{"id":174392,"date":"2026-09-17T21:55:02","date_gmt":"2026-09-18T03:55:02","guid":{"rendered":"https:\/\/tecscience.tec.mx\/en\/?post_type=sciencecommunication&p=174392"},"modified":"2026-09-18T16:51:15","modified_gmt":"2026-09-18T22:51:15","slug":"filamentous-fungus","status":"publish","type":"sciencecommunication","link":"https:\/\/tecscience.tec.mx\/en\/science-communication\/filamentous-fungus\/","title":{"rendered":"Thousands of Fungal Genes Under the Microscope"},"content":{"rendered":"\n

By Jos\u00e9 Manuel Villalobos-Escobedo<\/strong><\/a><\/p>\n\n\n\n

Filamentous fungi are involved in processes ranging from nutrient cycling<\/strong> and material decomposition<\/strong> to agriculture<\/strong> and human health<\/strong>. Some are allies of plants, helping control pests and pathogens<\/strong>; others can cause disease, harm amphibian and bat populations, and contribute to crop losses of up to 30% worldwide each year (1).<\/p>\n\n\n\n

Understanding what each of their genes does could help explain these capabilities, but the functions of most fungal genes remain unknown. Studying them one at a time is also slow and costly. Now, a new tool makes it possible to analyze thousands of genes simultaneously<\/strong> and determine which ones are essential for fungal growth under different conditions.<\/p>\n\n\n\n

The study, Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus<\/em><\/a>, presents a barcoded mutant library<\/strong> that allows researchers to study thousands of fungal genes at once and uncover their functions.<\/p>\n\n\n\n

The strategy involves disrupting different genes and assigning each mutant a unique genetic tag<\/strong>. Researchers can then track which mutants become more or less abundant as the fungus grows under different conditions, revealing which genes are required for survival and growth in each environment.<\/p>\n\n\n\n

\r\n \r\n \"\"\r\n <\/picture>
(Illustration: Courtesy of Jos\u00e9 Manuel Villalobos-Escobedo)<\/em><\/figcaption><\/figure>\n\n\n\n

Unlocking the hidden genes of a \u201cmold\u201d<\/h2>\n\n\n\n

The researchers created a library containing more than 83,000 mutants of <\/strong>Trichoderma atroviride<\/strong><\/em>, each identified by a unique DNA barcode<\/strong>. This filamentous fungus occurs naturally in soil and is used in agriculture as a biological control agent<\/strong> to help protect plants from microorganisms that can harm them.<\/p>\n\n\n\n

The researchers also adapted a strategy previously used in yeasts<\/strong> and bacteria<\/strong>, known as RB-TDNAseq, for use in this multicellular, multinucleate organism, T. atroviride<\/em>.<\/p>\n\n\n\n

The method uses the bacterium Agrobacterium tumefaciens<\/em> to insert DNA fragments<\/strong> carrying a unique tag, or \u201cbarcode,\u201d at different locations in the fungus\u2019s genome<\/strong>.<\/p>\n\n\n\n

Each insertion disrupts a different gene<\/strong>. Because every mutant carries its own barcode, thousands of mutants can be pooled into a single population, allowing researchers to track the behavior of each one using a high-throughput sequencing<\/strong> technique called BarSeq.<\/p>\n\n\n\n

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Agrobacterium tumefaciens-mediated fungal spore transformation protocol performed in a biosafety cabinet. (Photo: Courtesy)<\/em><\/figcaption><\/figure>\n\n\n\n

Using this approach, the researchers built a library of 83,311 insertions that disrupted 5,331 of the 11,863 predicted genes<\/strong> in the T. atroviride<\/em> genome.<\/p>\n\n\n\n

They then exposed this mixed population of mutants to different growth conditions<\/strong>\u2014including media lacking specific amino acids and media in which fructose or xylose was the only carbon source\u2014and tracked which mutants became less abundant under each condition. A decline indicated that the disrupted gene was required for growth in that environment.<\/p>\n\n\n\n

The analysis identified genes already known to be involved in the synthesis of sulfur-containing amino acids<\/strong>, confirming that the method was working as expected.<\/p>\n\n\n\n

It also uncovered genes involved in fructose metabolism<\/strong>, including a hexokinase required to process the sugar, as well as genes essential for using xylose, a major component of plant cell walls. These included a transcriptional regulator homologous to xlnR<\/strong> and a xylitol dehydrogenase<\/strong>.<\/p>\n\n\n\n

To validate these findings, the team turned to deletion mutants of the model fungus Neurospora crassa<\/em>. When the corresponding genes were missing, the mutants were unable to grow with xylose or xylan as a carbon source, just as the analysis predicted.<\/p>\n\n\n\n

\r\n \r\n \"\"\r\n <\/picture>
Mutagenized spores, collected in Falcon tubes<\/strong>, were used as the master library<\/strong> and stored at \u221280 \u00b0C<\/strong> for subsequent use as a mutant stock in BarSeq experiments. (Photo: Courtesy)<\/em><\/figcaption><\/figure>\n\n\n\n

