Status
v 4.0 Dec 2013. The v 3.0 assembly was reannotated with the current version of the JGI annotation pipeline. The resulting 11910 gene models include manually curated gene models and annotations mapped forward from v 3.0.
v 3.0 June 2008. This assembly of A. niger contains 8 chromosomes, made up of 21 scaffolds, and 3 unmapped scaffolds. 7 of the 8 chromosomes and 1 unmapped scaffold contain telomeres making A. niger's genome 34.85 MB in size.
This finished release includes 11197 gene models and annotations mapped from v1.0 annotations of this genome. This includes user-created gene models and manually curated annotations.
v.1.0 April 2006. The assembly release version 1.0 of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 8.9X. After trimming for vector and quality, 365,698 reads assembled into 143 scaffolds totaling 37.1 MB. Roughly half of the genome is contained in 6 scaffolds all at least 2.0 MB in length.
The current draft release, version 1.0, includes a total of 11,200 gene models predicted and functionally annotated using the JGI annotation pipeline.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 34.85 |
| Sequencing read coverage depth | 8.9 |
| # of contigs | 24 |
| # of scaffolds | 24 |
| # of scaffolds >= 2Kbp | 24 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 1.94 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 3.77, 3.76, 3.32 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | CombestEstClusters | 11078 | 11057 | 99.8% |
| Ests | pooled_clustered_ESTs | 51180 | 47681 | 93.2% |
| Ests | pooled_ESTs | 810840 | 778715 | 96.0% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1861 | 1567 |
| transcript | 1634 | 1392 |
| exon | 483 | 274 |
| intron | 97 | 64 |
| description: | ||
| protein length (aa) | 495 | 415 |
| exons per gene | 3.38 | 3 |
| # of gene models | 11910 |
Collaborators
Genome Reference(s)
Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.
Genome Res. 2011 Jun;21(6):885-97. doi: 10.1101/gr.112169.110
