Status
v1.0 (March 2011): The Acremonium alcalophilum genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. The nuclear genome sequence from this draft assembly was annotated using the JGI Genome Annotation Pipeline and custom analyses. Multiple ESTs sequencing technologies and EST cluster data sets were tested for gene modeling with this genome; the combined 454 and Illumina EST Clusters ("cap3_all", in the table below) was found best and used in gene modeling.
Summary statistics for the Acremonium alcalophilum v1.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 54.42 |
| Sequencing read coverage depth | 7.98x |
| # of contigs | 865 |
| # of scaffolds | 15 |
| # of scaffolds >= 2Kbp | 14 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 7.21 |
| # of gaps | 425 |
| % of scaffold length in gaps | 0.4% |
| Three largest Scaffolds (Mbp) | 11.08, 9.11, 7.21 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome | Notes |
| EstClusters | Acral1_EstClusters_cap3_all.fa | 16,004 | 12,195 | 76% | Illumina + 454 ests clustered by A. Tsang lab. |
| EstClusters | Acral1_EstClusters_cap3_illumina.fa | 19,647 | 14,705 | 75% | Illumina ests clustered by A. Tsang lab. |
| EstClusters | Acral1_EstClusters_454Isotigs_gte50.fasta | 11,550 | 11,388 | 99% | 454 ESTs clustered by JGI. |
| Ests | Acral1_Ests_CFFC_CGAN_good_ESTs.fasta | 1,336,020 | 1,283,166 | 96% | 454 ESTs sequenced by JGI. |
| Ests | Acral1_Ests_solexa_s_7.fasta, _s7_1.fasta, _s_7_2.fasta | 58,438,549 | 22,607,805 | 39% | Illumina ESTs provided by A. Tsang lab. |
| Note: All ESTs and EstClusters were mapped to the genomic assembly using BLAT and applying cutoffs of 95% identity and 80% coverage. | |||||
| Gene Models | FilteredModels2_2 | |
| length (bp) of: | average | median |
| gene | 2451 | 1923 |
| transcript | 1994 | 1614 |
| exon | 493 | 180 |
| intron | 152 | 71 |
| description: | ||
| protein length (aa) | 451 | 366 |
| exons per gene | 4.05 | 3 |
| # of gene models | 9491 |
Collaborators
- Adrian Tsang, Concordia University, Montreal, Canada
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
