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

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Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae). / Brandrud, Marie K.; Paun, Ovidiu; Lorenz, Richard; Baar, Juliane; Hedrén, Mikael.

I: Molecular Phylogenetics and Evolution, Vol. 136, 2019, s. 21-28.

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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T1 - Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)

AU - Brandrud, Marie K.

AU - Paun, Ovidiu

AU - Lorenz, Richard

AU - Baar, Juliane

AU - Hedrén, Mikael

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - Gymnadenia

KW - Nigritella

KW - Orchidaceae

KW - Phylogenomics

KW - Polyploidy

KW - RADseq

U2 - 10.1016/j.ympev.2019.03.018

DO - 10.1016/j.ympev.2019.03.018

M3 - Article

VL - 136

SP - 21

EP - 28

JO - Molecular Phylogenetics and Evolution

T2 - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

SN - 1095-9513

ER -