Plastid DNA sequencing and nuclear SNP genotyping help resolve the puzzle of central American Platanus

Castro, Olga De; Maio, Antonietta Di; García, José Armando Lozada; Piacenti, Danilo; Vázquez-Torres, Mario; Luca, Paolo De

doi:10.1093/aob/mct134

Cited by 16 publications

(10 citation statements)

References 35 publications

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“…The ‘old cultivars’ (group 6) formed an unstable subpopulation that was highly mixed with ‘modern cultivars’ (groups 4 and 5), which was also observed in the PCA, due to reduplicative hybridization among ‘old’ and ‘new’ cultivars, resulting in a highly admixed population. Similar results were also observed in the studies of Hibiscus rosa-sinensis [50] , Aechmea [51] and Platanus species [52] .…”

Section: Discussionsupporting

confidence: 89%

Application of Genomic SSR Locus Polymorphisms on the Identification and Classification of Chrysanthemum Cultivars in China

et al. 2014

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The Chinese traditional chrysanthemum is a notable group of chrysanthemums (Chrysanthemum×morifolium Ramat.) in which the phenotypic characteristics richly vary. At present, there is a serious controversy regarding homonyms and synonyms within this group. Moreover, the current international chrysanthemum classification systems are not comprehensive enough to be used on Chinese traditional chrysanthemums. Thus, we first identified a broad collection of 480 Chinese traditional chrysanthemum cultivars using the unique DNA fingerprints and molecular identities that were established by 20 simple sequence repeat markers. Five loci, which distinguished all of the selected cultivars, were identified as the core loci to establish unique fingerprints and molecular identities with 19 denary digits for each cultivar. A cluster analysis based on Nei's genetic distance indicated that the selected cultivars were clustered according to their horticultural classification. Population structure analysis was subsequently performed with K values ranging from 2 to 14, and the most likely estimate for the population structure was ten subpopulations, which was nearly consistent with the clustering result. Principal component analysis was further performed to verify the classification results. On the basis of the Q-matrices of K = 10, a total of 19 traits were found to be associated with 42 markers. Taken together, these results can serve as starting points for the identification and classification of chrysanthemums based on the polymorphism of microsatellite markers, which is beneficial to promote the marker-assisted breeding and international communication of this marvelous crop.

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Section: Discussionsupporting

confidence: 89%

Application of Genomic SSR Locus Polymorphisms on the Identification and Classification of Chrysanthemum Cultivars in China

et al. 2014

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“…Apart from that, in non-cloned sequences of rDNA SNPs are usually interpreted as the consequence of intragenomic polymorphism, which can be caused by repetitiveness in the genome (Drábková et al, 2009;Bailey et al, 2003). One of the reasons of intragenomic polymorphisms, which can be resulted in the SNP presence, is interpopulational and interspecific hybridization (Castro et al, 2013;Hodač et al, 2014). Resulting from that hybridization, there are three pathways of ribosomal DNA evolution (Hřibová et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…The presence of SNPs is usually considered as a consequence of intragenomic polymorphism caused by the presence of multiple rDNA copies in the genome at which copies with different alleles have emerged as a result of either the independent evolution (Bailey et al, 2003;Drábková et al, 2009) or hybridization between different populations and even species (Castro et al, 2013;Hodač et al, 2014). During the reconstruction of molecular phylogenies, sites with SNP are usually deleted, which decreases the resolution of phylogenetic trees (Frajman et al, 2009a).…”

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confidence: 99%

Differences of Atocion lithuanicum from A. armeria (Sileneae, Caryophyllaceae) and their hybrid by ITS1-ITS2 sequences and secondary structure of their transcripts

Martyniuk¹,

Karpenko²,

Tarieiev³

et al. 2018

Ukr. Bot. J.

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Atocion lithuanicum (Zapał.) Tzvel. was originally described by H. Zapałowicz (1911) from Lithuanian and Volhynian Polissia as Silene lithuanica Zapał. Later it was included in Atocion Adans. by Tzvelev (2001). This species is distributed on poor sandy soils in Poland, Lithuania, Ukraine, and Belarus. In Lithuania and Ukraine, this species is considered as a rare Sarmatian endemic species and is therefore protected (Red data..., 2007; Andrienko et al., 2009). Atocion lithuanicum is morphologically similar to A. armeria (L.) Raf., the latter taxon was described by Linnaeus as Silene armeria L. from England and France ("Anglia, Gallia") with its current native range throughout Southern and Central Europe (from the Pyrenees to the Balkans and northeastern Anatolia). Atocion armeria is also widely cultivated (Europe,

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“…ITS T was amplified by using plant universal primers that were reported in the literature {Forward-18S(3’) 5’-GGA GAA GTC GTA ACA AGG TTT CCG-3′, and Reverse-26S(5′)-internal 5’-TTC GCT CGC CGT TAC TAA GGG-3’} [28] and selective internal primers designed on Pinguicula sp. accessions from GenBank (Pingui_18Sfor 5’-AAG GAT CAT TGT CGA DWY Y-3’ and Pingui_26Srev 5’-TGR GGT CGC RRR IGT TGG CR-3’).…”

Section: Methodsmentioning

confidence: 99%

“…[14], Kondo & Shimai [15], Shimai & Kondo [16] and Shimai et al . [17]; (2) a complete GenBank nrDNA- Pinguicula database to be used for an exhaustive phylogenetic reconstruction; (3) completeness of information as a consequence of the biparental inheritance of nrDNA [6, 26, 27, 28]. In fact, cpDNA markers may cause confusion in inferring phylogenetic relationships in potentially hybrid/introgressed/polypoid taxa (e.g.…”

Section: Introductionmentioning

confidence: 99%

Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy

et al. 2016

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The genus Pinguicula (Lentibulariaceae) consists of about 100 carnivorous species, also known as butterworts. Eleven taxa are endemic to Italy, which represents a biodiversity hotspot for butterworts in Europe. The aim of our study was to provide a phylogenetic framework for the Italian endemics, in order to: a) investigate the relationships between species in this group; b) evaluate their actual taxonomic value. To achieve this, we analysed all the taxa endemic to Italy, along with several other species, by means of ITS nrDNA analysis. Our results clarify the relationships between Italian endemics and other Pinguicula taxa identifying a basal polytomy defined by five clades. All of the Italian endemics (with the exception of P. lavalvae) fall within a single large clade, which includes P. vulgaris and allied species. Among them, P. poldinii represents the most isolated lineage. Other taxa show strong molecular similarities and form a single subclade, although their taxonomic ranks can be retained. Pinguicula lattanziae sp. nov., seemingly endemic to Liguria (NW Italy), is also described.

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Plastid DNA sequencing and nuclear SNP genotyping help resolve the puzzle of central American Platanus

Cited by 16 publications

References 35 publications

Application of Genomic SSR Locus Polymorphisms on the Identification and Classification of Chrysanthemum Cultivars in China

Application of Genomic SSR Locus Polymorphisms on the Identification and Classification of Chrysanthemum Cultivars in China

Differences of Atocion lithuanicum from A. armeria (Sileneae, Caryophyllaceae) and their hybrid by ITS1-ITS2 sequences and secondary structure of their transcripts

Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy

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