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Announcements
- February 25-28, 2018
European Conference on Fungal Genetics, Haifa, Israel - March 13-16, 2018
Fungal genomics workshop @ JGI User Meeting, San Francisco, CA, U.S.A. - July 16-21, 2018
International Mycological Society Annual Meeting, San Juan, Puerto Rico
Releases
- March 7, 2024
Aspergillus fumigatus P4 SB v1.0 - March 7, 2024
Penicillium ribium P3 SB v1.0 - January 30, 2024
Trebouxiophyceae sp. bin 3300059473_978 v1.0 - January 30, 2024
Trebouxiophyceae sp. bin 3300059473_6682 v1.0 - January 30, 2024
Chlorellaceae sp. bin 3300059473_4402 v1.0
Benchmarking Fungal Annotation Pipeline
Complex intron-exon structure of eukaryotic genes makes their prediction challenging. Quality of gene prediction in eukaryotic genomes can be improved by combining different gene prediction approaches (ab initio, based on homology, ESTs, synteny, or their combinations) and experimental data (transcriptomics, proteomics, etc). In the course of fungal genome annotations we compared different gene predictors and annotation pipelines to assess and refine our annotation strategies for future genomes. Results of two such tests are presented here:
1. Annotation of Heterobasidion annosum genome (Dec 2008)
- Results: Several gene predictors and annotation pipelines were used in annotating the genome of fungus H. annosum v1.0 and accuracy of gene prediction was compared based on homology and EST support. Combination of tools used in the JGI annotation pipeline predicted larger sets of genes with best support.
EuGene
[1]GeneMark
[2]FgenesH
[3]JGI Pipe
[4,5]Number of predicted gene models 11,547 9,609 8,409 12,270 with partial EST support 5,544 3,829 4,567 5,248 with full length EST support 2,538 1,182 2,896 3,073 with homology support 6,758 6,043 5,750 7,214 with strong homology support (>80% aa identity, >80% coverage) 112 109 174 187 with homology and EST support 2,894 2,172 2,720 2,953 Average EST coverage per gene 77.7% 68.2% 80.8% 79.1% Supported splice sites 41,581 40,808 45,498 47,671 Average homology coverage per gene 64% 60% 68% 69%
EuGene models were built and provided by a collaborator. All models were used in JGI pipeline. EST support was computed based on 40,807 ESTs and 10,126 EST cluster consensus sequences mapped by BLAT; protein homology was computed by blast against NCBI NR. - Reference
2. Comparison of MAKER and JGI Annotation pipeline (Oct 2011)
- Results: Publicly available annotation pipeline MAKER[6] was compared with JGI annotation pipeline [4,5]. For Basidiomycete Dichomitus squalens , JGI pipeline predicted more genes with better support using several lines of evidence.
MAKER
[6]JGI Annotation pipeline
[4,5]Number of predicted gene models 9,940 12,290 with Swissprot hits 6,521 7,356 with non-repeat PFAM domains 5,365 6,010 with EST support 9,252 10,796 with >90% EST support 7,729 9,178 Number of unique PFAM domains 2,207 2,245 Average EST coverage per gene 93.0% 93.3% Splice sites supported by ESTs 99,627 102,200
Inputs: Aassembly v1.0 of D. squalens, 359,410 proteins seeds from NCBI NR, 16,501 EST cluster consensus sequences mapped by BLAT to the assembly. Mapper used the following gene predictors: Exonerate, FgenesH (same parameters as in JGI pipeline) and Augustus. All genes were blasted against the same Swissprot set of 530,264 protein sequences (downloaded Jul5 2011), EST sequences, and PFAM database(Pfam_v21)
- Reference:
- Schiex T, Moisan A, Rouzé P. (2001) Computational Biology, selected papers from JOBIM' 2000, no 2066 in LNCS. Springer Verlag; EuGène, an eukaryotic gene finder that combines several type of evidence; pp. 118–133.
- Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M. (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 18(12):1979-90.
- Solovyev V, Kosarev P, Seledsov I, Vorobyev D. (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol. 7 Suppl 1:S10.1-12.
- Grigoriev IV, Martinez DA, Salamov AA (2006) Fungal genomic annotation. In Applied Mycology and Biotechnology (Eds. Aurora, DK, Berka, RM, Singh, GB), Elsevier Press, Vol 6 (Bioinformatics), 123-142.
- http://genome.jgi.doe.gov/programs/fungi/FungalGenomeAnnotationSOP.pdf
- Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. (2008) MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18(1):188-96.