Characterization of fungus‐specific microsatellite markers in the lichen fungus <i>Usnea subfloridana</i> (Parmeliaceae)

Tõrra, Tiiu; Cornejo, Carolina; Cheenacharoen, Saran; Grande, Francesco Dal; Marmor, Liis; Scheidegger, Christoph

doi:10.3732/apps.1400034

Cited by 10 publications

(8 citation statements)

References 15 publications

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“…Particularly, the largest florida-subfloridana clade was reminiscent of the situation in another species pair, Usnea antarctica vs. U. aurantiacoatra, in which microsatellite markers and a RADseq approach demonstrated that the sexual and asexual morphs largely formed separate taxa (Lagostina et al 2018;Grewe et al 2018). Tõrra et al (2014) and Degtjarenko et al (2018Degtjarenko et al ( , 2019 developed microsatellite markers for the U. subfloridana complex, but did not report on their potential use to separate U. florida from U. subfloridana.…”

Section: Usnea Subgenus Neuropogon New Zealand Cladementioning

confidence: 98%

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

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We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.

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Section: Usnea Subgenus Neuropogon New Zealand Cladementioning

confidence: 98%

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Lücking¹,

Nadel²,

Araújo³

et al. 2020

Plant and Fungal Systematics

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“…The maximum number of alleles of the most variable marker found in the 264 specimens analyzed was five. This is considerably lower than the 11 alleles found in Lobaria pindarensis (Devkota et al 2014), 13 in both Nephroma laevigatum (Belinchón et al 2014) and Bryoria section Implexae (Nadyeina et al 2014a), 15 in Usnea subfloridana (Tõrra et al 2014) and 16 in Lobaria pulmonaria (Walser et al 2003;Werth et al 2013). However, the values are comparable to the three alleles found in Parmotrema tinctorum (Mansournia et al 2012), six in both Nephroma parile (Belinchón et al 2014) and Protoparmeliopsis muralis (Guzow-Krzemińska & Stocker-Wörgötter 2013) and eight in Lobarina scrobiculata (Prieto et al 2015).…”

Section: Specificity and Polymorphism Of The New Microsatellite Markersmentioning

confidence: 74%

“…2014) and Bryoria section Implexae (Nadyeina et al 2014 a ), 15 in Usnea subfloridana (Tõrra et al . 2014) and 16 in Lobaria pulmonaria (Walser et al . 2003; Werth et al .…”

Section: Discussionmentioning

confidence: 99%

Polymorphic fungus-specific microsatellite markers ofBactrospora dryinareveal multiple colonizations of trees

Nadyeina¹,

Zarabska-Bożejewicz

Wiedmer³

et al. 2017

The Lichenologist

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Bactrospora dryinais an epiphytic lichen-forming fungus specifically related to old-growth floodplain forests, which have dramatically declined in Europe over the past centuries. In order to promote conservation management of such forest remnants, we aimed to study population genetics of this rare and threatened lichen. The newly developed 16 microsatellite markers are specific for the mycobiont ofB. dryinaand reliably amplify either single fruiting bodies or a sterile thallus. This allows the use of these markers for the identification of sterile crusts and for quantification of recent dispersal of the species into restored habitats. We tested the markers in 264 samples collected from 10 pedunculate oak trees growing in three localities in north-eastern Switzerland. All markers were polymorphic and showed two to five alleles per locus, and unbiased gene diversity varied from 0·06 to 0·71 over three populations. The relatively low number of alleles inB. dryinais possibly the consequence of colonization of secondary habitats created by forest management. Although oaks were largely covered with a single, continuousB. dryinacolony, the microsatellite markers identified single or complex multi-genotype colonizations per tree. For future population genetic studies, we recommend collection of 5–15 specimens from one tree which would enable detection of 60–80% of the multilocus genotypes present. Hierarchical AMOVA revealed high variation (70%) on host trees, and a relatively high differentiation (12%) among the three locations in NE Switzerland indicated limited gene flow between those regions. Thus, the newly developed markers showed their applicability in population genetics at different spatial scales. They will play an important role in monitoring habitat restoration for the conservation ofB. dryinaand associated forests and riverscapes.

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“…The total genomic DNA was extracted using PowerPlant Pro DNA Isolation Kit and DNeasy Plant Mini Kit (MO BIO Laboratories, Inc., Qiagen, USA), according to the manufacturer’s protocol. Seven fungal microsatellite loci ( Us02 , Us03 , Us04 , Us05 , Us06 , Us08 and Us09 ) were amplified in two multiplex PCR using QIAGEN Multiplex PCR Kit, following the instructions described in Tõrra et al (2014) and Degtjarenko et al (2016). Fragment lengths of PCR products were determined on a 3730xl DNA Analyzer (Applied Biosystems) with LIZ-500 as the internal size standard.…”

Section: Methodsmentioning

confidence: 99%

Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island

Degtjarenko

Jüriado

Mandel

et al. 2019

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Understanding the distribution of genetic patterns and structure is an essential target in population genetics and, thereby, important for conservation genetics. The main aim of our study was to investigate the population genetics of Usnea subfloridana, a widespread lichenised fungus, focusing on a comparison of genetic variation of its populations amongst three geographically remote and disconnected regions, in order to determine relationships amongst environmental data, variation in lichen secondary chemistry and microsatellite data in genotyped populations. In all, 928 Usnea thalli from 17 populations were genotyped using seven specific fungal microsatellite markers. Different measures of genetic diversity (allelic richness, private allelic richness, Nei’s unbiased genetic diversity and clonal diversity) were calculated and compared between lichen populations. Our results revealed a low genetic differentiation of U. subfloridana populations amongst three distant areas in Estonia and also a high level of gene flow. The results support suggestion of the long-range vegetative dispersal of subpendulous U. subfloridana via symbiotic propagules (soralia, isidia or fragments of thalli). Our study has also provided evidence that environmental variables, including mean annual temperature and geographical longitude, shape the genetic structure of U. subfloridana populations in Estonia. Additionally, a weak but statistically significant correlation between lichen chemotypes and microsatellite allele distribution was found in genotyped specimens.

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Characterization of fungus‐specific microsatellite markers in the lichen fungus Usnea subfloridana (Parmeliaceae)

Cited by 10 publications

References 15 publications

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Two decades of DNA barcoding in the genus Usnea (Parmeliaceae): how useful and reliable is the ITS?

Polymorphic fungus-specific microsatellite markers ofBactrospora dryinareveal multiple colonizations of trees

Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island

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