Table 2.
Whole‐genome sequencing of phytopathogenic fungi registered on NCBI platforms (up to 1 October 2019) and summary of the related genetic markers.
| Species | ID number | Number of sequenced strains | Representative strain | Size (Mb) | GC% | Genes | Proteins | Specific genetic markers |
|---|---|---|---|---|---|---|---|---|
| Penicillium | ||||||||
| P. expansum | ID11336 | 9 | MD‐8 | 32.36 | 47.5 | 11 060 | 11 060 | Polygalacturonase (Hesham et al., 2011); PatF (Tannous et al., 2015); idh, 18S, β‐tubulin, calmodulin (De et al., 2016; Rharmitt et al., 2016); ITS1‐ITS4 (Hammami et al., 2017) |
| P. digitatum | ID13384 | 3 | Pd1 | 26.05 | 48.9 | 8962 | 8961 | PdCYP51 (Hamamoto et al., 2001); β‐tubulin (Oshikata et al., 2013); Pdcyt b (Zhang et al., 2009); ITS (Liu et al., 2017); RPB1, cmd (Chen et al., 2017b) |
| P. griseofulvum | ID43141 | 2 | PG3 | 29.14 | 47.3 | 9630 | 9630 | ITS and IAO (Shi et al., 2011) |
| P. citrinum | ID40785 | 2 | JCM 22607 | 34.00 | 45.9 | – | – | msdC (Yoshida and Ichishima, 1995); ITS (Song et al., 2018) |
| P. italicum | ID34360 | 3 | GL‐Gan1 | 31.03 | 45.8 | – | – | ITS (Youssef et al., 2010); RPB1‐1, cmd‐3 (Chen et al., 2017b); RPB1, RPB2 (Chen et al., 2019) |
| Alternaria | ||||||||
| A. alternata | ID11201 | 6 | SRC1lrK2f | 32.99 | 51.4 | 13 577 | 13 466 | endopolygalacturonase (Garganese et al., 2016); glyceraldehyde 3‐phosphate dehydrogenase (Gpd), Alt a1 (Gherbawy et al., 2018); AaSdhB, AaSdhC, AaSdhD (Lichtemberg et al., 2018); β‐tubulin (Basim et al., 2018); ITS1, ITS4, histone 3 (Wang et al., 2019) |
| A. arborescens | ID12091 | 5 | EGS 39‐128 | 33.89 | 50.9 | – | – | ITS (Lorenzini and Zapparoli, 2014); endopolygalacturonase (Garganese et al., 2016); Alt a1, calmodulin, plasma membrane ATPase (Elfar et al., 2018); elongation factor, β‐tubulin, glyceraldehyde‐3‐phosphate dehydrogenase (Somma et al., 2019) |
| A. brassicicola | ID865 | 2 | Abra43 | 31.04 | 50.8 | – | – | Cutinase A (Gachon and Saindrenan, 2004); Microsatellite locus ABS28 (Singh et al., 2014); ITS4, ITS5 (Gao et al., 2014) |
| A. solani | ID65961 | 2 | NL03003 | 32.78 | 51.3 | – | – | ITS1, ITS2 (Zur et al., 2002); Alt_a1, ITS‐ptAs (Gu et al., 2017); histidine kinase (HK1) (Khan et al., 2018) |
| A. tenuissima | ID76065 | 7 | FERA 1166 | 35.70 | 51.1 | 13 653 | 13 575 | ITS1, ITS4 (You et al., 2014); AM‐toxin (Andersen et al., 2006); histone (Kou et al., 2014) |
| Aspergillus | ||||||||
| A. flavus | ID360 | 60 | NRRL3357 | 36.89 | 48.3 | 13 485 | 13 485 | aflS, aflO (Degola et al., 2007); ITS, pksA, omtA (Yin et al., 2009b); β‐tubulin (Zarrinfar et al., 2015); aflatoxin biosynthesis gene cluster (Callicott and Cotty, 2015); aflQ (Mahmoud, 2015); ITS1, ITS4 (Mylroie et al., 2016); aflR –aflJ intergenic region (Atoui and El Khoury, 2017); ITS, aflP(1), aflM, aflA, aflD, aflP(3), aflP(2), aflR (Al‐Shuhaib et al., 2018); norA, omtA (Hua et al., 2018) |
