Taxonomic notes in American Polystachya (Orchidaceae): the identity of P. foliosa (Hook.) Rchb.f. and the reestablishment of P. caracasana Rchb.f

Peraza-Flores, Lizandro N.; Carnevali, Germán; Romero‐González, Gustavo A.

doi:10.3159/torrey-d-11-00029.1

Cited by 7 publications

(7 citation statements)

References 13 publications

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“…This can be seen in the herbarium identifications that sometimes consider them as two distinct species, but sometimes as the same species. The same occurs with P. foliosa , a name which would only be correctly applied to plants from the Amazon basin, the Guyana Shield and the West Indies ( Peraza-Flores, Fernández-Concha & Romero-González, 2011 ). This circumscription is not accepted by Mytnik-Ejsmont (2011) , who considers P. estrellensis and P. foliosa to be synonymous.…”

Section: Discussionmentioning

confidence: 93%

The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

Abreu

Alves

Cardoso

et al. 2018

PeerJ

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BackgroundCurrent evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic.MethodsWe generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops).ResultsWe retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species.DiscussionOur results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.

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Section: Discussionmentioning

confidence: 93%

The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

Abreu

Alves

Cardoso

et al. 2018

PeerJ

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“…Author details 1 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China. 2 Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China. 3 University of Chinese Academy of Sciences, Beijing, 100049, China.…”

Section: Availability Of Data and Materialsmentioning

confidence: 99%

“…The genus Polystachya Hook (1824: 103; Orchidaceae) comprises approximately 240 species, of which most species are distributed in Africa, a few ones extend to tropical and subtropical Americas, and only three species in Asia [1][2][3][4][5][6]. It is di cult to give exact number of species of the genus for while some species are widespread, others are narrow endemics.…”

Section: Introductionmentioning

confidence: 99%

“…It is di cult to give exact number of species of the genus for while some species are widespread, others are narrow endemics. Furthermore, the taxonomic nomenclature of the genus is also complex since there are about 500 names available associated with the currently recognized species [2,7]. Representatives of the genus are usually epiphytic, occasionally lithophytic or terrestrial perennial herbs [8,9] (http://powo.science.kew.org/taxon/325981-2;http://www.theplantlist.org/tpl1.1/search?q=Polystachya).…”

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confidence: 99%

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Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

Jiang

Tian

Yang

et al. 2021

Preprint

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Background: Polystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the centre of diversity in Africa. Chloroplast (cp) genomes of plants are highly conserved and can provide much more informative DNA sites and generate much better resolution for plant phylogenies. However, for Polystachya, the whole cp genome including its structure features are yet unknown and its phylogenetic placement of the genus within the Orchidaceae is still unclear.Results: In this study, the complete cp genomes of six Polystachya species were assembled based on genome skimming. We subjected them to comparative genomic analyses and reconstructed their phylogenetic relationships. The results exhibited that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had almost similar GC content of 36.9%-37.0%. Gene annotation revealed 113 unique genes. In additions, 19 genes are duplicated in the inverted regions, and 17 gene possessed intron. Comparative analysis of the overall sequence identity among six complete cp genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR region among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out specific SSR and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis suggested that the six Polystachya species formed a monophyletic clade and had more closely related to tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 cp genome sequences were generally consistent with previous studies and robust. Conclusions: Our study reported the complete cp genomes of the six Polystachya species, and provided detailed structural analysis and comparative analysis results, which can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the present results further demonstrate the phylogenetic position of Polystachya.

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“…2019 2,2-5 × 2,5-3,7 mm, trilobado, labelo apresentando de cinco a oito venações base truncada, margem repanda ou sinuada; lobo mediano 2,2-5 × 1,2-2,7 mm, oblongo, ovado ou elíptico, ápice obtuso, arredondado, retuso ou emarginado; lobos laterais 1-1,2 × 0,7-1,5 mm, ovados ou oblongos; margem inteira, ápice arredondado, obtuso; calo 0,5 mm, elíptico, estreito-elíptico, base truncada, ápice retuso a acuminado, não atingindo o centro do labelo; superfície coberta por pseudopólen, disposto por todo o comprimento do labelo, geralmente cobrindo os lobos laterais, sendo mais densamente cobrindo o calo. Polystachya caracasana não é endêmica do Brasil, no Neotrópico possui distribuição no México, Republica Dominicana, Honduras, Jamaica, Porto Rico, Costa Rica, Panamá, Antilhas, Granada, Trinidad e Tobago, Colômbia, Venezuela, Guiana, Suriname, Guiana Francesa, Brasil, Equador e Paraguai (Mytnik-Ejsmont 2011;Peraza-Flores et al 2011). No Brasil sua distribuição se dá por quase todo o território nacional, exceto nos estados Ceará, Rio de Janeiro, Mato Grosso, Rondônia, Sergipe, Pernambuco, Paraíba e Rio Grande do Norte (BFG 2018).…”

Section: Chave De Identificação Das Espécies Do Gênerounclassified

O gênero Polystachya (Orchidaceae, Polystachyinae) no estado do Paraná, Brasil

Machnicki-Reis

Smidt

2019

Rodriguésia

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Resumo Polystachya compreende cerca de 200 espécies epífitas e terrestres, com distribuição Pantropical. As espécies do gênero destacam-se pois nem o pedúnculo e nem o ovário ressupinam, de modo que o labelo está posicionado na parte superior da flor. O objetivo deste estudo foi realizar o tratamento taxonômico de Polystachya no estado do Paraná, apresentando descrições, pranchas, mapas de distribuição, chave de identificação, estado de conservação e comentários para cada espécie. São encontradas quatro espécies para o estado do Paraná, sendo o primeiro registro de P. rupicola. O gênero ocorre predominantemente na Floresta Ombrófila Densa, com alguns registros na Floresta Ombrófila Mista e em Estepe Gramíneo Lenhosa no estado. De acordo com os critérios da IUCN, P. rupicola é considerada como criticamente em perigo, P. caespitosa, P. caracasana e P. concreta como em perigo, devido a destruição do habitat e coleta indiscriminada. É proposta a lectotipificação para P. caespitosa.

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Taxonomic notes in American Polystachya (Orchidaceae): the identity of P. foliosa (Hook.) Rchb.f. and the reestablishment of P. caracasana Rchb.f

Cited by 7 publications

References 13 publications

The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

The use of chloroplast genome sequences to solve phylogenetic incongruences inPolystachyaHook (Orchidaceae Juss)

Comparative And Phylogenetic Analyses of Six Kenya Polystachya (Orchidaceae) Species Based On The Complete Chloroplast Genome Sequences

O gênero Polystachya (Orchidaceae, Polystachyinae) no estado do Paraná, Brasil

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