Info • Mucor lusitanicus CBS277.49 v2.0
Please note that this organism is for archival use only. Please see the current Mucor lusitanicus CBS277.49 v3.0 site for the latest data and information.

Status

Assembly v2 (28 Dec 2009) is an improved assembly produced by the JGI Finishing Pipeline. 26 scaffolds and 36.6 Mbp were assembled.
Main genome scaffold total 26
Main genome contig total 26
Main genome scaffold sequence total 36.6 Mbp
Main genome contig sequence total 36.6 Mbp
Estimated % sequence bases in gaps 0.0 %
Main genome scaffold N50 / L50 4 / 4.3 Mbp
Main genome contig N50 / L50 4 / 4.3 Mbp
Number of scaffolds >50 Kbp 15
% main genome in scaffolds >50 99.7%
% ESTs aligned to scaffolds 95%

The draft assembly release version 1.0 (12 Mar 2009) of whole genome shotgun reads was constructed with Arachne, using paired end sequencing reads at an average coverage of 9.49X. After trimming for vector and quality, the sequencing reads assembled into 23 main genome scaffolds totaling 36.5 MB. Roughly half of the genome is contained in 4 scaffolds all at least 4.3 Mbp in length.

Annotation v2 (28 Dec 2009) is a consensus gene set predicted by the JGI Annotation Pipeline, using a variety of cDNA-based, protein-based, and ab initio gene modelers, as well as Annotation v1 genes mapped onto the v2 scaffolds. After filtering for homology and expression support, a total of 11719 genes were structurally and functionally annotated.

# of genes 11719
Gene density 320.3 genes / Mbp scaffold
Ave.gene length 1429.3 nt
Ave. protein length 379.5 aa
Ave. exon frequency 3.8 exons / gene
% genes with introns 83%
% models with start+stop codons 85%
% genes with NR hits 82%
% genes with Pfam domains 64%
% genes with TM domains 18%
% genes with ESTs 33%
% genes in multigene families 72%

The draft annotation release version 1.0 (12 Mar 2009) of the v1.0 assembly was produced by the JGI Annotation Pipeline, using a variety of cDNA/EST-based, homology-based, and ab initio gene predictors. After filtering for EST and homology support, a total of 10930 genes were structurally and functionally annotated. 83% of the genes have homology support, 61% have Pfam support, and 36% have EST support.

Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV
Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication.
Curr Biol. 2016 Jun 20;26(12):1577-1584. doi: 10.1016/j.cub.2016.04.038

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.