Article (Scientific journals)
Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon
Magain, Nicolas; Miadlikowska, Jolanta; Mueller, Olaf et al.
2017In Molecular Phylogenetics and Evolution, 117 (12), p. 10-29
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Abstract :
[en] Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to >10 kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. As a proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) – a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.
Disciplines :
Phytobiology (plant sciences, forestry, mycology...)
Author, co-author :
Magain, Nicolas  ;  Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - aCREA-Ulg
Miadlikowska, Jolanta
Mueller, Olaf
Gajdeczka, Michael
Truong, Camille
Salamov, Asaf A.
Dubchak, Inna
Grigoriev, Igor V.
Goffinet, Bernard
Sérusiaux, Emmanuël ;  Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - aCREA-Ulg
Lutzoni, François
Language :
English
Title :
Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon
Publication date :
December 2017
Journal title :
Molecular Phylogenetics and Evolution
ISSN :
1055-7903
eISSN :
1095-9513
Publisher :
Academic Press, San Diego, United States - California
Special issue title :
25th Anniversary Issue of Molecular Phylogenetics and Evolution
Volume :
117
Issue :
12
Pages :
10-29
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 27 September 2017

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