Decoding the chromosome-scale genome of the nutrient-rich Agaricus subrufescens: a resource for fungal biology and biotechnology

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology Pub Date : 2023-11-01 DOI:10.1016/j.resmic.2023.104116

Carlos Godinho de Abreu , Luiz Fernando Wurdig Roesch , Fernando Dini Andreote , Saura Rodrigues Silva , Tatiana Silveira Junqueira de Moraes , Diego Cunha Zied , Félix Gonçalves de Siqueira , Eustáquio Souza Dias , Alessandro M. Varani , Victor Satler Pylro

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引用次数: 0

Abstract

Agaricus subrufescens, also known as the “sun mushroom,” has significant nutritional and medicinal value. However, its short shelf life due to the browning process results in post-harvest losses unless it's quickly dehydrated. This restricts its availability to consumers in the form of capsules. A genome sequence of A. subrufescens may lead to new cultivation alternatives or the application of gene editing strategies to delay the browning process. We assembled a chromosome-scale genome using a hybrid approach combining Illumina and Nanopore sequencing. The genome was assembled into 13 chromosomes and 31 unplaced scaffolds, totaling 44.5 Mb with 96.5% completeness and 47.24% GC content. 14,332 protein-coding genes were identified, with 64.6% of the genome covered by genes and 23.41% transposable elements. The mitogenome was circularized and encoded fourteen typical mitochondrial genes. Four polyphenol oxidase (PPO) genes and the Mating-type locus were identified. Phylogenomic analysis supports the placement of A. subrufescens in the Agaricomycetes clade. This is the first available genome sequence of a strain of the “sun mushroom.” Results are available through a Genome Browser (https://plantgenomics.ncc.unesp.br/gen.php?id=Asub) and can support further fungal biological and genomic studies.

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解码营养丰富的亚陆生蘑菇的染色体规模基因组：真菌生物学和生物技术的资源。

蘑菇，也被称为“太阳蘑菇”，具有重要的营养和药用价值。然而，由于褐变过程，它的保质期很短，除非迅速脱水，否则会导致收获后的损失。这限制了其以胶囊形式提供给消费者。亚绿曲霉的基因组序列可能会带来新的栽培选择或应用基因编辑策略来延缓褐变过程。我们使用Illumina和Nanopore测序相结合的混合方法组装了染色体规模的基因组。基因组被组装成13条染色体和31个未放置的支架，总计44.5Mb，完整性为96.5%，GC含量为47.24%。鉴定出14332个蛋白质编码基因，其中64.6%的基因组被基因覆盖，23.41%的转座子被转座子覆盖。线粒体基因组被循环化，编码了14个典型的线粒体基因。鉴定了4个多酚氧化酶（PPO）基因和交配型基因座。系统发育基因组分析支持A.subrufscens在琼脂分支中的定位。这是“太阳蘑菇”菌株的第一个可用基因组序列。结果可通过基因组浏览器获得(https://plantgenomics.ncc.unesp.br/gen.php?id=Asub)并且可以支持进一步的真菌生物学和基因组研究。

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来源期刊

Research in microbiology 生物-微生物学

CiteScore

4.10

自引率

3.80%

发文量

审稿时长

16 days

期刊介绍： Research in Microbiology is the direct descendant of the original Pasteur periodical entitled Annales de l''Institut Pasteur, created in 1887 by Emile Duclaux under the patronage of Louis Pasteur. The Editorial Committee included Chamberland, Grancher, Nocard, Roux and Straus, and the first issue began with Louis Pasteur''s "Lettre sur la Rage" which clearly defines the spirit of the journal:"You have informed me, my dear Duclaux, that you intend to start a monthly collection of articles entitled "Annales de l''Institut Pasteur". You will be rendering a service that will be appreciated by the ever increasing number of young scientists who are attracted to microbiological studies. In your Annales, our laboratory research will of course occupy a central position, but the work from outside groups that you intend to publish will be a source of competitive stimulation for all of us."That first volume included 53 articles as well as critical reviews and book reviews. From that time on, the Annales appeared regularly every month, without interruption, even during the two world wars. Although the journal has undergone many changes over the past 100 years (in the title, the format, the language) reflecting the evolution in scientific publishing, it has consistently maintained the Pasteur tradition by publishing original reports on all aspects of microbiology.