Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)

[Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densif...

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Vydané v:	Molecular phylogenetics and evolution Ročník 136; s. 21 - 28
Hlavní autori:	Brandrud, Marie K., Paun, Ovidiu, Lorenz, Richard, Baar, Juliane, Hedrén, Mikael
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	United States Elsevier Inc 01.07.2019
Predmet:	allopolyploidy allozymes analytical methods Biologi Biological Sciences Biological Systematics Biologisk systematik clearcutting diploidy genetic variation genome genomics Geography Gymnadenia Gymnadenia conopsea Likelihood Functions loci microsatellite repeats Natural Sciences Naturvetenskap Nigritella Orchidaceae Orchidaceae - genetics Phylogenomics Phylogeny Polyploidy Principal Component Analysis RADseq Restriction Mapping ribotypes sequence analysis Sequence Analysis, DNA single nucleotide polymorphism tetraploidy RADseq Polyploidy Gymnadenia Orchidaceae Nigritella Phylogenomics
ISSN:	1055-7903, 1095-9513, 1095-9513
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Abstract	[Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densiflora from G. conopsea s.str. is supported.•Affiliation of Nigritella polyploid taxa into three distinct groups is supported. The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.
AbstractList	The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported. The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported. [Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may explain discordant tree topologies.•An origin of Gymnigritella runei from extant G. conopsea and N. nigra is supported.•The separation of G. densiflora from G. conopsea s.str. is supported.•Affiliation of Nigritella polyploid taxa into three distinct groups is supported. The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically distinct, it has been suggested that the separating characters are easily modifiable and subject to rapid evolutionary change. So far, molecular phylogenetic studies have either given support for the inclusion of Nigritella in Gymnadenia, or for their separation as different genera. To resolve this issue, we analysed data obtained from Restriction-site associated DNA sequencing, RADseq, which provides a large number of SNPs distributed across the entire genome. To analyse samples of different ploidies, we take an analytical approach of building a reduced genomic reference based on de novo RADseq loci reconstructed from diploid accessions only, which we further use to map and call variants across both diploid and polyploid accessions. We found that Nigritella is distinct from Gymnadenia forming a well-supported separate clade, and that genetic diversity within Gymnadenia is high. Within Gymnadenia, taxa characterized by an ITS-E ribotype (G. conopsea s.str. (early flowering) and G. odoratissima), are divergent from taxa characterized by ITS-L ribotype (G. frivaldii, G. densiflora and late flowering G. conopsea). Gymnigritella runei is confirmed to have an allopolyploid origin from diploid Gymnadenia conopsea and tetraploid N. nigra ssp. nigra on the basis of RADseq data. Within Nigritella the aggregation of polyploid members into three clear-cut groups as suggested by allozyme and nuclear microsatellite data was further supported.
Author	Paun, Ovidiu Lorenz, Richard Brandrud, Marie K. Hedrén, Mikael Baar, Juliane
AuthorAffiliation	1 Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria 3 Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden 2 AHO Baden-Württemberg, Leibnizstrasse 1, D-69459 Weinheim, Germany
AuthorAffiliation_xml	– name: 1 Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria – name: 3 Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden – name: 2 AHO Baden-Württemberg, Leibnizstrasse 1, D-69459 Weinheim, Germany
Author_xml	– sequence: 1 givenname: Marie K. surname: Brandrud fullname: Brandrud, Marie K. organization: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria – sequence: 2 givenname: Ovidiu surname: Paun fullname: Paun, Ovidiu organization: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria – sequence: 3 givenname: Richard surname: Lorenz fullname: Lorenz, Richard organization: AHO Baden-Württemberg, Leibnizstrasse 1, D-69459 Weinheim, Germany – sequence: 4 givenname: Juliane surname: Baar fullname: Baar, Juliane organization: Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria – sequence: 5 givenname: Mikael surname: Hedrén fullname: Hedrén, Mikael email: mikael.hedren@biol.lu.se organization: Department of Biology, University of Lund, Sölvegatan 37, SE-223 62 Lund, Sweden
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Keywords	RADseq Polyploidy Gymnadenia Orchidaceae Nigritella Phylogenomics
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Snippet	[Display omitted] •RADseq supports a sister relationship of the orchid genera Gymnadenia and Nigritella.•Restricted gene flow between the two genera may... The orchid genus Nigritella is closely related to Gymnadenia and has from time to time been merged with the latter. Although Nigritella is morphologically...
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SubjectTerms	allopolyploidy allozymes analytical methods Biologi Biological Sciences Biological Systematics Biologisk systematik clearcutting diploidy genetic variation genome genomics Geography Gymnadenia Gymnadenia conopsea Likelihood Functions loci microsatellite repeats Natural Sciences Naturvetenskap Nigritella Orchidaceae Orchidaceae - genetics Phylogenomics Phylogeny Polyploidy Principal Component Analysis RADseq Restriction Mapping ribotypes sequence analysis Sequence Analysis, DNA single nucleotide polymorphism tetraploidy
Title	Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)
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