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

Henry, Peter; Kaur, Sukhwinder; Pham, Quyen Anh Tran; Barakat, Radwan; Brinker, Samuel; Haensel, Hannah; Daugovish, Oleg; Epstein, Lynn

doi:10.1186/s12864-020-07141-5

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

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 function^f
Gene	Avg. cpm^b in planta	Avg. cpm in vitro	LogFC	Adjusted P-value	Cellular local-ization^c	Protein mass, kDa	No. cyste-ine resi-dues	Lineage-specific (LS) Accessory, host-specific (HS) Accessory, or Core chromosome no.^d	Contig: start bp^e	Postulated function^f
NS.09678^g	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.06282^g	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.06525^g,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.05812^g	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.06635^g	6133	0.2	13.5	5.5E-10	secr	13.8	6	HS Acc	SS17:1461842	Effector
NS.06362^g	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.06821^g,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.06691^g,i	2938	0.0	13.0	4.6E-09	secr	12.5	7	HS Acc	SS17:1661252	Effector
NS.12180^j	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.06820^h	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.06376^g	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.11338^k	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

^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
^bcpm, normalized as the number of reads per million fungal reads
^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
^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
^eSS Superscaffold; uni Unitig
^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
^gThe terminus of a miniature impala (mimp) transposable element is within 2.5 kb upstream of the ORF start
^hNS.06820 and NS.06821 are adjacent to each other
ⁱPGN.06691 and NS.06525 are adjacent to each other
^jThe translated gene model was annotated by Panther as a Tc1_like DDE_3 and is contained within a RepeatMasker-annotated TcMar-Tc1
^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

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ISSN: 1471-2164

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