Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
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DOI：
10.1101/gr.112169.110
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发表时间：
2011-06-01
期刊：
影响因子：
7
通讯作者：
Baker, Scott E.
中科院分区：
文献类型：
--
作者：
Andersen, Mikael R.;Salazar, Margarita P.;Baker, Scott E.
丝状真菌尼日尔在其表型上表现出很大的多样性。它是全球发现的海洋和陆地菌株，产生大量的有机酸和水解酶，一些菌株表现出致病性。虽然工业产酶A.尼日尔菌株（CBS 513.88）已经测序，该物种的多功能性和多样性迫使进行额外的探索。因此，我们进行了产酸A的全基因组测序。尼日尔野生型菌株（ATCC 1015），并产生非常高质量的基因组序列。只有15个缺口存在于序列中，一半的端粒区域已被阐明。此外，来自ATCC 1015的序列信息用于改进CBS 513.88的基因组序列。染色体水平的比较发现了几个基因组重排，缺失，一个明确的情况下，应变特定的水平基因转移，并确定了0.8 Mb的新序列。发现两种菌株之间的每种酶的单核苷酸多态性（SNPs/kb）异常高（平均值：7.8，最大值：160个SNPs/kb）。物种内的高变异与外代谢物分析和遗传学证实。等位基因的详细列表被生成，并且观察到基因型差异在酸产生和蛋白质合成所必需的代谢途径中积累。转录组分析支持与产生蛋白质的CBS 513.88菌株中的葡糖淀粉酶A、tRNA-内切酶和蛋白质转运蛋白中丰富的氨基酸的生物合成相关的基因的上调。我们的结果和数据集从这个综合系统生物学分析导致真菌进化的快照，并将支持进一步优化基于丝状真菌的细胞工厂。
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.