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Title: Annotation and analysis of the geome of Phycomyces blakesleeanus, a model photoresponsive zygomycete

Abstract

Light induces in P. blakesleeanus multiple developmental and biochemical responses (sporangiophore growth and development, beta-carotene synthesis). P. blakesleeanus is an intensively studied, experimentally tractable model organism, and whole-genome analysis is expected to further elucidate the signaling pathways underlying its photoregulation. To this end, the genome was sequenced to 7.49X depth and assembled into 475 scaffolds totaling 56Mbp, and 47847 ESTs were assembled from cDNAs of light and dark cultures. We combined into a single annotation pipeline a variety of gene modeling methods (homology-based, EST-based, and ab initio), and predicted 14792 protein-coding genes. Many of these gene predictions are supported by homology in nr (68percent), by Pfam domains (44percent), or by ESTs (35percent). We next assigned GO terms to 41percent of the proteins and EC numbers to 16percent. We then distributed these annotations to the Phycomyces consortium, along with tools to curate them manually. We expect that the annotation will provide a solid platform for expression analysis. In addition to its value as a model organism, P. blakesleeanus is the second zygomycete with a sequenced genome, after the related Rhizopus oryzae. We therefore will present preliminary results of comparative analysis between the two zygomycetes.

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1167446
Report Number(s):
LBNL-6850E
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: Fungal Genetics Conference - 2007, Pacific Grove, CA, March 20 - 25, 2007
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS; Phycomyces blakesleeanus, Joint Genome Institute, zygomycete

Citation Formats

Kuo, Alan, Salamov, Asaf, Pangilinan, Jasmyn, Lindquist, Erika, Shapiro, Harris, Baker, Scott, Corrochano, Luis, and Grigoriev, Igor. Annotation and analysis of the geome of Phycomyces blakesleeanus, a model photoresponsive zygomycete. United States: N. p., 2007. Web.
Kuo, Alan, Salamov, Asaf, Pangilinan, Jasmyn, Lindquist, Erika, Shapiro, Harris, Baker, Scott, Corrochano, Luis, & Grigoriev, Igor. Annotation and analysis of the geome of Phycomyces blakesleeanus, a model photoresponsive zygomycete. United States.
Kuo, Alan, Salamov, Asaf, Pangilinan, Jasmyn, Lindquist, Erika, Shapiro, Harris, Baker, Scott, Corrochano, Luis, and Grigoriev, Igor. Mon . "Annotation and analysis of the geome of Phycomyces blakesleeanus, a model photoresponsive zygomycete". United States. doi:. https://www.osti.gov/servlets/purl/1167446.
@article{osti_1167446,
title = {Annotation and analysis of the geome of Phycomyces blakesleeanus, a model photoresponsive zygomycete},
author = {Kuo, Alan and Salamov, Asaf and Pangilinan, Jasmyn and Lindquist, Erika and Shapiro, Harris and Baker, Scott and Corrochano, Luis and Grigoriev, Igor},
abstractNote = {Light induces in P. blakesleeanus multiple developmental and biochemical responses (sporangiophore growth and development, beta-carotene synthesis). P. blakesleeanus is an intensively studied, experimentally tractable model organism, and whole-genome analysis is expected to further elucidate the signaling pathways underlying its photoregulation. To this end, the genome was sequenced to 7.49X depth and assembled into 475 scaffolds totaling 56Mbp, and 47847 ESTs were assembled from cDNAs of light and dark cultures. We combined into a single annotation pipeline a variety of gene modeling methods (homology-based, EST-based, and ab initio), and predicted 14792 protein-coding genes. Many of these gene predictions are supported by homology in nr (68percent), by Pfam domains (44percent), or by ESTs (35percent). We next assigned GO terms to 41percent of the proteins and EC numbers to 16percent. We then distributed these annotations to the Phycomyces consortium, along with tools to curate them manually. We expect that the annotation will provide a solid platform for expression analysis. In addition to its value as a model organism, P. blakesleeanus is the second zygomycete with a sequenced genome, after the related Rhizopus oryzae. We therefore will present preliminary results of comparative analysis between the two zygomycetes.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Mar 19 00:00:00 EDT 2007},
month = {Mon Mar 19 00:00:00 EDT 2007}
}

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