Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species†

IF 3 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Molecular omics Pub Date : 2024-08-20 DOI:10.1039/D4MO00108G

Freddy Castillo-Alfonso, Cecilio Valadez-Cano, Gabriela Cejas-Añón, José Utrilla, Juan-Carlos Sigala Alanis, Sylvie Le Borgne, Alfonso Mauricio Sales-Cruz, Gabriel Vigueras-Ramírez and Roberto Olivares-Hernández

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引用次数: 0

Abstract

The basidiomycete fungus Leucoagaricus gongylophorus is able to grow in the fungus garden of leaf-cutter ants. This mutualistic interaction has driven the evolutionary adaptation of L. gongylophorus, shaping its metabolism to produce enzymes adept at lignocellulosic biomass degradation. In this study, we undertook the comprehensive sequencing, assembly, and functional annotation of the genome of L. gongylophorus strain LEU18496, mutualistic fungus of the Atta mexicana. Our genomic analyses revealed a distinctive bimodal nature to the genome: a predominant region characterized by AT enrichment and low genetic density, alongside a smaller region exhibiting higher GC content and higher genetic density. The presence of transposable elements (TEs) within the AT-enriched region suggests genomic compartmentalization, facilitating differential evolutionary rates. With a gene count of 6748, the assembled genome of L. gongylophorus LEU18496 surpasses previous reports for this fungal species. Inspection of genes associated with central metabolism unveiled a remarkable abundance of carbohydrate-active enzymes (CAZymes) and fungal oxidative lignin enzymes (FOLymes), underscoring their pivotal roles in the life cycle of this fungus.

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Leucoagaricus gongylophorus LEU18496（一种迪卡里亚互生物种）的测序、组装和基因组注释。

基生真菌Leucoagaricus gongylophorus能够在切叶蚁的真菌花园中生长。这种互惠互利的互动关系推动了褐飞虱的进化适应，使其新陈代谢产生了善于降解木质纤维素生物质的酶。在这项研究中，我们对墨西哥蚁的互生真菌 L. gongylophorus 菌株 LEU18496 的基因组进行了全面测序、组装和功能注释。我们的基因组分析表明，该基因组具有独特的双峰性质：一个主要区域以 AT 富集和低遗传密度为特征，另一个较小区域则表现出较高的 GC 含量和较高的遗传密度。富含 AT 的区域内存在转座元件（TE），这表明基因组区隔化促进了不同的进化速度。L. gongylophorus LEU18496基因组的基因数量为6748个，超过了之前关于该真菌物种的报道。对与中央代谢有关的基因的检查发现了大量的碳水化合物活性酶（CAZymes）和真菌氧化木质素酶（FOLymes），强调了它们在该真菌生命周期中的关键作用。

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来源期刊

Molecular omics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

5.40

自引率

3.40%

发文量

期刊介绍： Molecular Omics publishes high-quality research from across the -omics sciences. Topics include, but are not limited to: -omics studies to gain mechanistic insight into biological processes – for example, determining the mode of action of a drug or the basis of a particular phenotype, such as drought tolerance -omics studies for clinical applications with validation, such as finding biomarkers for diagnostics or potential new drug targets -omics studies looking at the sub-cellular make-up of cells – for example, the subcellular localisation of certain proteins or post-translational modifications or new imaging techniques -studies presenting new methods and tools to support omics studies, including new spectroscopic/chromatographic techniques, chip-based/array technologies and new classification/data analysis techniques. New methods should be proven and demonstrate an advance in the field. Molecular Omics only accepts articles of high importance and interest that provide significant new insight into important chemical or biological problems. This could be fundamental research that significantly increases understanding or research that demonstrates clear functional benefits. Papers reporting new results that could be routinely predicted, do not show a significant improvement over known research, or are of interest only to the specialist in the area are not suitable for publication in Molecular Omics.