| A. niger | ID429 | 14 | FDAARGOS_311 | 35.74 | 49.7 | 11 602 | 11 190 | ITS (Gonzalez‐Salgado et al., 2005); aclF1 (Tuntevski et al., 2013); β‐tubulin gene (Mirhendi et al., 2016); calmodulin gene (Das et al., 2017); benA (von Hertwig et al., 2018) |
| A. parasiticus | ID12976 | 3 | SU‐1 | 39.47 | 48.1 | 8645 | 8645 | nor‐1, ver‐1, omt‐1, apa‐2 (Chen et al., 2002); aflR (Somashekar et al., 2004); ITS (Luo et al., 2009); aflC, norA (Yin et al., 2015); aflR‐aflJ intergenic region (Atoui and El Khoury, 2017) |
| A. tubingensis | ID18109 | 2 | CBS 134.48 | 35.15 | 49.2 | 12 592 | 12 319 | ITS (Medina et al., 2005); sequence‐characterized amplified region (SCAR) (Giaj Merlera et al., 2015); calmodulin (Palumbo and O'Keeffe, 2015); β‐tubulin (Mirhendi et al., 2016) |
| A. carbonarius | ID947 | 1 | ITEM 5010 | 36.15 | 51.6 | 11 735 | 11 478 | Calmodulin (Palumbo and O'Keeffe, 2015); ITS (Tryfinopoulou et al., 2015); acOTApks, acOTAnrps, acpks, laeA, veA (El Khoury et al., 2016) |
| A. westerdijkiae | ID40399 | 1 | CBS 112803 (Abdel‐Wahhab et al., 2016) | 36.07 | 50.2 | – | – | ITS (Gil‐Serna et al., 2009); pks, p450‐B03 (Gil‐Serna et al., 2011); β‐tubulin (Durand et al., 2019) |
| Fusarium | ||||||||
| F. oxysporum | ID707 | 115 | f. sp. lycopersici 4287 (Ma et al., 2010) | 61.39 | 48.4 | 27 347 | 27 347 | FOW1 (Li et al., 2014); IGS, TEF‐1α, β‐tubulin gene (Kim et al., 2017b); Tfo1 insertion (Ortiz et al., 2017); Bik (Pugliese et al., 2013); ITS (Wu et al., 2019); Ef1α (Chen et al., 2017a); SIX4, SIX5 (Ayukawa et al., 2016); SIX1, SIX3 (Debbi et al., 2018); FEM1, HPEG (van Dam et al., 2018); FocScF/FocScR (Singh and Kapoor, 2018) |
| F. solani (Nectria haematococca) | ID 537 | 3 | 77‐13‐4 (Coleman et al., 2009) | 51.29 | 50.8 | 15 708 | 15 708 | FS1/FS2 (Casasnovas et al., 2013); EF‐1α (Muraosa et al., 2014); ITS (de Souza et al., 2017); RPB (Chitrampalam et al., 2018) |
| F. fujikuroi | ID 13188 | 15 | IMI 58289 (Wiemann et al., 2013) | 43.83 | 47.5 | 14 943 | 14 810 | histone H3 (Steenkamp et al., 1999); MAT allele (Steenkamp et al., 2000); ITS (Llorens et al., 2006); gaoB (Faria et al., 2012); β2‐tubulin (Zhang et al., 2015); TEF 1‐α (Carneiro et al., 2017) |
| F. verticillioides | ID 488 | 4 | 7600 (Ma et al., 2010) | 41.84 | 48.7 | 20 574 | 20 574 | EF‐1α (Wu et al., 2016); FUM1, FUM19 (Omori et al., 2018); ITS (Jedidi et al., 2018); calmodulin (Mulè et al., 2004); EGFP (Gai et al., 2018) |
