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Affymetrix Maize/Ustilago maydis "All Genes" Genome Array v7 (updated 8/2/10)

Brent Kronmiller, Mendel Biotechnology, Hayward, CA
Roger Wise, USDA-ARS / Iowa State University, Ames, IA

Affymetrix "100" format Gene Level Array; 2,598,544 probes
  • 5 µm feature size
  • 103,262 probe sets
  • 20 → 25 X 25nt probes/probe set optimally spaced 5' → 3'
  • GC binned background set (~17,000 probes)
  • Whole transcript (random primed) labeling

Section 1 (S1 prefix):
    (from Chengzhi Liang, Shiran Pasternak; Joshua Stein; Doreen Ware; Cold Spring Harbor Laboratory and USDA-ARS, Cold Spring Harbor, NY 11724)

Evidence-based gene builds from 16,606 B73 BACS (based on 4a.53 release; captures 95% of maize genes)

Probes designed off all exons of 91,435 evidence-based genes obtained from Maizesequence.org. 32,540 protein-encoding genes within the 91,435 are the core reference set published in Science (2009) 326:1112-1115. After removal of duplicates, 91,381 were submitted for probe-set selection. 81,130 were successfully tiled 5' → 3' within the exon space (Average 22 probes/gene). 1,751,449 probes.

Section 1b/c (S1b/c prefix):
    (filtered by Brent Kronmiller; Mendel Biotechnology, Hayward, CA)

15,299 Maizesequence.org Fgenesh ab initio gene predictions were aligned via BLASTn to two public mRNA seq experiments:
    1) Shoot (SRX012380) and root (SRX012381) from 14-day old B73 maize seedlings (SRP001359; Ref) and
    2) B73 leaf developmental gradient: SRX018907, SRX018905, SRX018904, SRX018903, SRX018902, SRX018901 (SRP002265 Description; Data).
7,296 of these 15,299 Fgenes sh predictions were selected by the criteria of perfect alignment to the RNA seq reads and were submitted for probe-set selection. 7,066 were successfully tiled 5' → 3' within the exon space (Average 22 probes/gene). 155,497 probes
Section 2 (S2 prefix):
    (from Shiran Pasternak; Joshua Stein; Doreen Ware; Cold Spring Harbor Laboratory, NY 11724 via Yeisoo Yu, Arizona Genomics Institute, Tucson AZ)

14,963 full length B73 cDNAs from the Arizona Genomics Institute were compared against the evidence-based gene builds on the 4a.53 BAC-based physical map (Section 1) to remove redundancy. 381 unique AGI FLcDNAs were submitted for probe-set selection. 379 were successfully tiled 5' → 3' within the exon space (Average 19 probes/gene). 7,206 probes.

Section 3 (S3 prefix):
    (from Shiran Pasternak; Joshua Stein; Doreen Ware; Cold Spring Harbor Laboratory, NY 11724 via Dick Flavell, CERES)

34,477 full length B73 cDNAs from CERES were compared against the evidence-based gene builds on the 4a.53 BAC-based physical map (Section 1) to remove redundancy. 1,685 CERES FLcDNAs were retained. After removal of duplicates, 1,676 were submitted for probe-set selection. 1,615 were successfully tiled 5' → 3' within the exon space (Average 21 probes/gene). 33,592 probes

Section 4 (S4 prefix):
    (from Jon Duvick; PlantGDB, Iowa State University, Ames, IA 50011)

All cDNAs not represented on BAC-based physical map: All B73 cDNAs found in GenBank were compared against the evidence-based gene builds and full-length cDNAs (Sections 1, 2, 3) to identify additional unique genes. 63,918 cDNAs were obtained from GenBank using the following query:
("Zea mays"[ORGN] AND biomol_mRNA[PROP] AND (B73[All Fields] OR flavell[All Fields])) NOT srcdb_refseq[prop] not (mitochondri* or chloroplast*). These were compared to 134,099 transcripts from the maizesequence.org evidence-based gene builds with blastn with a cut-off of 1-e20. 1,627 new cDNAs were identified. After removal of duplicates, 1,283 were submitted for probe-set selection. 1,252 were successfully tiled 5' → 3' within the exon space (Average 23 probes/gene). 28,544 probes

Section 5 (S5 prefix):
    (from Jon Duvick, PlantGDB, Iowa State University, Ames, IA 50011)

