Info • Phycomyces blakesleeanus NRRL1555 v2.0

Status

Assembly v2 (1 March 2010) is an improved assembly produced by the JGI Finishing Pipeline. 80 scaffolds and 53.9 Mbp were assembled.

Main genome scaffold total 80
Main genome contig total 350
Main genome scaffold sequence total 53.9 Mbp
Main genome contig sequence total 53.4 Mbp
Estimated % sequence bases in gaps 1.1 %
Main genome scaffold N50 / L50 11 / 1.5 Mbp
Main genome contig N50 / L50 41 / 370.4 kbp
Number of scaffolds >50 Kbp 51
% main genome in scaffolds >50 99.4 %
% ESTs aligned to scaffolds 98 %

 

Assembly v1 (September 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 ~7.49X. After trimming for vector and quality, 506287 reads assembled into 475 main genome scaffolds totaling 55.9 Mbp. Roughly half of the genome is contained in 15 scaffolds all at least 1.0 MB in length.

Annotation v2 (1 March 2010) 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 to the v2 scaffolds. After filtering for homology and expression support, a total of 16528 genes were structurally and functionally annotated:
# of genes 16528
Gene density 306.4 genes / Mbp scaffold
Ave.gene length 1627.7 nt
Ave. protein length 352.8 aa
Ave. exon frequency 4.5 exons / gene
% genes with introns 89 %
% models with start+stop codons 90 %
% genes with NR hits 67 %
% genes with Pfam domains 44 %
% genes with TM domains 16 %
% genes with ESTs 33 %
% genes in multigene families 76 %


Annotation v1 (November 2006): The draft annotation, version 1.0, includes a total of 14,792 gene models predicted and functionally annotated using the JGI Annotation Pipeline.

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.