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Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii.
- Source :
-
Eukaryotic cell [Eukaryot Cell] 2005 Feb; Vol. 4 (2), pp. 455-64. - Publication Year :
- 2005
-
Abstract
- Blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. Its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. To contribute to the understanding of the complexity of the B. emersonii genome, we present here a survey of expressed sequence tags (ESTs) from various stages of the fungal development. Nearly 20,000 cDNA clones from 10 different libraries were partially sequenced from their 5' end, yielding 16,984 high-quality ESTs. These ESTs were assembled into 4,873 putative transcripts, of which 48% presented no matches with existing sequences in public databases. As a result of Gene Ontology (GO) project annotation, 1,680 ESTs (35%) were classified into biological processes of the GO structure, with transcription and RNA processing, protein biosynthesis, and transport as prevalent processes. We also report full-length sequences, useful for construction of molecular phylogenies, and several ESTs that showed high similarity with known proteins, some of which were not previously described in fungi. Furthermore, we analyzed the expression profile (digital Northern analysis) of each transcript throughout the life cycle of the fungus using Bayesian statistics. The in silico approach was validated by Northern blot analysis with good agreement between the two methodologies.
- Subjects :
- Amino Acid Sequence
Animals
Databases, Nucleic Acid
Genes, Fungal
Humans
Life Cycle Stages genetics
Molecular Sequence Data
Oligonucleotide Array Sequence Analysis
Sequence Alignment
Blastocladiella genetics
Blastocladiella physiology
Expressed Sequence Tags
Gene Expression Profiling
Genome, Fungal
Sequence Analysis, DNA
Subjects
Details
- Language :
- English
- ISSN :
- 1535-9778
- Volume :
- 4
- Issue :
- 2
- Database :
- MEDLINE
- Journal :
- Eukaryotic cell
- Publication Type :
- Academic Journal
- Accession number :
- 15701807
- Full Text :
- https://doi.org/10.1128/EC.4.2.455-464.2005