The first whole genome sequencing of historical lichen specimens enables genome-wide analysis of fungal and algal symbionts

The first whole genome sequencing of historical lichen specimens enables genome-wide analysis of fungal and algal symbionts | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL Ecology and Evolution This is a preprint and has not been peer reviewed. Data may be preliminary. 22 January 2025 V1 Latest version Share on The first whole genome sequencing of historical lichen specimens enables genome-wide analysis of fungal and algal symbionts Authors : Mieko Kono 0000-0003-4402-9545 [email protected] , Yoshihito Ohmura 0000-0003-2557-2761 , and Yohey Terai 0000-0003-3353-3420 Authors Info & Affiliations https://doi.org/10.22541/au.173757880.08532665/v1 Published Ecology and Evolution Version of record Peer review timeline 428 views 162 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract With the advent of high-throughput sequencing techniques, natural history museums and herbaria have become new frontiers for genetic research. Genomic information from historical specimens has provided evidence to solve significant questions in broad research areas. However, access to such valuable genetic resources remains limited in lichens due to experimental challenges in extracting and amplifying highly degraded DNA in historical specimens. So far, only a handful of studies have reported successful sequencing of several short genetic markers from historical lichen specimens despite the increasing importance of genetic information in lichenology. Here, we aim to establish an efficient method for sequencing the whole genome of historical lichen specimens. We modified a method used in ancient DNA studies and sequenced the whole genome of 75-year-old Usnea hakonensis specimens, including the holotype. Our approach shows that 3.9 % and 9.8 % of the total sequenced reads originate from the genomes of U. hakonensis fungal (mycobiont) and algal (photobiont) symbionts. The mycobiont- and photobiont-derived reads are comprised of DNA fragments shorter than 45 bp, covering 77 % and 93 % of the mycobiont and photobiont reference genomes in average coverage of 27x and 45x, respectively. We retrieved 792,245 Single Nucleotide Variants (SNVs) to perform phylogenetic analysis of the mycobiont. We also demonstrated experimental modifications that improved proportions of symbionts-derived reads within sequenced data. We believe that our method is applicable to lichen specimens in a broad range of age and taxonomic groups, thereby potentially converting historical lichen specimens into resources of genome-wide studies. Supplementary Material File (main_document.doc) Download 315.00 KB Information & Authors Information Version history V1 Version 1 22 January 2025 Peer review timeline Published Ecology and Evolution Version of Record 22 Sep 2025 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection Ecology and Evolution Keywords genetics method development multiple terrestrial Authors Affiliations Mieko Kono 0000-0003-4402-9545 [email protected] SOKENDAI View all articles by this author Yoshihito Ohmura 0000-0003-2557-2761 National Museum of Nature and Science View all articles by this author Yohey Terai 0000-0003-3353-3420 SOKENDAI View all articles by this author Metrics & Citations Metrics Article Usage 428 views 162 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Mieko Kono, Yoshihito Ohmura, Yohey Terai. The first whole genome sequencing of historical lichen specimens enables genome-wide analysis of fungal and algal symbionts. Authorea . 22 January 2025. DOI: https://doi.org/10.22541/au.173757880.08532665/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. 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