Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Neubig, Kurt M.; Whitten, W. Mark; Carlsward, Barbara S.; Blanco, Mario A.; Endara, Lorena; Williams, Norris H.; Moore, Michael J.

doi:10.1007/s00606-008-0105-0

Cited by 145 publications

(136 citation statements)

References 25 publications

(28 reference statements)

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“…A ca. 1500 bp portion of 3' portion of ycf1 was amplified and sequenced using the primers and protocols in Neubig et al (2009a). A list of taxa, vouchers, and GenBank numbers is presented in Table 1.…”

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confidence: 99%

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Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Whitten¹,

Neubig²,

Williams³

2014

Lankesteriana

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Relationships among all subtribes of Neotropical Cymbidieae (Orchidaceae) were estimated using combined matK/ycf1 plastid sequence data for 289 taxa. The matrix was analyzed using RAxML. Bootstrap (BS) analyses yield 100% BS support for all subtribes except Stanhopeinae (87%). Generic relationships within subtribes are highly resolved and are generally congruent with those presented in previous studies and as summarized in Genera Orchidacearum. Relationships among subtribes are largely unresolved. The Szlachetko generic classification of Maxillariinae is not supported. A new combination is made for Maxillaria cacaoensis J.T.Atwood in Camaridium.

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confidence: 99%

“…The matK matrix was trimmed to eliminate a region of ambiguous alignment in the first 100 bp. Polystachya was chosen as the outgroup based upon broader sampling (Neubig et al 2009a). Matrices and a list of vouchers are deposited in the Dryad Digital Repository (http://doi.org/10.5061/dryad.2rm60) or are available from the author.…”

mentioning

confidence: 99%

Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Whitten¹,

Neubig²,

Williams³

2014

Lankesteriana

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“…DNA amplification and sequencing was carried out following published primers and methods, with modifications when necessary (matK+trnK, atpB-rbcL, rpoC1 and ITS from Whitten et al 2007; ycf1 from Neubig et al 2009; ETS from Monteiro et al 2010). Electropherograms were assembled and edited using Geneious Pro 5.0.3 (Drummond et al 2010); alignments were generated using MUSCLE (Edgar 2004) and adjusted by eye using MacClade (Maddison & Maddison 2005).…”

Section: Methodsmentioning

confidence: 99%

Molecular phylogenetics of <i>mormolyca</i> (orchidaceae: maxillariinae) based on combined molecular data sets

Arévalo

Cameron

2013

Lankesteriana

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ABstrAct. The Neotropical orchid genus Mormolyca Fenzl, as currently circumscribed, encompasses a diverse group of ca. 27species. Many of these were included traditionally in Maxillaria sect. Rufescens, when similarity of floral morphology was considered foremost in their classification rather than the evolutionary history of the taxa. In order to begin revising species delimitation and clarifying the evolution and biology of the genus, we present a phylogenetic hypothesis using sequence data from five plastid loci (rpoC1, matK gene and flanking trnK intron, atpB-rbcL intergenic spacer, and the 3' portion of ycf1) and the nuclear ribosomal internal and external transcribed spacers (ITS, ETS). Resulting trees using both Bayesian and parsimony inference are congruent with each other, and generally well resolved. Based on current level of sampling across Maxillariinae, these molecular data support the monophyly of Mormolyca and shed light on the interspecific phylogenetic patterns within the genus. These include an early divergent paraphyletic grade of Mormolyca species successively sister to a clade with at least two definable subclades within. The latter are characterized by two different flower morphologies that are likely related to their pollination systems. Although not all relationships within the genus are fully resolved or supported, these results offer a first glimpse into the phylogeny of a small group of epiphytic orchids characterized by an unusually high level of variable vegetative characters, floral fragrance profiles, and pollination systems.

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“…ycf1: Another locus that is "more variable than matK" [71] or "any existing plastid candidate barcodes and can serve as a barcode for land plants", that was ycf1, proposed as a barcode by Dong, et al (2015) [15]. Within the plastid genome, ycf1 spans the small single copy (SSC) and the inverted repeat (IR) regions.…”

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Review on molecular markers for identification of Orchids

Vu¹,

Le²,

Nguyen³

et al. 2017

VJSTE

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Abstract:Orchidaceae is one of the most valuable plant groups all over the world, and is also an impressively large and complex family of flowering plants. Effective molecular tools used for the identification of orchid species should be developed to support traditional morphological approaches. This study reviews most of the DNA fragments that have been used as taxon identifiers in researches conducted on Orchidaceae in order to assess potential molecular markers and metric measurements for the identification of orchid species.

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Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

Cited by 145 publications

References 25 publications

Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Generic and Subtribal relationShipS in neotropical cymbidieae (orchidaceae) baSed on matK/ycf1 plaStid data

Molecular phylogenetics of <i>mormolyca</i> (orchidaceae: maxillariinae) based on combined molecular data sets

Review on molecular markers for identification of Orchids

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