Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat

Nguyen, Hai D. T.; Sultana, Tahera; Kesanakurti, Prasad; Hambleton, Sarah

doi:10.1186/s43008-019-0011-9

Table 4 Best primers and probes sequences for targetting the best genes unique to each species to give amplicon sizes approximately between 100 bp to 150 bp

From: Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat

		Orthogroup putative function		Effector analysis^c
Species	Orthogroup ID	InterProScan^a	NCBI blastp nr database^b	Prediction	Probability	Forward Primer	Probe	Reverse Primer
Tilletia caries	OG0010723	Unknown	hypothetical protein	Non-effector	0.71	TGTCTGCTACCTTTCTTTGGGTT	CGGTCAGCATATCTAGCGTCGCAGCCT	ACCTAGTTCGCAGGAAGAATGTT
	OG0010724	Unknown	GTPase	Non-effector	0.69	TAGTGGATCGACAACGGAAAACT	GTGATGTGGCGAAAACCATCGGGAGCC	AGCTCATCAATCAGCTCGAACAG
	OG0010727	Unknown	hypothetical protein	Non-effector	0.66	CTGAAATTGCTGTCATCTGGGTG	ACCAGTCCTCGCCTACCTTGATAGCCA	AACTAGACTCTGGTTAGACGTGC
	OG0010729	Contains signal peptide	hypothetical protein	Effector	0.68	TTCTTATCTGCCCTTACCTGCTG	TATCCACGTCACTCAAGCCTTGCGCCT	CAGCCATAACAATCGCATACAGG
	OG0010739	Contains DNA binding domain	XRE family transcriptional regulator	Non-effector	0.63	CCAAAGGCGATATGAGCGTCTC	CCTGAAGCTGGTCAAGGCCGGACATCA	CTCGTCGAGGATGTCTTCAATCG
	OG0010773	Contains EamA domain	EamA family transporter	Non-effector	0.91	TCCAAATCCAGTAGCCAATGAGG	TCGAGAAGATGGCGGCGTTGTCGATCT	GGAGATTTATGTGCGGACATTGG
	OG0010825	Unknown	DUF2384 domain-containing protein	Non-effector	0.59	GCTCAAAACGATACCAGGCATAG	GCGGTTCCACCTTGCTGAGCACCTCTA	CCGCATGGAATCAGATGACATTC
	OG0010847	Unknown	hypothetical protein	Non-effector	0.81	CCTGTAGCAACTTCGTCAGATCC	GTTCGCTGCCATCGACGAGCTGCTTTG	AGCAGATCATCGTTCAGAACCTT
	OG0010878	Contains domain associated eicosanoid/glutathione metabolism	MAPEG family protein	Non-effector	0.90	CAAGATCAACCAATGGACCTTGC	GAGTGTCGGTGCTGGCAGTTTGATGGC	GGTGAGAAAGAACTCCTCATGCT
	OG0010879	Contains PDZ domain	hypothetical protein	Non-effector	0.54	TTCATCTTCAGGCTGACCAAAGT	GCGCCACAGATCGCCGGAATTGTATGA	GGAAGCGAGACGAGCAAATATTC
	OG0010908	Contains signal peptide	hypothetical protein	Effector	0.65	TGAACCATCGGCTTTCTTAGTCA	GCTCCCAACGACAGAAGCTGCTCCTCA	GATGTCACTTGCTACGGCTACTA
	OG0010935	Unknown	hypothetical protein	Unlikely effector	0.51	GACACTCGACCGCTATCTTCAAG	CCGGAAAAGGGTGCCGTCACTCAGGAA	CCGAAATCAATGCACGGTCATAT
	OG0010940	Unknown	hypothetical protein	Effector	0.66	CGTAGAGTCGCCTCGAGAAATTA	TCATGGGCCAATCCTCCAATGCGAACA	GGAGCTTATCTGTAACCGCAAAA
	OG0010947	Unknown	hypothetical protein	Unlikely effector	0.50	GATAGCCTTGATAATGCCGATGC	GAGATCCGAGACTGCCCGGCTGACGTT	TATAATCGACGATGAGCTACGGC
	OG0011035	Unknown	No significant hits found	Non-effector	0.74	GATTCAAAATCGCGGGACAGTAC	ATCAGGGCGAGCCTGTGATACACGGTG	TCCAAAGATCAAGCTGGCGATTA
	OG0011043	ABC-2 transporter	ABC transporter permease	Non-effector	0.89	CATCCATTGTTGATGCTGCTCTT	CTGACGTCGATCACCTTCAGCCTCGCT	CAGGCTCAATTGCTCGAAATTCT
	OG0011044	Aspartic peptidase	TIGR02281 family clan AA aspartic protease	Unlikely effector	0.55	CCTGAGTTCATCCGTCTGCATC	GCAGCGAACTCAGGCTCGACAAGAAGC	GATCATGCGAACCAATGTCGAG
Tilletia controversa	OG0009908	Unknown	hypothetical protein	Effector	0.69	CTTGACTCTCCAGTGGTCGAAG	GGAACTCCCGTCAAGACAACAGCGACG	TTCACGTACTACCTCAAGGACAG
Tilletia laevis	OG0009501	Unknown	hypothetical protein	Effector	0.68	CGCAAACTGGAATGGACCATACT	ATTCTACGCGCAACGGTCTGCAAGAGG	GTTGTAAACTCGATCCGCATTCG
Tilletia laevis	OG0009526	Unknown	No significant hits found	Non-effector	0.94	GTGAGGAATTACGATCTGTCCCC	TACCCGATGAGATGCGTTCGGCTGGTC	GATCCCACATACCAGAGTTCCAG
Tilletia indica	OG0009272	Unknown	hypothetical protein	Non-effector	0.92	GAGGACCTTCAAGATCTGACAGG	ACACCTAGGCCACTCCCTATCCAGCCA	CTGATGATCTTGCCCGGTTTTAC
Tilletia walkeri	OG0010415	Contains signal peptide	hypothetical protein	Unlikely effector	0.53	TCAACTACTTCGACTCCTCCTCC	CTTCCGTGATCCCGTCAACGTCGGACT	GCGACACCATCCTTAGTTGTGTA
	OG0010423	Contains signal peptide	hypothetical protein	Non-effector	0.94	ATCTTCTACCCAATCACCTGCAG	GCCCAGCAAGGTGTTTTTGGCCAAGGA	ATAGCATCACTGATGAGCGTCTG
	OG0010431	Contains signal peptide	hypothetical protein	Non-effector	0.52	TTTCGATCACAGGACCAAGGATC	ACTTGAGGCCAGGGTGTCACATAGGCG	GCACTTCTACCTTTCTACCCCTT

^aPutative function determined with Interproscan(https://www.ebi.ac.uk/interpro/search/sequence-search)
^bPutative function determined from NCBI’s blastp analyses on the nr database. Only results with alignment scores of > 80 were considered
^cEffector probability determined by effectorP 2.0 (http://effectorp.csiro.au)

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ISSN: 2210-6359

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