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      Characterization of microsatellite loci in the Himalayan lichen fungus Lobaria pindarensis (Lobariaceae) 1

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          Abstract

          • Premise of the study: Microsatellite loci were developed for the rare, Himalayan, endemic haploid lichen fungus, Lobaria pindarensis, to study its population subdivision and the species’ response to forest disturbance and fragmentation.

          • Methods and Results: We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data and assessed them in 109 individuals. The number of alleles per locus ranged from three to 11 with an average of 6.9. Nei’s unbiased gene diversity, averaged over loci, ranged from 0.514 to 0.685 in the three populations studied. The cross-amplification success with related species ( L. chinensis, L. gyrophorica, L. isidiophora, L. orientalis, L. pulmonaria, L. spathulata, and Lobaria sp.) was generally high and decreased with decreasing relationship to L. pindarensis.

          • Conclusions: The new markers will allow the study of genetic diversity and differentiation within L. pindarensis across its distribution. Moreover, they will enable us to study the effects of forest management on the genetic population structure of this tree-colonizing lichen and to carry out population genetic studies of related species in East Asia.

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          Arlequin (version 3.0): An integrated software package for population genetics data analysis

          Laurent Excoffier, Guillaume Laval, Stefan Schneider (2007)
          Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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            msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.

            Brant C Faircloth (2008)
            msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine. msatcommander accepts as input DNA sequence data in single-sequence or concatenated, fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface for msatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8. msatcommander is available from http://code.google.com/p/msatcommander/. © 2007 The Author.
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              Vertical and horizontal photobiont transmission within populations of a lichen symbiosis.

              F Dal Grande, I Widmer, H. H. Wagner … (2012)
              Lichens are widespread symbioses and play important roles in many terrestrial ecosystems. The genetic structure of lichens is the result of the association between fungal and algal populations constituting the lichen thallus. Using eight fungus- and seven alga-specific highly variable microsatellite markers on within-population spatial genetic data from 62 replicate populations across Europe, North America, Asia and Africa, we investigated the contributions of vertical and horizontal transmission of the photobiont to the genetic structure of the epiphytic lichen Lobaria pulmonaria. Based on pairwise comparisons of multilocus genotypes defined separately for the mycobiont and for the photobiont, we inferred the transmission mode of the photobiont and the relative contribution of somatic mutation and recombination. After constraining the analysis of one symbiont to pairs of individuals with genetically identical symbiotic partners, we found that 77% of fungal and 70% of algal pairs were represented by clones. Thus, the predominant dispersal mode was by means of symbiotic vegetative propagules (vertical transmission), which dispersed fungal and algal clones co-dependently over a short distance, thus shaping the spatial genetic structure up to distances of 20m. Evidence for somatic mutation generating genetic diversity was found in both symbionts, accounting for 30% of pairwise comparisons in the alga and 15% in the fungus. While the alga did not show statistically significant evidence of recombination, recombination accounted for 7.7% of fungal pairs with identical algae. This implies that, even in a mostly vegetatively reproducing species, horizontal transmission plays a role in shaping the symbiotic association, as shown in many coral and other symbioses in nature. © 2012 Blackwell Publishing Ltd.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Appl Plant Sci
                Journal ID (iso-abbrev): Appl Plant Sci
                Journal ID (publisher-id): apps
                Title: Applications in Plant Sciences
                Publisher: Botanical Society of America
                ISSN (Electronic): 2168-0450
                Publication date Collection: May 2014
                Publication date (Electronic): 5 April 2014
                Volume: 2
                Issue: 5
                Electronic Location Identifier: apps.1300101
                Affiliations
                [2 ]Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
                [3 ]Central Department of Botany, Tribhuvan University, Kirtipur, Nepal
                [4 ]Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
                [5 ]Research Centre for Applied Science and Technology (RECAST), Tribhuvan University, Kirtipur, Nepal
                Author notes
                [1]

                The authors thank the Genetic Diversity Centre, ETH Zurich, for technical assistance; the Swiss National Science Foundation (grant JRP IZ70Z0_131338/1 to C.S.); the European Commission (Marie Curie Actions “Lichenomics” to S.W.); and the Department of National Parks and Wildlife Conservation, Ministry of Forest and Soil Conservation, Government of Nepal, and the National Trust for Nature Conservation, Nepal, for providing collecting permits in the study areas.

                [6 ]Author for correspondence: christoph.scheidegger@ 123456wsl.ch
                Article
                Publisher ID: apps1300101
                DOI: 10.3732/apps.1300101
                PMC ID: 4103109
                SO-VID: d85de282-6646-48ca-b387-7ca92ad7862e
                Copyright © © 2014 Devkota et al. Published by the Botanical Society of America
                License:

                This work is licensed under a Creative Commons Attribution License (CC-BY-NC-SA).

                History
                Date received : 23 December 2013
                Date accepted : 6 February 2014
                Categories
                Subject: Primer Note

                Keywords: ascomycetes,himalayas,lichen-forming fungi,lobaria pindarensis,microsatellites,population subdivision
                Data availability:
                Keywords: ascomycetes, himalayas, lichen-forming fungi, lobaria pindarensis, microsatellites, population subdivision

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