Non-B73 genes; located on physical map or not: All non-B73 maize cDNAs found in GenBank were compared against the evidence-based gene builds and full-length cDNAs (Sections 1, 2, 3) and cDNAs not found on BAC-based physical map (Section 4) to identify unique genes. 81,886 cDNAs were obtained from GenBank using the following query:
("Zea mays"[ORGN] AND biomol_mRNA[PROP] NOT (B73[All Fields] OR flavell[All Fields])) NOT srcdb_refseq[prop] not (mitochondri* or chloroplast*). These were compared to 134,099 transcripts from the maizesequence.org evidence-based gene builds and 1,627 new B73 cDNAs with blastn with a cut-off of 1-e20. 13,788 non-B73 cDNAs were identified. After removal of duplicates, 13,753 were submitted for probe-set selection. 13,623 were successfully tiled 5' → 3' within the exon space (Average 25 probes/gene). 336,890 probes
Section 6 (S6x prefix):
    (from James Allen, University of Missouri; Columbia, MO 65205; Brent Kronmiller, Roger Wise; Iowa State University and USDA-ARS, Ames, IA, 50011)

Mitochondrion - 60+ transcriptional units +/- 200nt; T-urf13 region [Genbank Accession M12582] tiled
  • Five maize cytoplasms (NB, NA, CMS-C, CMS-S, CMS-T) and presumed progenitor subspecies: Zm ssp. parviglumis, Z. luxurians, Z. perennis and Tripsacum dactyloides
6a - Mitochondrial genes, 67 genes (Average 23 probes per transcriptional unit) 1,557 probes
6b - Mitochondrial edits, 140 edits 1,680 probes
6c - T-urf13: GenBank M12582 (Turf 2H3) tiled (1bp overlaps, both sense and antisense directions; takes into account rf1, rf8, rf* splice sites) 6,598 probes

Section 7 (S7x prefix):
    (from Zhangjun Fei, David Stern; Boyce Thompson Institute for Plant Research; Cornell University; Ithaca, NY 14853)

7a - Chloroplast, 119 transcriptional units. 102 were successfully tiled. (Average 24 probes/gene). 2,465 probes.
7b - Chloroplast edits, 36 edits, 432 probes

Section 8 (S8 prefix):
    (from Regina Baucom, James Estill, Jeff Bennetzen; University of Georgia; Athens, GA, 30602)

Retrotransposon sequences and annotations for 581 maize repetitive element families were obtained from the Bennetzen lab (Baucom et al. 2009 PLoS Genet 5(11): e1000732. doi:10.1371/journal.pgen.1000732). After removal of duplicates, 579 were submitted for probe-set selection. 571 were successfully tiled in two 500bp regions surrounding the primer-binding site. (Average 23 probes/gene). 13,337 probes.

Section 9 (S9x prefix):
    (from Brent Kronmiller, Roger Wise; Iowa State University and USDA-ARS, Ames, IA, 50011)

9a - 58 evidence-based liberal gene calls from the maize B73 rf1-C1 and rf1-C2 finished supercontigs (Ref). These genes were not included in the evidence-based gene builds in Section 1. After removal of duplicates, 57 were submitted for probe-set selection. 55 were successfully tiled (Average 23 probes/gene). 1,250 probes
9b - SNPs derived from B73 (rf1) - Wf9-BG (Rf1) comparison treated as edits. 48 probes
Section 10 (S10 prefix):
    (from Shiran Pasternak; Joshua Stein; Doreen Ware; Cold Spring Harbor Laboratory, NY, 11724)

222 maize miRNA genes were provided by the Ware lab (Zhang et al. 2009. PLoS Genetics 5(11): e1000716.doi:10.1371/journal.pgen.1000716.). Ten probes designed on each miRNA precursor sequences from both the "+" and "-" stands (444 total). 150 miRNA of these are the core reference set published in Science (2009) 326:1112-1115. 3,446 probes
Section 11 (S11 prefix):
    (from Thomas Lubberstedt; Iowa State University, Ames, IA 50011)
  • The maize dwarf mosaic virus sequence was treated as one gene for probe design.
  • Sporisorium sorghi virus sequence was treated as one gene for probe design.
121 probes

Section 12 (S12 prefix):
    reporter genes commonly used in plant transformation experiments (Average 12 probes/gene). 726 probes

Ustilago maydis:

6,785 genes (17,493 exons) originally used for the 9-fungal genome array (H.C. Kistler, ARS CDL, University of Minnesota, St. Paul) in collaboration with Li-Jun Ma (Broad Institute), Jin-Rong Xu (Purdue University), Ulrich Gueldener (MIPS) were re-tiled at 34 probes per gene to increase sensitivity for in planta expression experiments. 230,290 probes
 
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