Table 1.
List of candidate genes identified based on the T‐DNA insertion sites in the random mutants that showed compromised virulence on tomato.
| T‐DNA insertion within the CDS | ||||||
|---|---|---|---|---|---|---|
| Mutant | Old locus† | New locus‡ | Annotation | Expression§ | CDS¶ | |
| 78 | Not available | VDAG_JR2_Chr1g08240 | Glycoside hydrolase | + | – | |
| 73 | Not available | VDAG_JR2_Chr1g08240 | Glycoside hydrolase | + | – | |
| 407 | VDAG_00500 | VDAG_JR2_Chr1g19180 | Carboxypeptidase D | + | – | |
| 659 | VDAG_02200 | VDAG_JR2_Chr2g03300 | α/β‐Hydrolase fold family | – | – | |
| SD‐133 | VDAG_04418 | VDAG_JR2_Chr3g02140 | Ran GTPase‐activating protein 1 | + | – | |
| 444‐B | VDAG_08830 | VDAG_JR2_Chr3g07650 | Acetate kinase | + | – | |
| 211 | VDAG_06985 | VDAG_JR2_Chr4g06020 | Leucine‐rich repeat protein | + | – | |
| 375 | VDAG_07314 | VDAG_JR2_Chr4g10770 | Copper amine oxidase 1 | + | – | |
| 416 | VDAG_10292 | VDAG_JR2_Chr5g06230 | Conserved hypothetical protein | – | – | |
| 174 | VDAG_05684 | VDAG_JR2_Chr5g09640 | Hypothetical protein | + | – | |
| 657‐2 | VDAG_04769 | VDAG_JR2_Chr6g09500 | Phospho‐2‐dehydro‐3‐deoxyheptonate aldolase | + | – | |
| 367 | VDAG_06253 | VDAG_JR2_Chr7g00300 | Cyclic nucleotide‐binding protein | + | – | |
| 618 | VDAG_08151 | VDAG_JR2_Chr8g01560 | Hypothetical protein | + | – | |
| 48 | VDAG_08150 | VDAG_JR2_Chr8g01570 | CaiB/BaiF family enzyme | – | – | |
| T‐DNA insertion in intergenic region | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Upstream direction | Downstream direction | |||||||||||
| Mutant | Dist.* | Old locus† | New locus‡ | Annotation | Expression§ | CDS¶ | Dist.† | Old locus | New locus‡ | Annotation | Expression§ | CDS¶ |
| 459‐1 | 2485 | VDAG_00838 | VDAG_JR2_Chr1g01770 | Predicted protein | + | – | 1784 | VDAG_00839 | VDAG_JR2_Chr1g01780 | Transcription initiation factor TFIID subunit 12 | + | – |
| 143 | 374 | VDAG_00843 | VDAG_JR2_Chr1g01820 | Not annotated | + | – | 100 | VDAG_00844 | VDAG_JR2_Chr1g01830 | Exosome complex exonuclease | + | – |
| SD‐102 | 270 | VDAG_00599 | VDAG_JR2_Chr1g20260 | Histidinol‐phosphate aminotransferase | + | – | 746 | VDAG_00600 | VDAG_JR2_Chr1g20270 | Acetyl esterase | + | – |
| 44 | 545 | VDAG_08030 | VDAG_JR2_Chr1g22770 | Deuterolysin metalloprotease | – | – | 669 | VDAG_08031 | VDAG_JR2_Chr1g22760 | SAFF domain containing protein | + | – |
| 11 | 100 | VDAG_08003 | VDAG_JR2_Chr1g23050 | F‐box protein | – | – | 3330 | VDAG_08988 | VDAG_JR2_Chr1g23040 | UMTA methyltransferase | + | – |
| SD‐107 | 165 | VDAG_07796 | VDAG_JR2_Chr1g25310 | Hydrolase | + | – | 1586 | VDAG_07797 | VDAG_JR2_Chr1g25300 | Briggsae CBR‐SMU‐2 protein | + | – |
| 182 | 470 | VDAG_09439 | VDAG_JR2_Chr2g01480 | SMC N‐terminal‐containing protein | + | – | 257 | VDAG_09440 | VDAG_JR2_Chr2g01470 | SGT1‐like protein | + | – |
| 525 | 895 | VDAG_02343 | VDAG_JR2_Chr2g01760 | Cell wall glucanase | + | 100 | 71 | VDAG_02344 | VDAG_JR2_Chr2g01750 | Phosphoribosylglycinamide formyltransferase | + | – |
| SD‐7 | 215 | VDAG_02014 | VDAG_JR2_Chr2g05250 | Myb‐like DNA‐binding protein | + | – | 1004 | VDAG_02015 | VDAG_JR2_Chr2g05240 | Zinc NFX1‐type‐containing protein | – | – |
| 540 | 622 | VDAG_01960 | VDAG_JR2_Chr2g05800 | KH domain containing protein | + | – | 336 | VDAG_01961 | VDAG_JR2_Chr2g05790 | DUF974 protein | + | – |
| 402 | 1788 | VDAG_01891 | VDAG_JR2_Chr2g06520 | Domain‐containing protein | + | 400 | 1318 | VDAG_01892 | VDAG_JR2_Chr2g06510 | Hypothetical protein | + | 100 |
