Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain

Braumann, Ilka; Berg, M. A.; Kempken, Frank

doi:10.1007/s00438-008-0367-9

Cited by 13 publications

(6 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The presence and functionality of transposons are qualitatively and quantitatively less complex in the genome of ATCC 1015 than in CBS 513.88 (Supplemental Table 11). Such a different distribution of transposons between strains has been observed before (Braumann et al 2008) and was described to be inducible by mutagenesis and other stress-induced conditions (Strand and McDonald 1985). However, the number and scale of differences make a recent mutagenesis program unlikely to be the basis for the multiple HGT events.…”

Section: Discussionmentioning

confidence: 87%

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

322

276

View full text Add to dashboard Cite

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

show abstract

Section: Discussionmentioning

confidence: 87%

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Andersen

Salazar²,

Schaap³

et al. 2011

Genome Res.

322

276

View full text Add to dashboard Cite

show abstract

“…Some Smini1 and Smini3 repeats possess 5 bp target site duplications suggesting that they may be transposons or integrated elements caused by transposition. In some cases, point mutations may have modified target site duplications, or recombination may have occurred as has been shown for Aspergillus niger [65]. As Smini1 and Smini3 are both uniform in size (with the exception of some truncated elements), they may be solo-LTRs rather than mini-transposons such as the guest element of N. crassa [66].…”

Section: Resultsmentioning

confidence: 96%

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

et al. 2010

Self Cite

View full text Add to dashboard Cite

Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30–90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in ∼4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for comparative studies to address basic questions of fungal biology.

show abstract

“…Ogasawara et al (2009) described at least 16 apparently unmutated copies of an active Tc1/ Mariner element ''Crawler" in an industrial A. oryzae strain, but this element is represented by only two degenerate fragments in the sequenced A. oryzae genome. Braumann et al (2008a) reported the occurrence of RIP-like mutations in an ANiTa family (Copia superfamily) in the industrial A. niger CBS-513.88 strain, but again this family is represented by only a few solo LTRs in the ATCC-1015 sequence (Braumann et al, 2008b). In the CBS-513.88 sequence there are a number of near-identical, apparently unmutated copies and one (ANiTaR1) that differs from the rest by one transversion and multiple transitions with dinucleotide preference: CpG > CpA > CpC > CpT (see Table 3 for re-analysis).…”

Section: A Oryzae a Flavus Aspergillus Carbonarius Aspergillus Amentioning

confidence: 97%

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

Clutterbuck

2011

Fungal Genetics and Biology

119

133

View full text Add to dashboard Cite

Strain-specific retrotransposon-mediated recombination in commercially used Aspergillus niger strain

Cited by 13 publications

References 34 publications

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

Comparative genomics of citric-acid-producingAspergillus nigerATCC 1015 versus enzyme-producing CBS 513.88

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

Contact Info

Product

Resources

About