Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

被引：277

作者：

Andersen, Mikael R. ^{[2
]}

Salazar, Margarita P. ^{[2
]}

Schaap, Peter J. ^{[3
]}

van de Vondervoort, Peter J. I. ^{[4
]}

Culley, David ^{[1
]}

Thykaer, Jette ^{[2
]}

Frisvad, Jens C. ^{[2
]}

Nielsen, Kristian F. ^{[2
]}

Albang, Richard ^{[5
]}

Albermann, Kaj ^{[5
]}

Berka, Randy M. ^{[6
]}

Braus, Gerhard H. ^{[7
]}

Braus-Stromeyer, Susanna A. ^{[7
]}

Corrochano, Luis M. ^{[8
]}

Dai, Ziyu ^{[1
]}

van Dijck, Piet W. M. ^{[9
]}

Hofmann, Gerald ^{[10
]}

Lasure, Linda L. ^{[1
]}

Magnuson, Jon K. ^{[1
]}

Menke, Hildegard ^{[4
]}

Meijer, Martin ^{[11
]}

Meijer, Susan L. ^{[2
]}

Nielsen, Jakob B. ^{[2
]}

Samson, Rob A. ^{[11
]}

Stam, Hein ^{[4
]}

Tsang, Adrian ^{[12
]}

van den Brink, Johannes M. ^{[13
]}

Atkins, Alex ^{[14
]}

Aerts, Andrea ^{[14
]}

Shapiro, Harris ^{[14
]}

Pangilinan, Jasmyn ^{[14
]}

Salamov, Asaf ^{[14
]}

Lou, Yigong ^{[14
]}

Lindquist, Erika ^{[14
]}

Lucas, Susan ^{[14
]}

Grimwood, Jane ^{[15
]}

Grigoriev, Igor V. ^{[14
]}

Kubicek, Christian P. ^{[16
]}

Martinez, Diego ^{[17
,18
]}

van Peij, Noel N. M. E. ^{[4
]}

Roubos, Johannes A. ^{[4
]}

Nielsen, Jens ^{[2
]}

Baker, Scott E. ^{[1
]}

机构：

[1] Pacific NW Natl Lab, Fungal Biotechnol Team, Richland, WA 99352 USA

[2] Tech Univ Denmark, Dept Syst Biol, Ctr Microbial Biotechnol, DK-2800 Kongens Lyngby, Denmark

[3] Wageningen Univ, Microbiol Lab, Sect Fungal Genom, NL-6703 HB Wageningen, Netherlands

[4] DSM Biotechnol Ctr, NL-2600 MA Delft, Netherlands

[5] Biomax Informat AG, D-82152 Martinsried, Germany

[6] Novozymes Inc, Davis, CA 95616 USA

[7] Univ Gottingen, D-37077 Gottingen, Germany

[8] Univ Seville, Dept Genet, E-41080 Seville, Spain

[9] DSM Nutr Prod, NL-2600 MA Delft, Netherlands

[10] Novozymes AS, DK-4400 Kalundborg, Denmark

[11] CBS Fungal Biodivers Ctr, NL-3584 CT Utrecht, Netherlands

[12] Concordia Univ, Ctr Struct & Funct Genom, Montreal, PQ H4B 1R6, Canada

[13] Chr Hansen AS, DK-2970 Horsholm, Denmark

[14] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA

[15] Stanford Human Genome Ctr, Joint Genome Inst, Palo Alto, CA 94304 USA

[16] Vienna Univ Technol, Res Area Gene Technol & Appl Biochem, Inst Chem Engn, A-1060 Vienna, Austria

[17] Los Alamos Natl Lab, Los Alamos, NM 87545 USA

[18] Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA

来源：

GENOME RESEARCH | 2011年 / 21卷 / 06期

关键词：

FUNGAL METABOLITE; LIQUID-CHROMATOGRAPHY; GENES; EXPRESSION; IDENTIFICATION; MYCOTOXINS; KARYOTYPE; REVEALS; CLONING; SAFETY;

D O I：

10.1101/gr.112169.110

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 whole-genome 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.

引用

页码：885 / 897

页数：13

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