Table 2.

Secreted proteins considered as rust effector candidates in transcriptome studies.

Species	Interaction, biological stage	Transcriptome approach	Number of transcripts detected	Detailed analysis of CSEPs	Publication
Hemileia vastatrix	Infected leaves	454-pyrosequencing GS-FLX titanium	6,763 fungal transcripts	382 predicted CSEPs	Fernandez et al. (2012)
H. vastatrix	Urediniospores and appressoria	454-pyrosequencing GS-FLX titanium	9,234 unique fungal transcripts	516 predicted CSEPs; abondant among the most highly expressed genes, particularly in planta	Talhinhas et al. (2014)
Melampsora larici-populina	Laser capture microdissection of infected leaves	Custom whole-genome oligoarrays	7,288 to 8,145 transcripts expressed in uredinia or in mesophyll tissues	19 CSEPs in the 25 most highly up-regulated transcripts in palisade mesophyll (haustoria) compared to uredinia	Hacquard et al. (2010)
M. larici-populina	Infected leaves, urediniospores	Custom whole-genome oligoarrays	>7,500 transcripts expressed in each biological condition tested	509 of 1,184 predicted CSEP genes expressed in planta; 50 CSEP among the top 100 genes up-regulated in planta	Duplessis et al. (2011a)
M. larici-populina	Time-course infection of leaves	Custom whole-genome oligoarrays	<500 early expressed transcripts; up to 8 326 transcripts in planta	270 CSEP genes specifically expressed in planta; distinct sets of >500 CSEP genes coordinately expressed along the time course	Duplessis et al. (2011b)
M. larici-populina	Early infected leaves	454-pyrosequencing GS-FLX titanium	90,398 contigs; 649 reads aligned to 361 fungal genes	19 early expressed CSEP genes among 40 fungal genes supported by more than 3 reads	Petre et al. (2012)
M. larici-populina	Telia (autumn)	Custom whole-genome oligoarrays	9,588 transcripts expressed in telia	11 SSP genes specifically expressed in telia; 113 SSP genes up-regulated in telia vs. uredinia	Hacquard et al. (2013)
Phakopsora pachyrhizi	Purified haustoria	454-pyrosequencing GS-FLX titanium	4,483 P. pachyrhizi unique contigs	156 contigs encoding CSEPs	Link et al. (2014)
P. pachyrhizi	Infected leaves	Illumina GA II	32,940 P. pachyrhizi contigs	176 predicted CSEP genes	Tremblay et al. (2012)
P. pachyrhizi	Time-course infection of leaves	Illumina GA II	Up to 12,284 P. pachyrhizi transcripts expressed	Not mentioned	Tremblay et al. (2013)
Puccinia graminis f. sp.tritici	Infected leaves, urediniospores	Custom whole-genome oligoarrays	9,818 transcripts expressed in total	442 of 1,106 predicted CSEP genes expressed in planta; 29 CSEPs in top-100 in planta up-regulated genes	Duplessis et al. (2011a)
Puccinia striiformis f. sp. tritici (5 isolates)	Infected leaves and purified haustoria	Illumina Genome Analyzer II	12–28.8 Millions reads from infected leaves and purified haustoria	933 CSEPs; 57 and 31 CSEP genes induced or repressed in haustoria vs. in planta, respectively	Cantu et al. (2013)
P. striiformis f. sp. tritici	Purified haustoria and urediniospores	454-pyrosequencing GS-FLX titanium and Illumina GA II	12,282 transcripts from combined transcriptomes	437 Haustoria Secreted Proteins (HSP); expression confirmed for 71 HSP genes by RT-qPCR	Garnica et al. (2013)
Puccinia triticina (6 isolates)	Infected leaves	Illumina RNA-Seq	222,571 fungal reads	543 CSEP transcripts (445 shared by the 6 isolates)	Bruce et al. (2014)
Uromyces appendiculatus	Purified haustoria	454-pyrosequencing GS-FLX Titanium	7,582 U. appendiculatus contigs	413 contigs encoding CSEPs	Link et al. (2014)

This table compiles the most recent genome-scale transcriptome studies in rust fungi (i.e., custom genome oligarrays and 454/Illumina-based RNA-Seq). Identification of expressed CSEPs is detailed. See Duplessis et al. (2012) for a detailed analysis of previous transcriptome studies in rust fungi based on Sanger expressed sequence tags or cDNA-arrays.