Next Generation Sequencing of Ancient Fungal Specimens: The Case of the Saccardo Mycological Herbarium

Forin, Niccolò; Nigris, Sebastiano; Voyron, Samuele; Vizzini, Alfredo; Casadoro, Giorgio; Baldan, Barbara

doi:10.3389/fevo.2018.00129

Cited by 31 publications

(20 citation statements)

References 59 publications

(60 reference statements)

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“…Lactifluus deceptivus was described by Peck (1885), and Hesler and Smith (1979) designated a lectotype (Peck s.n., NYS-F-000959). Samples this old have both time and conservation related DNA damage, besides exogenous DNA contamination, that makes nucleic acid extraction and amplification challenging (Forin et al 2018). Therefore, Illumina Miseq sequencing was chosen as an alternative to the conventional Sanger sequencing to overcome these problems for the type specimen of L. deceptivus.…”

Section: Discussionmentioning

confidence: 99%

Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity

et al. 2019

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The ectomycorrhizal genus Lactifluus is known to contain many species complexes, consisting of morphologically very similar species, which can be considered cryptic or pseudocryptic. In this paper, a thorough molecular study is performed of the clade around Lactifluus deceptivus (originally described by Peck from North America) or the deceptive milkcaps. Even though most collections were identified as L. deceptivus, the clade is shown to contain at least 15 species, distributed across Asia and America, indicating that the L. deceptivus clade represents a species complex. These species are morphologically very similar and are characterized by a tomentose pileus with thinwalled hyphae and a velvety stipe with thick-walled hyphae. An ITS1 sequence was obtained through Illumina sequencing for the lectotype of L. deceptivus, dating from 1885, revealing which clade represents the true L. deceptivus. In addition, it is shown that three other described species also belong to the L. deceptivus clade: L. arcuatus, L. caeruleitinctus and L. mordax, and molecularly confirmed that L. tomentoso-marginatus represents a synonym of L. deceptivus. Furthermore, two new Neotropical species are described: Lactifluus hallingii and L. domingensis.

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Section: Discussionmentioning

confidence: 99%

Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity

et al. 2019

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“…DNA was extracted with the CTAB protocol described in Forin et al [ 11 ]. In order to prepare the libraries for a paired-end sequencing using the Illumina MiSeq technology 2 × 300 bp, ITS1 and ITS2 regions were amplified using a two-step PCR process [ 12 ].…”

Section: Methodsmentioning

confidence: 99%

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

et al. 2021

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In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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“…Other HTS platforms, for example various Illumina machines, should be explored to assess if these can overcome some of the drawbacks with the Ion Torrent PGM. Using the Illumina MiSeq technology, Forin et al (2018) managed to obtain ITS2 sequences of century-old fungal collections, indicating the potential success of this approach also for historical lichen specimens. Furthermore, single-read sequencing technologies, such as implemented in the PacBio (Pacific Biosciences) and MinION (Oxford nanopore technologies) should be tested with lichen material.…”

Section: Drawbacks Potential Improvements and Future Use Of The Appmentioning

confidence: 99%

DNA Sequencing Historical Lichen Specimens

et al. 2019

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Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.

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Next Generation Sequencing of Ancient Fungal Specimens: The Case of the Saccardo Mycological Herbarium

Cited by 31 publications

References 59 publications

Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity

Looks can be deceiving: the deceptive milkcaps (Lactifluus, Russulaceae) exhibit low morphological variance but harbour high genetic diversity

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

DNA Sequencing Historical Lichen Specimens

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