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Table 4 Thirty-five up-expressed potential effectors or pathogenicity/virulence factors in Foa race 4 in plantaa

From: Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii

  EdgeR analysis of 3’TagSeq Predicted protein Genome location Postulated functionf
Gene Avg. cpmb in planta Avg. cpm in vitro LogFC Adjusted P-value Cellular local-izationc Protein mass, kDa No. cyste-ine resi-dues Lineage-specific (LS) Accessory, host-specific (HS) Accessory, or Core chromosome no.d Contig: start bpe
NS.09678g 25,300 2284 2.46 2.5E-07 secr 12.8 3 Core chr13, OUT SS4:3084010 Effector
NS.05815 18,471 1.2 13.2 1.3E-08 secr 30.0 8 HS Acc SS14:228927 SIX1 effector
PGN.06282g 18,379 0.1 15.4 4.5E-09 secr 5.6 0 HS Acc SS17:11497 Effector
NS.06742 14,139 5.3 10.0 2.2E-09 secr 29.0 8 LS Acc SS19:499478 Effector
NS.14450 12,854 598 3.20 1.7E-04 intra 3.6 5 Core chr10, W/IN uni19:1108440 Unknown, but not secreted
NS.06525g,i 11,596 3.1 10.7 1.4E-09 secr 12.8 3 HS Acc SS17:1662847 Effector
PGN.05952 9116 2.7 10.5 4.5E-09 secr 12.5 6 HS Acc SS14:222108 Effector
NS.05812g 7873 5.3 9.5 2.1E-10 intra 15.2 0 HS Acc SS14:223943 Unknown, but not secreted
PGN.20363 7809 0.4 12.95 4.8E-08 secr 10.8 8 Core chr4, W/IN uni7:4951240 Effector
PGN.05922 7745 36 6.5 1.4E-09 secr 11.9 6 HS Acc SS14:122611 Effector
PGN.15680 6730 57 5.65 1.5E-09 secr 12.4 8 Core chr10, W/IN uni19:3727811 Effector
PGN.06635g 6133 0.2 13.5 5.5E-10 secr 13.8 6 HS Acc SS17:1461842 Effector
NS.06362g 5038 0.1 13.2 2.0E-08 secr 9.9 6 HS Acc SS17:1000217 Effector
PGN.09917 4632 480 2.23 1.3E-08 secr 12.8 7 Core chr13, OUT SS4:3084950 Effector
NS.05829 4407 0.3 12.1 6.4E-08 secr 30.5 8 HS Acc SS14:278932 SIX1 effector
PGN.07042 4099 1.1 10.7 1.2E-09 secr 13.7 6 LS Acc SS19:912650 Effector
NS.06821g,h 3935 0.1 13.1 7.1E-09 intra 31.3 0 LS Acc SS19:758783 Abhydrolase_1
NS.10798 3622 158 3.33 5.5E-06 secr 45.2 12 Core chr11, OUT SS5:2865460 Metalloproteinase
NS.17257 2979 2.3 9.17 2.5E-10 secr 51.2 3 Core chr12, W/IN uni26:1845597 Amine oxidase or dehydrogenase
PGN.06691g,i 2938 0.0 13.0 4.6E-09 secr 12.5 7 HS Acc SS17:1661252 Effector
NS.12180j 2830 14.0 6.5 6.0E-08 intra 28.0 3 Acc uni111:57177 Transposase
NS.01422 2533 121 3.01 8.6E-05 secr 25.2 7 Core chr5, W/IN SS10:4596446 Effector
NS.09643 2463 0.3 11.07 5.4E-08 secr 29.3 8 Core chr13, OUT SS4:2943454 Effector; F. oxysporum f. sp. vasinfectum Pep1 homolog
NS.16793 2461 0.2 11.61 1.5E-07 secr 18.2 14 Core chr12, W/IN uni26:670796 Effector
NS.06528 2038 55.7 3.8 1.6E-07 secr? 15.1 9 HS Acc SS17:1671928 Effector
NS.06820h 1874 0.1 12.3 4.0E-08 intra 33.9 3 LS Acc SS19:758056 Alcohol dehydrogenase GroES-like domain & NAD(P) binding (Panther)
PGN.06376g 1768 0.2 11.6 1.9E-08 secr 12.3 8 HS Acc SS17:415228 Effector
NS.14958 1743 1.6 8.82 1.3E-07 TM 69.0 11 Core chr10, W/IN uni19:2687638 Polyol transporter
NS.07235 1665 45.3 4.1 2.3E-07 intra 81.2 3 LS Acc SS2:1462982 Catalase/peroxidase
NS.06359 1636 1.0 9.4 2.6E-09 secr 73.2 12 HS Acc SS17:990399 Extracellular glucosidase
NS.17886 1589 4.5 6.1 5.7E-04 Intra/nuclear 106.7 9 LS Acc uni56:301050 Unknown, but not an effector
NS.15045 1545 95 2.93 4.0E-08 secr 28.8 0 Core chr10, W/IN uni19:2886040 Effector; related to early nodulin 75 precursor
NS.11338k 1262 2.7 6.7 8.5E-04 intra 119.6 11 LS Acc SS6:142150 Retrotransposon
PGN.05959 1060 0.8 9.4 8.2E-08 secr 9.8 4 HS Acc SS14:239989 Effector
PGN.06650 1040 0.0 11.6 4.6E-09 secr 12.3 8 HS Acc SS17:1511396 Effector
  1. aGenes 1) had significantly (adjusted P < 0.05) higher expression in planta in celery crowns than in vitro; 2) accounted for more than 0.1% of the total fungal reads in planta and 3) were not “house-keeping” genes
  2. bcpm, normalized as the number of reads per million fungal reads
  3. cintra, intracellular, based on WoLF PSORT and the absence of a secretion signal and a transmembrane domain; secr, secreted based on SignalP-5.0; secr?, based on the absence of a secretion signal by SignalP but an extrascellular localization by WoLF PSORT; TM, transmembrane based on Geneious TMHMM prediction
  4. dBased on comparisons with progressiveMauve of Foa race 4 with the Fol 4287 reference. Contigs were categorized as follows: core, on contigs that are homologs of Fol chromosomes; or Acc, accessory contigs (no homology to a core chromosome). Genes in core chromosomes were further designated as W/IN, within the core region, i.e., within a progressiveMauve colinear block, or OUT, outside of the core region, i.e., between colinear blocks
  5. eSS Superscaffold; uni Unitig
  6. fDNA and predicted amino acid sequences were BLASTed on GenBank and analyzed with Geneious InterProScan and Panther. Genes that were identified as putative effectors were secreted (SignalP-5.0, 2), had a molecular mass < 35 kDa, and have no known biochemical function
  7. gThe terminus of a miniature impala (mimp) transposable element is within 2.5 kb upstream of the ORF start
  8. hNS.06820 and NS.06821 are adjacent to each other
  9. iPGN.06691 and NS.06525 are adjacent to each other
  10. jThe translated gene model was annotated by Panther as a Tc1_like DDE_3 and is contained within a RepeatMasker-annotated TcMar-Tc1
  11. kThe translated gene model was annotated by Panther as an integrase/ribonuclease Gag-Pol related retrotransposon/DNA-RNA polymerase with reverse transcriptase_2. The gene model is contained within a RepeatMasker-annotated 5614 bp Long Terminal Repeat/Copia transposon that is bounded by 95% identical 140 bp terminal repeats