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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 and Hedrén, Mikael LU (2019) In Molecular Phylogenetics and Evolution 136. p.21-28
Abstract

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... (More)

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.

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organization
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type
Contribution to journal
publication status
published
subject
keywords
Gymnadenia, Nigritella, Orchidaceae, Phylogenomics, Polyploidy, RADseq
in
Molecular Phylogenetics and Evolution
volume
136
pages
8 pages
publisher
Elsevier
external identifiers
  • scopus:85063742817
ISSN
1055-7903
DOI
10.1016/j.ympev.2019.03.018
language
English
LU publication?
yes
id
15cbc27e-c577-4948-ac1b-4d3c1511a7f1
date added to LUP
2019-04-23 09:50:50
date last changed
2019-05-14 04:53:46
@article{15cbc27e-c577-4948-ac1b-4d3c1511a7f1,
  abstract     = {<p>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.</p>},
  author       = {Brandrud, Marie K. and Paun, Ovidiu and Lorenz, Richard and Baar, Juliane and Hedrén, Mikael},
  issn         = {1055-7903},
  keyword      = {Gymnadenia,Nigritella,Orchidaceae,Phylogenomics,Polyploidy,RADseq},
  language     = {eng},
  pages        = {21--28},
  publisher    = {Elsevier},
  series       = {Molecular Phylogenetics and Evolution},
  title        = {Restriction-site associated DNA sequencing supports a sister group relationship of Nigritella and Gymnadenia (Orchidaceae)},
  url          = {http://dx.doi.org/10.1016/j.ympev.2019.03.018},
  volume       = {136},
  year         = {2019},
}