Category Archives: Genomics

Colletotrichum genome sequencing

The genome of Colletotrichum graminicola will be sequenced in 2007.  The project is supported by the National Research Initiative of the USDA Cooperative State Research, Education and Extension Service, (grant number 2007-35600-17829). The principal investigators of the grant are Lisa Vaillancourt (University of Kentucky), Li-Jun Ma (the Broad Institute of MIT and Harvard), Martin Dickman (Institute for Plant Genomics and Biotechnology, Texas A&M University), Jeffrey Osborn (University of Kentucky), and Michael Thon (Texas A&M University).

The objectives of the project are:

  1. Produce and release to the public sequence reads from 8X shotgun coverage of the genome of C. graminicola strain M1.001.
  2. Construct a high quality draft assembly and annotation, and make this accessible to the public via the Broad Institute’s Fungal Genomics website.
  3. An optical map and an EST resource will be developed to further validate and enhance these data. The map and the EST data will also be publicly released.
  4. Lay the groundwork for a comparative genomics resource at Texas A&M University focused on understanding the evolutionary and functional relationships among hemibiotrophy and other plant-parasitic fungal lifestyles.
  5. Develop an educational unit for Appalachian high school teachers and students that provides a solid understanding of genomics and bioinformatics and how basic genomics research contributes to the advancement of the science of agriculture.

Overview of Sequencing: Genome Seqencing: Our goal is to produce a total of ~615,000 reads representing ~8x coverage in Q20 bases and ~64x in physical coverage. Two plasmid libraries with insert sizes of 4 and 10 kb will be used to provide the majority of sequence coverage. Fosmids, which contain 40kb average inserts from randomly sheared genomic DNA, provide long-range linking information that allows large scaffold sizes to be achieved.The Broad’s assembly program, Arachne, will be used to assemble the Colletotrichum genome sequence. To provide an independent view of the genome and a measure of the quality of the genome assembly, an optical map will be commissioned from OpGen Inc. (Madison, WI, The quality of the Broad assembly will be assessed by comparing the predicted restriction fragment lengths from the assembled genome with the observed fragment lengths in the optical map. The map also provides a means to anchor sequence to the genome, adding order and orientation to the sequence contigs where there previously was none.The Calhoun whole genome analysis system will be used to identify repeat features, call genes using a variety of gene prediction tools, assign functional annotation to genes, predicts protein domains, and provides access to genome annotation data and support various analyses.EST Sequencing: EST sequences developed at the University of Kentucky will be used to train the gene prediction algorithm. We propose to sequence both ends of a total of 15,000 clones. The sequences will be collated into unigene sets with the aid of stackPACK. BLAST and conserved domain and Prosite signature motif searches will provide information about possible functional classes.

Anticipated Timeline:

Spring 2007:

  • Optical Map of the genome
  • Whole Genome Shotgun Sequencing

Fall 2007

  • Genome Assembly
  • EST Resource
  • Design, develop, and implement the educational curriculum

Spring 2008

  • Automated Annotation of the genome
  • Assess High School student participants

Fall 2008

  • Comparative Genomics web site