| 417 | 88 | VDAG_01651 | VDAG_JR2_Chr2g09280 | F‐box protein | + | – | 731 | VDAG_01652 | VDAG_JR2_Chr2g09270 | Cytochrome p450 protein | – | – |
| 622 | 700 | Not available | VDAG_JR2_Chr3g02050 | Unknown | + | – | 101 | VDAG_04427 | VDAG_JR2_Chr3g02040 | AGC/AKT protein kinase | + | – |
| SD‐89 | 335 | VDAG_07703 | VDAG_JR2_Chr4g00600 | Transcriptional regulatory protein pro‐1 | – | – | 423 | VDAG_07704 | VDAG_JR2_Chr4g00580 | Pathway‐specific nitrogen regulator | + | – |
| SD‐78 | 1214 | VDAG_07011 | VDAG_JR2_Chr4g05750 | Subunit of Golgi mannosyltransferase complex | + | – | 1914 | VDAG_07012 | VDAG_JR2_Chr4g05740 | Fungal‐specific transcription factor | + | – |
| 414 | 4 | Not available | VDAG_JR2_Chr4g08330 | Myomesin | – | – | 1466 | Not available | VDAG_JR2_Chr4g08340 | UMTA methyltransferase | – | – |
| 584 | 51 | VDAG_09007 | VDAG_JR2_Chr4g08540 | Family protein | + | – | 1221 | VDAG_09008 | VDAG_JR2_Chr4g08550 | Zinc‐binding dehydrogenase | + | – |
| 534 | 737 | VDAG_09007 | VDAG_JR2_Chr4g08540 | Family protein | + | – | 535 | VDAG_09008 | VDAG_JR2_Chr4g08550 | Zinc‐binding dehydrogenase | + | – |
| 199 | 64 | VDAG_05141 | VDAG_JR2_Chr5g01900 | Low‐affinity potassium transport protein | – | – | 703 | VDAG_05142 | VDAG_JR2_Chr5g01910 | Sodium ion/H ion antiporter | + | – |
| 412 | 1647 | VDAG_09301 | VDAG_JR2_Chr5g03950 | Potassium sodium efflux p‐type fungal type | + | – | 1459 | VDAG_09302 | VDAG_JR2_Chr5g03940 | Glycoside hydrolase family 43 protein | + | 100 |
| 550 | 78 | VDAG_04591 | VDAG_JR2_Chr6g07500 | Calmodulin | + | – | 667 | VDAG_04592 | VDAG_JR2_Chr6g07510 | AP‐1 complex subunit γ‐1 | + | – |
| SD‐94 | 716 | VDAG_04810 | VDAG_JR2_Chr6g09950 | NADPH dehydrogenase | + | – | 1014 | VDAG_04811 | VDAG_JR2_Chr6g09960 | Hypothetical protein | – | 100 |
| 75 | 1060 | VDAG_09054 | VDAG_JR2_Chr6g10940 | Ubiquitin fusion degradation protein | + | – | 196 | VDAG_09055 | VDAG_JR2_Chr6g10930 | Ubiquitin fusion degradation protein | + | – |
| 374 | 1023 | VDAG_06275 | VDAG_JR2_Chr7g00090 | Maintenance of telomere capping 1 | + | – | 279 | VDAG_06276 | VDAG_JR2_Chr7g00080 | Major facilitator superfamily transporter | + | – |
| 389 | 56 | VDAG_06010 | VDAG_JR2_Chr7g02960 | NAD‐dependent epimerase dehydratase | + | – | 2363 | VDAG_06011 | VDAG_JR2_Chr7g02950 | Squalene synthetase | + | – |
| 438 | 977 | VDAG_10534 | VDAG_JR2_Chr7g06650 | CTP synthase | + | – | 55077 | VDAG_06595 | VDAG_JR2_Chr7g06640 | SAD1/UNC protein | + | – |
| 59 | 47 | VDAG_10192 | VDAG_JR2_Chr7g10460 | Benzoate 4‐monooxygenase cytochrome P450 | – | – | 1565 | VDAG_10193 | VDAG_JR2_Chr7g10450 | Cellulose‐binding family II | + | – |
| 646 | 246 | VDAG_10191 | VDAG_JR2_Chr7g10470 | Methyltransferase | + | – | 422 | VDAG_10192 | VDAG_JR2_Chr7g10460 | Benzoate 4‐monooxygenase cytochrome p450 | – | – |
| 575 | 466 | VDAG_03431 | VDAG_JR2_Chr8g09910 | Vegetative cell wall protein gp1‐like | – | – | 1040 | VDAG_03432 | VDAG_JR2_Chr8g09920 | DUF221 protein | + | – |
*Distance from the T‐DNA to the coding sequence (CDS).
†Locus corresponds to the Verticillium dahliae strain VdLs.17 assembly deposited at http://genome.jgi.doe.gov/programs/fungi/ (Klosterman et al., 2011).
‡Locus corresponds to the Verticillium dahliae strain JR2 assembly deposited at http://fungi.ensembl.org/ (Faino et al., 2015).
§Evidence for in planta expression.
¶Evidence for expression in the region between T‐DNA and the closest open reading frame (ORF). Distances from T‐DNA are indicated in base pairs (bp).