Beyond these specific examples, the study\u2019s most significant contribution is methodological. The plasmid library, containing nearly 290 million unique DNA barcodes<\/strong>, together with the optimized transformation protocol, could be adapted to other species<\/strong> of filamentous fungi\u2014not just members of the genus Trichoderma<\/em>.<\/p>\n\n\n\n

The same strategy has already been used to generate a comparable library in a different thermophilic fungus, providing evidence that the approach can be transferred across a broad range of fungal species<\/strong>.<\/p>\n\n\n\n

This platform provides a foundation for large-scale studies of gene function in fungi with medical, agricultural, and biotechnological applications<\/strong>.<\/p>\n\n\n\n

In the long term, the approach could help identify targets for new antifungal treatments<\/strong> for humans, animals, and plants; improve biological control agents such as Trichoderma<\/em>; and support the development of fungal strains optimized to produce enzymes or other compounds of industrial interest.<\/p>\n\n\n\n

\r\n \r\n \"\"\r\n <\/picture>
Culture of mutant-group spores<\/strong> growing under conditions lacking different amino acids. (Photo: Courtesy).<\/em><\/figcaption><\/figure>\n\n\n\n

References<\/h4>\n\n\n\n
    \n
  1. Huberman LB, Villalobos-Escobedo JM, Skerker JM, Shi R, Rico-Ram\u00edrez AM, Adams CA, Arkin AP, Deutschbauer AM, Glass NL. Barcoded mutant library enables high-throughput functional genomics in a filamentous fungus<\/a>. PNAS. 2026;123(35):e2616888123.<\/li>\n<\/ol>\n\n\n\n


    Author<\/strong><\/h4>\n\n\n\n

    Jos\u00e9 Manuel Villalobos-Escobedo.<\/strong> Research professor at the Institute for Obesity Research<\/a> at Tecnol\u00f3gico de Monterrey, where he leads the Functional Genomics for Bioprospecting Laboratory. His research combines functional genomics, metagenomics, and metabolic modeling to study fungi and bacteria with applications in biotechnology.<\/p>\n","protected":false},"excerpt":{"rendered":"

    A new tool lets researchers probe thousands of genes in a filamentous fungus at once, revealing which ones are essential for growth and what roles they play.<\/p>\n","protected":false},"author":18,"featured_media":174393,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","format":"standard","meta":{"_acf_changed":false,"_eb_attr":"","footnotes":""},"categories":[93],"tags":[166],"class_list":["post-174392","sciencecommunication","type-sciencecommunication","status-publish","format-standard","has-post-thumbnail","hentry","category-biotechnology","tag-institute-for-obesity-research"],"acf":[],"yoast_head":"\nA Fungus\u2019s Hidden Genes | TecScience<\/title>\n<meta name=\"description\" content=\"A new tool lets researchers probe thousands of genes in a filamentous fungus at once, revealing which ones are essential for growth and what roles they play.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/tecscience.tec.mx\/en\/science-communication\/filamentous-fungus\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Thousands of Fungal Genes Under the Microscope\" \/>\n<meta property=\"og:description\" content=\"A new tool lets researchers probe thousands of genes in a filamentous fungus at once, revealing which ones are essential for growth and what roles they play.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/tecscience.tec.mx\/en\/science-communication\/filamentous-fungus\/\" \/>\n<meta property=\"og:site_name\" content=\"TecScience\" \/>\n<meta property=\"article:modified_time\" content=\"2026-09-18T22:51:15+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/tecscience.tec.mx\/en\/wp-content\/uploads\/sites\/9\/2026\/09\/filamentous-fungus.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"750\" \/>\n\t<meta property=\"og:image:height\" content=\"500\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"5 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/\",\"url\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/\",\"name\":\"A Fungus\u2019s Hidden Genes | TecScience\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/#primaryimage\"},\"image\":{\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/09\\\/filamentous-fungus.jpg\",\"datePublished\":\"2026-09-18T03:55:02+00:00\",\"dateModified\":\"2026-09-18T22:51:15+00:00\",\"description\":\"A new tool lets researchers probe thousands of genes in a filamentous fungus at once, revealing which ones are essential for growth and what roles they play.\",\"breadcrumb\":{\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/science-communication\\\/filamentous-fungus\\\/#primaryimage\",\"url\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/09\\\/filamentous-fungus.jpg\",\"contentUrl\":\"https:\\\/\\\/tecscience.tec.mx\\\/en\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2026\\\/09\\\/filamentous-fungus.jpg\",\"width\":750,\"height\":500,\"caption\":\"The study focused on Trichoderma atroviride, a filamentous fungus that occurs naturally in soil and is used in agriculture as a biological control agent because it helps protect plants from other microorganisms that can damage them. 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