Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

Table 2 Gene prediction statistics for Pyrenophora tritici-repentis isolates

Isolate	M4 PacBio	^aBFPV1	BFPV2	134	239	5213	11137	86-124	AR CrossB10	DW5	DW7	SD20
Protein coding genes	13,797	12,171	11,969	11,072	11,239	11,142	11,034	12,525	12,086	10,880	10,908	10,715
Total length CDS (Mb)	18.22	16.40	17.46	15.82	15.96	15.91	15.86	15.82	15.49	15.51	15.25	13.85
^bGenes (K) Supported by RNA-seq	7.8	^e7.8	^e8.3	7.1	7.1	7.1	7.2	^e9.0	^e9.0	7.0	^e8.6	^e7.1
% Complete ^fBUSCO	92.1	93.5	93.7	94.3	94	93.7	94.5	88.6	88.7	92.2	91.1	74.4
^cPredicted effectors	224	260	179	188	190	193	184	246	227	186	191	184
^dSupported by proteogenomics	1568	N/A	N/A	N/A	N/A	N/A	1868	N/A	N/A	1681	N/A	N/A
Predicted effectors supported by proteogenomics	79	N/A	N/A	N/A	N/A	N/A	78	N/A	N/A	97	N/A	N/A

^aGenBank version 1.0, ^bNo. of genes with RNA-seq support (100%). ^cNo. of genes with effector prediction (EffectorP score >= 0.5). ^dNo. Genes with proteogenomics support overlap on same strand. ^eRNA-seq data pooled. ^fBenchmarking Universal Single-Copy Orthologs (BUSCO)

ISSN: 1471-2164