaling; metabolic process; ATP generation; carbohydrates / polysaccharides; nucleoside/nucleotides; peptidyl-proline; response to chemical; tRNA binding; chemotaxis
 GO:0022411 cellular component disassembly 0.0168/8.44e-4 6/0 800/1810 over
 GO:0032984 macromolecular complex disassembly 0.0168/8.44e-4 6/0 800/1810 over
 GO:0043241 protein complex disassembly 0.0168/8.44e-4 6/0 800/1810 over
 GO:0023052 signaling 0.0496/0.0031 18/14 788/1796 over
 GO:0007165 signal transduction 0.0496/0.0031 18/14 788/1796 over
 GO:0006090 pyruvate metabolic process 0.0086/3.44e-4 13/5 793/1805 over
 GO:0006096 glycolytic process 0.0149/5.74e-4 17/10 789/1800 over
 GO:0006733 oxidoreduction coenzyme metabolic process 0.0343/0.0018 8/2 798/1808 over
 GO:0044264 cellular polysaccharide metabolic process 0.0149/7.01e-4 9/2 797/1808 over
 GO:0006757 ATP generation from ADP 0.0078/3.08e-4 11/3 795/1807 over
 GO:0016052 carbohydrate catabolic process 0.0359/0.0020 10/4 796/1806 over
 GO:0005976 polysaccharide metabolic process 0.0359/0.0020 9/3 797/1807 over
 GO:0006165 nucleoside diphosphate phosphorylation 0.0168/8.36e-4 11/4 795/1806 over
 GO:0009132 nucleoside diphosphate metabolic process 0.0066/2.55e-4 10/2 796/1808 over
 GO:0009135 purine nucleoside diphosphate metabolic process 0.0066/2.55e-4 10/2 796/1808 over
 GO:0009179 purine ribonucleoside diphosphate metabolic process 0.0066/2.55e-4 10/2 796/1808 over
 GO:0009185 ribonucleoside diphosphate metabolic process 0.0383/0.0022 13/7 793/1803 over
 GO:0019362 pyridine nucleotide metabolic process 0.0383/0.0022 13/7 793/1803 over
 GO:0046496 nicotinamide nucleotide metabolic process 0.0066/2.58e-4 7/0 799/1810 over
 GO:0003755 peptidyl-prolyl cis-trans isomerase activity 0.0066/2.58e-4 7/0 799/1810 over
 GO:0000413 protein peptidyl-prolyl isomerization 0.0066/2.58e-4 7/0 799/1810 over
 GO:0016859 cis-trans isomerase activity 0.0383/0.0022 13/7 793/1803 over
 GO:0018208 peptidyl-proline modification 0.0168/8.36e-4 11/4 795/1806 over
 GO:0042221 response to chemical 0.0454/0.00275 5/0 801/1810 over
 GO:0000049 tRNA binding 0.0454/0.00275 5/0 801/1810 over
 GO:0006935 chemotaxis 0.0454/0.00275 5/0 801/1810 over
 GO:0040011 locomotion 0.0168/8.44e-4 6/0 800/1810 over
 GO:0042330 taxis 0.0168/8.44e-4 6/0 800/1810 over
Specific to the subclade I.3 from subsp. pauca: transport, recombination, organelle part
 GO:0006310 DNA recombination 0.0093/5.91e-4 0/12 1147/1281 under
 GO:0006812 cation transport 0.0368/0.0029 2/15 1145/1278 under
 GO:0015672 monovalent inorganic cation transport 0.0282/0.0022 1/13 1146/1280 under
 GO:0034220 ion transmembrane transport 0.0089/5.56e-4 2/19 1145/1274 under
 GO:0098655 cation transmembrane transport 0.0167/0.0012 1/14 1146/1279 under
 GO:0098660 inorganic ion transmembrane transport 0.0103/6.72e-4 1/15 1146/1278 under
 GO:0098662 inorganic cation transmembrane transport 0.0488/0.0040 1/12 1146/1281 under
 GO:0008324 cation transmembrane transporter activity 0.0282/0.0022 1/13 1146/1280 under
 GO:0044422 organelle part 0.0167/0.0012 1/14 1146/1279 under
 GO:0044446 intracellular organelle part 0.0167/0.0012 1/14 1146/1279 under
Specific to the CFBP 8072 genome from subsp. pauca: nucleoside and carboxylic acid biosynthetic processes
 GO:0009142 nucleoside triphosphate biosynthetic process 0.0303/0.0020 0/8 1205/1024 under
 GO:0072330 monocarboxylic acid biosynthetic process 0.0158/9.28e-4 0/9 1205/1023 under
Specific to the Hib4 genome from subsp. pauca: response to stress, transfer/transport activity, iron-sulfur binding, component assembly/organization
 GO:0006950 response to stress 1.39e-4/1.05e-5 1/17 1323/1047 under
 GO:0006979 response to oxidative stress 0.0279/0.0034 0/7 1324/1057 under
 GO:0033554 cellular response to stress 0.0153/0.0017 1/11 1323/1053 under
 GO:0008565 protein transporter activity 0.0279/0.0034 1/10 1323/1054 under
 GO:0009055 electron transfer activity 0.0279/0.0034 0/7 1324/1057 under
 GO:0015197 peptide transporter activity 0.0153/0.0017 1/11 1323/1053 under
 GO:0016667 oxidoreductase activity, acting on a sulfur group of donors 0.0135/0.0015 0/8 1324/1056 under
 GO:0051540 metal cluster binding 0.0055/5.56e-4 2/14 1322/1050 under
 GO:0051536 iron-sulfur cluster binding 0.0055/5.56e-4 2/14 1322/1050 under
 GO:0051539 4 iron, 4 sulfur cluster binding 0.0279/0.0034 1/10 1323/1054 under
 GO:0022607 cellular component assembly 0.0023/2.15e-4 1/13 1323/1051 under
 GO:0043933 macromolecular complex subunit organization 0.0066/6.79e-4 0/9 1324/1055 under
  1. 1Complete datasets are provided in Additional file 7
  2. 2Annot test/ref.: number of GO-associated CDS in the list of CDS harboring specific mers (query) / number of GO-associated CDS in the reference genome
  3. 3Non-annot test/ref.: number of non-annotated (no GOs) CDS in the list of CDS harboring specific mers (query) / number of non-annotated (no GOs) CDS in the reference genome