What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence

Mannhaupt, Gertrud; Montrone, Corinna; Haase, Dirk; Mewes, Hans‐Werner; Aign, Verena; Hoheisel, Jörg D.; Fartmann, Berthold; Nyakatura, Gerald; Kempken, Frank; Maier, Jutta; Schulte, Ulrich

doi:10.1093/nar/gkg293

Cited by 62 publications

(43 citation statements)

References 87 publications

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“…Another gyspy-like element is inserted 100 bp upstream of a 'hybrid' peroxidase gene pc.91.32.1 (Supplementary Table 1 online). The occurrence of intact transposons and other highly conserved repetitive elements is in marked contrast to the recently sequenced N. crassa genome, where repeat-induced point mutations (RIP) have greatly reduced the frequency of repeats greater than 400 bp [6][7][8] .…”

Section: A R T I C L E Smentioning

confidence: 96%

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

et al. 2004

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Section: A R T I C L E Smentioning

confidence: 96%

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

et al. 2004

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“…Of this number, 1074 had a homolog in at least one plant or one animal genome of those tested above, demonstrating that this proteobacterial set of just over 1000 genes was conserved among eukaryotes tested. Similarly, Mannhaupt et al (2003) found that of the homologs of N. crassa present in other eukaryotes (EMBL database), 33% could also be found in prokaryotes (e-value £ 1E-8).…”

Section: Prokaryotic Homologsmentioning

confidence: 59%

Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

Hsiang

Baillie

2005

J Mol Evol

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Abstract. The purpose of this research was to search for evolutionarily conserved fungal sequences to test the hypothesis that fungi have a set of core genes that are not found in other organisms, as these genes may indicate what makes fungi different from other organisms. By comparing 6355 predicted or known yeast (Saccharomyces cerevisiae) genes to the genomes of 13 other fungi using Standalone TBLASTN at an e-value <1E-5, a list of 3340 yeast genes was obtained with homologs present in at least 12 of 14 fungal genomes. By comparing these common fungal genes to complete genomes of animals (Fugu rubripes, Caenorhabditis elegans), plants (Arabidopsis thaliana, Oryza sativa), and bacteria (Agrobacterium tumefaciens, Xylella fastidiosa), a list of common fungal genes with homologs in these plants, animals, and bacteria was produced (938 genes), as well as a list of exclusively fungal genes without homologs in these other genomes (60 genes). To ensure that the 60 genes were exclusively fungal, these were compared using TBLASTN to the major sequence databases at GenBank: NR (nonredundant), EST (expressed sequence tags), GSS (genome survey sequences), and HTGS (unfinished high-throughput genome sequences). This resulted in 17 yeast genes with homologs in other fungal genomes, but without known homologs in other organisms. These 17 core, fungal genes were not found to differ from other yeast genes in GC content or codon usage patterns. More intensive study is required of these 17 genes and other common fungal genes to discover unique features of fungi compared to other organisms.

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“…Roughly twice as many fragments would be needed for equal confidence in detecting an element representing 0.25% of the genome. In fungi examined to date, Class II elements are generally below this threshold (Kidwell, 2002;Mannhaupt et al, 2003), and therefore their presence in M. violaceum cannot be excluded without a more detailed study.…”

Section: Discussionmentioning

confidence: 99%

Repetitive DNA in the automictic fungus Microbotryum violaceum

Hood

2005

Genetica

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The small genomes of fungi are expected to have little repetitive content other than rDNA genes. Moreover, among asexual or highly selfing lineages, the diversity of repetitive elements is also expected to be very low. However, in the automictic fungus Microbotryum violaceum, a very large proportion of random DNA fragments from the autosomes and the fungal sex chromosomes are repetitive in nature, either as retrotransposon or helicase sequences. Among the retrotransposon sequences, examples were found from each major kind of elements, including copia, gypsy, and non-LTR sequences. The most numerous were copialike elements, which are believed to be rare in fungi, particularly among basidiomycetes. The many helicase sequences appear to belong to the recently discovered Helitron type of transposable elements. Also, sequences that could not be identified as a known type of gene were also very repetitive within the database of random fragments from M. violaceum. The differentiated pair of fungal sex chromosomes and suppression of recombination may be the major forces determining the highly repetitive content in the small genome of M. violaceum.

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What's in the genome of a filamentous fungus? Analysis of the Neurospora genome sequence

Cited by 62 publications

References 87 publications

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

Comparison of the Yeast Proteome to Other Fungal Genomes to Find Core Fungal Genes

Repetitive DNA in the automictic fungus Microbotryum violaceum

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