Genomic features of lichen-associated black fungi.

IF 3.7 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
IUBMB Life Pub Date : 2025-01-01 DOI:10.1002/iub.2934
Victoria Keller, Anjuli Calchera, Jürgen Otte, Imke Schmitt
{"title":"Genomic features of lichen-associated black fungi.","authors":"Victoria Keller, Anjuli Calchera, Jürgen Otte, Imke Schmitt","doi":"10.1002/iub.2934","DOIUrl":null,"url":null,"abstract":"<p><p>Lichens are mutualistic associations consisting of a primary fungal host, and one to few primary phototrophic symbiont(s), usually a green alga and/or a cyanobacterium. They form complex thallus structures, which provide unique and stable habitats for many other microorganisms. Frequently isolated from lichens are the so-called black fungi, or black yeasts, which are mainly characterized by melanized cell walls and extremophilic lifestyles. It is presently unclear in which ways these fungi interact with other members of the lichen symbiosis. Genomic resources of lichen-associated black fungi are needed to better understand the physiological potential of these fungi and shed light on the complexity of the lichen consortium. Here, we present high-quality genomes of 14 black fungal lineages, isolated from lichens of the rock-dwelling genus Umbilicaria. Nine of the lineages belong to the Eurotiomycetes (Chaetothyriales), four to the Dothideomycetes, and one to the Arthoniomycetes, representing the first genome of a black fungus in this class. The PacBio-based assemblies are highly contiguous (5-42 contigs per genome, mean coverage of 79-502, N50 of 1.0-7.3 mega-base-pair (Mb), Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness generally ≥95.4%). Most contigs are flanked by a telomere sequence, suggesting we achieved near chromosome-level assemblies. Genome sizes range between 26 and 44 Mb. Transcriptome-based annotations yielded ~11,000-18,000 genes per genome. We analyzed genome content with respect to repetitive elements, biosynthetic genes, and effector genes. Each genome contained a polyketide synthase gene related to the dihydroxynaphthalene-melanin pathway. This research provides insights into genome content and metabolic potential of these relatively unknown, but frequently encountered lichen associates.</p>","PeriodicalId":14728,"journal":{"name":"IUBMB Life","volume":"77 1","pages":"e2934"},"PeriodicalIF":3.7000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664114/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IUBMB Life","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/iub.2934","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Lichens are mutualistic associations consisting of a primary fungal host, and one to few primary phototrophic symbiont(s), usually a green alga and/or a cyanobacterium. They form complex thallus structures, which provide unique and stable habitats for many other microorganisms. Frequently isolated from lichens are the so-called black fungi, or black yeasts, which are mainly characterized by melanized cell walls and extremophilic lifestyles. It is presently unclear in which ways these fungi interact with other members of the lichen symbiosis. Genomic resources of lichen-associated black fungi are needed to better understand the physiological potential of these fungi and shed light on the complexity of the lichen consortium. Here, we present high-quality genomes of 14 black fungal lineages, isolated from lichens of the rock-dwelling genus Umbilicaria. Nine of the lineages belong to the Eurotiomycetes (Chaetothyriales), four to the Dothideomycetes, and one to the Arthoniomycetes, representing the first genome of a black fungus in this class. The PacBio-based assemblies are highly contiguous (5-42 contigs per genome, mean coverage of 79-502, N50 of 1.0-7.3 mega-base-pair (Mb), Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness generally ≥95.4%). Most contigs are flanked by a telomere sequence, suggesting we achieved near chromosome-level assemblies. Genome sizes range between 26 and 44 Mb. Transcriptome-based annotations yielded ~11,000-18,000 genes per genome. We analyzed genome content with respect to repetitive elements, biosynthetic genes, and effector genes. Each genome contained a polyketide synthase gene related to the dihydroxynaphthalene-melanin pathway. This research provides insights into genome content and metabolic potential of these relatively unknown, but frequently encountered lichen associates.

与地衣相关的黑色真菌的基因组特征。
地衣是由一个初级真菌宿主和一个或几个初级光合共生体(通常是绿藻和/或蓝藻)组成的共生体。它们形成复杂的菌体结构,为许多其他微生物提供独特而稳定的栖息地。通常从地衣中分离出来的是所谓的黑色真菌,或黑色酵母,其主要特征是细胞壁变黑,生活方式极端。目前还不清楚这些真菌是如何与地衣共生的其他成员相互作用的。为了更好地了解这些真菌的生理潜能和揭示地衣联盟的复杂性,需要地衣相关黑色真菌的基因组资源。在这里,我们提出了14个黑色真菌谱系的高质量基因组,分离自地衣的岩石居住属脐衣。其中9个系属于Eurotiomycetes (Chaetothyriales), 4个系属于Dothideomycetes, 1个系属于Arthoniomycetes,代表了该类别黑真菌的第一个基因组。基于pacbio的序列高度连续(每个基因组5-42个contigs,平均覆盖率为79-502,N50为1.0-7.3兆碱基对(Mb), Benchmarking Universal单拷贝Orthologs (BUSCO)完整性一般≥95.4%)。大多数contigs的两侧都有一个端粒序列,这表明我们获得了接近染色体水平的组装。基因组大小在26到44 Mb之间。基于转录组的注释每个基因组产生约11,000-18,000个基因。我们分析了基因组中重复元素、生物合成基因和效应基因的含量。每个基因组包含一个与二羟基萘-黑色素通路相关的聚酮合成酶基因。这项研究提供了对这些相对未知但经常遇到的地衣相关物的基因组内容和代谢潜力的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
IUBMB Life
IUBMB Life 生物-生化与分子生物学
CiteScore
10.60
自引率
0.00%
发文量
109
审稿时长
4-8 weeks
期刊介绍: IUBMB Life is the flagship journal of the International Union of Biochemistry and Molecular Biology and is devoted to the rapid publication of the most novel and significant original research articles, reviews, and hypotheses in the broadly defined fields of biochemistry, molecular biology, cell biology, and molecular medicine.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信