| F. proliferatum | ID 2434 | 13 | ET1 (Niehaus et al., 2016) | 45.21 | 48.1 | 16 509 | 16 143 | Calmodulin (Mulè et al., 2004); ISR (Borrego‐Benjumea et al., 2014); SSR (Moncrief et al., 2016); tef‐1α, FUM1 (Galvez et al., 2017); FUM19 (Proctor and Vaughan, 2017); ITS (Jedidi et al., 2018) |
| F. graminearum | ID 58 | 11 | PH‐1 (Cuomo et al., 2007) | 36.67 | 48.3 | 13 334 | 13 334 | MGB (Waalwijk et al., 2004); gaoA (de Biazio et al., 2008); cyp51A, beta‐tubulin (Yin et al., 2009a); TRI12 (Nielsen et al., 2012); MAT (Demeke et al., 2010); PKS13 (Atoui et al., 2012); Tri7, Tri13 (Tralamazza et al., 2016); TRI (Wang and Cheng, 2017); ITS (Jedidi et al., 2018); tef‐1α (Garmendia et al., 2018) |
| Colletotrichum | ||||||||
| C. acutatum | ID38530 | 2 | 1 | 52.13 | 51.7 | – | – | ITS (Talhinhas et al., 2002); beta‐tubulin 2 (Talhinhas et al., 2005); CaInt2 (Jelev et al., 2008); BenA (Polizzi et al., 2011); beta‐tubulin (TUB), GAPDH (Karimi et al., 2019); MAT1‐2 (Furuta et al., 2017) |
| C. gloeosporioides | ID17739 | 6 | TYU | 53.01 | 49.6 | – | – | RAPD (Pileggi et al., 2009); CgInt (Lopes et al., 2010); β‐tubulin (TUB), actin (ACT), GPDH (Ramdeen and Rampersad, 2013); act, cal, gapdh, gs, ITS, tub2 (Sharma et al., 2017) |
| C. coccodes | ID56076 | 2 | NJ‐RT1 | 50.12 | 53.8 | – | – | RAPD (Dauch et al., 2003); ITS (Baysal‐Gurel et al., 2014); CAL, ITS, TUB2 (Silva et al., 2018) |
| C. fructicola | ID57524 | 3 | 15060 (Aguilar‐Pontes et al., 2018) | 55.92 | 53.2 | – | – | ITS (Li et al., 2013); ACT, CAL, CHS‐1, ITS, TUB, GAPDH (Gan et al., 2017) |
| Monilinia | ||||||||
| M. fructicola | ID54919 | 2 | LMK 125 | 44.68 | 40.1 | – | – | MO368‐1, Laxa (Cote et al., 2004); 18S rDNA (Fulton and Brown, 1997); β‐tubulin (Fan et al., 2014); ITS (Guinet et al., 2016); laccase‐2 (Wang et al., 2018b); cytochrome b (Ortega et al., 2019) |
| M. laxa | ID56076 | 2 | EBR‐Ba11b | 41.84 | 40.2 | – | – | 18S rDNA (Fulton and Brown, 1997); MO368‐1, Laxa (Cote et al., 2004); ISSR and RAPD (Fazekas et al., 2014); ITS (Guinet et al., 2016); laccase‐2 (Wang et al., 2018b); SCAR (Ortega et al., 2019) |
| M. fructigena | ID66926 | 3 | ASM290963v1 | 39.33 | 41.7 | – | – | 18S rDNA (Fulton and Brown, 1997); MO368‐1, Laxa (Cote et al., 2004); β‐tubulin (Fan et al., 2014); ITS (Guinet et al., 2016); laccase‐2 (Wang et al., 2018b) |
| M. polystroma | ID66925 | 1 | ASM290964v1 | 44.63 | 39.2 | – | – | MO368‐1, Laxa (Cote et al., 2004); ITS (Guinet et al., 2016); laccase‐2 (Wang et al., 2018b) |
| Botrytis | ||||||||
| B. cinerea | ID494 | 4 | B05.10 | 42.63 | 42.0 | 13 703 | 13 703 | EcoRI (Rigotti et al., 2002); IGS, SCAR (Suarez et al., 2005); IGS (Diguta et al., 2010); G3PDH, HSP60, RPB2, NEP1, NEP2 (Fan et al., 2015); ITS, β‐tubulin (Reich et al., 2016); necrosis, nep1 (Munoz et al., 2016) |