Table 2.

Positively Selected Genes That Were Deleted in Sporisorium reilianum f. sp. zeae and Their Selection Criteria

Family	Gene ID	Gene Description	dN/dS	Species with Detected Positive Selectiona	Number of Paralogs in Srzb	Virulence Phenotype of Candidate Gene Deletion	Closest Ortholog in Ustilago maydisc
FAM001428	sr10529	Conserved hypothetical protein	31.1469	Srz and Srr	0	Virulence abolished	UMAG_01375 (pit2)i
FAM005472	sr10059	Conserved hypothetical Ustilaginaceae-specific protein	6.53881	Srz and Srr	0	Virulence unaffected	UMAG_05306 (cluster 19A)j
FAM000532	sr10182	Conserved hypothetical protein	1.57473	Srr	10f	Virulence unaffected	UMAG_00492
FAM002067	sr12968	Conserved hypothetical protein	37.9007	Srr	0	Virulence unaffected	UMAG_02006
FAM003728	sr14558	Conserved hypothetical protein	24.355	Srz	0	Virulence unaffected	UMAG_03564
FAM004113	sr14944	Conserved hypothetical Ustilaginaceae-specific protein	4.30527	Srz and Srr	0	Virulence unaffected	UMAG_04034 (cluster 11–16)k
FAM003465	sr14347	Conserved hypothetical protein	544.37	Srz	5g	Virulence unaffected	UMAG_03349
FAM001868	sr12897	Conserved hypothetical protein	999d	Srr	0	Virulence unaffected	UMAG_01820
FAM000842	sr12084	Conserved hypothetical protein	999e	Srz	2h	Virulence unaffected	UMAG_00792 (cluster 1–32)k

^aSpecies are S. reilianum f. sp. zeae (Srz) and S. reilianum f. sp. reilianum (Srr).

^bBased on BLASTp search with an e-value cutoff of 0.001.

^cBased on BLASTp search.

^dMaximum value allowed by the PartNH program.

^eInfinity due to low value of d_S.

^fThe ten paralogs include: sr13431, sr11876, sr16607, sr11405, sr10621, sr16723, sr16877, 13293, sr11163.2, and sr15970.

^gThe five paralogs include: sr12257, sr11661, sr13976, sr14607, and sr11273.

^hThe two paralogs include: sr12085 and sr12086.

ⁱAs described in Doehlemann et al. (2011) and Mueller et al. (2013).

^jAs described in Kämper et al. (2006).

^kAs described in Schirawski et al. (2010).