University of Kentucky College of Agriculture

COLLETOTRICHUM GENES AND

GENOME RESOURCES

 

Complete Genome Sequence:
Colletotrichum graminicola strains M1.001 and M5.001. Sequencing of M1.001 was funded by the USDA-NRI, and was a collaborative effort of the Broad Institute, Lisa Vaillancourt, Martin Dickman, and Mike Thon. M5.001 data were donated by Pioneer, a Dupont Company.

C. graminicola EST DATA:
2380 EST sequences generated from strain M5.001 by Pioneer, a Dupont Company, are available on NCBI GSS. The sequences were produced from mRNAs collected from mycelium and conidiating cultures.

102 partial cDNA sequences encoding secreted proteins identified by yeast signal sequence trap technique (described in the article by Krijger et al., 2008) are available on the NCBI nucleotide database, Genbank accession numbers AM944392-AM944494
Krijger, J., Horbach, R., Behr, M., Schweizer, P., Deising, H., Wirsel, S. 2008. The yeast signal sequence trap identifies secreted proteins of the hemibiotrophic corn pathogen Colletotrichum graminicola. Molecular Plant Microbe Interactions 21(10): 1325-1336

EST data from other Colletotrichum species

C. acutatum
1003 EST, Woobong Choi, on NCBI dbEST (germinating spores).

C. gloeosporioides
1029 EST, Dov Prusky, on NCBI dbEST (fungus treated with alkaline condition).

C. gloeosporioides f. sp. aeschynomene
1413 EST unigenes, Amir Sharon, on COGEME

C. trifolii
540 EST unigenes, Deborah Samac, on COGEME and on NCBI dbEST.

C. graminicola full-length and partial gene sequences on GenBank:

β-tubulin 1 (TUB1) M34491

β-tubulin 2 (TUB2) M34492

pyrimidine biosynthetic gene (orotate phosphoribosyl transferase) S47907

chitin synthase V (chsA) DQ132981

chitin synthase A (chsI) AY052545

chitin synthase B (chsIII) AY052546

chitin synthase C (chsV) AY052547

cytochrome B (partial) AY285743

superoxide dismutase (sod2) AF430836

phosphopantetheinyl transferase (PPT1) DQ028305

Elongation Factor 2 (EF2) DQ512324

Heterotrimeric G protein gene (CGG1) similar to Aspergillus nidulans FadA EU589331

BOup2* gene, similar to 3-phytase A (myo-inositol hexakisphosphate phosphohydrolase A) in SwissProt Accession Number O00107 DQ512320

BOup6* gene, similar to acid phosphatase PHO1 in SwissProt Accession Number P52291 DQ512321

BOdown1* gene, similar to Aspergillus fumigatus Af293 extracellular lipase in XP_754236 DQ512322

BOdown198* gene DQ512325

BOup 1* gene DQ512319

BOdown 2* gene DQ512323

* BO refers to “breakout zone”, “up” is up-regulated and “down” is down-regulated. These genes were differentially regulated during biotrophic growth in maize stalks, as reported in the article by Tang, W., Coughlan, S., Crane, E., Beatty, M. and Duvick, J. 2006. The application of laser microdissection to in planta gene expression profiling of the maize anthracnose stalk rot fungus Colletotrichum graminicola, Molecular Plant Microbe Interactions 19(11), 1240-1250

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Genes from other Colletotrichum species in Genbank, by category:

 

DIFFERENTIALLY EXPRESSED cDNA SEQUENCES: Isolated using differential hybridization techniques.

C. lagenarium

Produced during appressorial development

cad1

cad2

C. lindumuthianum

Biotrophy-related

cih1

C. gloeosporioides

Hard-surface contact induced in avocado strain

chip2

chip3

chip5

malonyl CoA-acyl carrier protein transacylase

ubiquitin-conjugating enzyme

Produced during appressorial development in avocado strain

cap3

cap5

cap20

cap22

Nitrogen-starvation induced in Stylosanthes strain

mRNA U94187

glutamine rich gene (U94186)

mRNA U94185

mRNA U94184

mRNA U94183

mRNA U94182

mRNA U94181

mRNA U94180

SIGNALING GENES

Kinases

MAP kinase from C. lagenarium

MAPKK from C. gloeosporioides

histidine kinase from C. gloeosporioides

kinase TB3 from C. trifolii

serine-threonine protein kinase from C. trifolii

serine-threonine protein kinase from C. lindemuthianum

cAMP-dependent protein kinase: regulatory subunit from C. trifolii

cAMP-dependent protein kinase: catalytic subunit from C. trifolii

Calcium signaling

calmodulin from C. trifolii

calmodulin from C. gloeosporioides

calmodulin-dependent protein kinase from C. gloeosporioides

Ras homologs

from C. trifolii

from C. lagenarium

CYTOSKELETON GENES

Actin

from C. gloeosporioides

Tubulin

β-tubulin 1 from C. gloeosporioides

β-tubulin 2 from C. gloeosporioides

β-tubulin 1 from C. graminicola

β-tubulin2 from C. graminicola

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DEGRADATIVE ENZYMES

Pectin lyase

C. gloeosporioides f.sp.malvae pectin lyase 1

C. gloeosporioides uncharacterized strain; pectin lyase A

Pectate lyase

C. gloeosporioides f.sp. malvae pectate lyase 1

C. gloeosporioides f.sp. malvae pectate lyase 2

C. gloeosporioides avocado strain; pectate lyase B

C. gloeosporioides uncharacterized strain; pectate lyase

C. magna pectate lyase

Endopolygalacturonase

C. gloeosporioides avocado strain; polygalacturonase

C. magna endopolygalacturonase

C. lindemuthianum endopolygalacturonase 1

C. lindemuthianum endopolygalacturonase 2

Cutinase

C. capsici papaya strain cutinase

C. gloeosporioides papaya strain; cutinase

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GENOMICS:

The Sorghum bicolor EST database. Compiled by M.-M. Cordonnier-Pratt, A. Gingle, R. Dean, M. Sudman, and L.H. Pratt. This collection of more than 10,000 EST sequences is available from GenBank.

Two-week-old sorghum plants (BTX 623 cultivar) were infected with pathogen (isolate FRM42I of Colletotrichum graminicola (note, should be C. sublineolum) which is a sorghum isolate). RNA was prepared from infected leaves harvested from 45 seedlings 48 hours after inoculation. Note: young seedlings (2 weeks old) exhibit juvenile resistant reaction, which is an incompatible interaction. As they grow older (4 weeks or older), plants resume susceptiblity to anthracnose disease. The library was made from poly-A RNA in the cloning vector lambda ZAP II. Clones to be sequenced were prepared by mass excision.