Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA

Sun, Yu-Shan; Skinner, Daniel Z.; Liang, G. H.; Hulbert, Scot H.

doi:10.1007/bf00226978

Cited by 717 publications

(374 citation statements)

References 25 publications

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“…The ITS region consisted of the 3' and 5' ends of the 18S and 26S ribosomal RNA genes, respectively, the internal transcribed spacers (ITS1 and ITS2), and the intervening 5.8S gene of the nuclear ribosomal multigene family. Amplifications of this region were performed using primers 17SE and 26SE (Sun et al 1994). We used an internal fragment of approximately 630 bp of the matK gene, amplified with primers matK-F2 and matK-R2 (Batista et al 2013), which approximately corresponds to the region widely used for barcoding land plants (Chase et al 2007).…”

Section: Methodsmentioning

confidence: 99%

From Cuba to most of the neotropic: habenaria bicornis (orchidaceae) is widespread from Mexico to southeastern Brazil

Batista¹,

Proite²,

Carvalho³

et al. 2014

Lankesteriana

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Habenaria bicornis fue descrita por primera vez en 1835, para Cuba, y era conocida apenas para este país y unos pocos registros de Panamá, de 1920. En el presente estudio, demostramos que H. bicornis y H. goyazensis, esta última conocida para Brasil y Guiana, son específicas y la especie se distribuye desde México hasta el sudeste de Brasil. El modelado de nicho y la recolección de datos indican que esta especie posee una preferencia por sabanas húmedas de tierras bajas y es predicho que su distribución incluye gran parte del Neotrópico con hábitats favorables. Los análisis filogenéticos moleculares con secuencias del ADN nuclear (ITS) y plastidial (matK) ubicaron H. bicornis en una posición aislada próximo a la base del clado Neotropical, aunque con bajo soporte. En términos de su morfología, sus relaciones no están aclaradas, ya que no hay similitudes evidentes entre H. bicornis y los subclados básales o cualquier otro subclado Neotropical. Los análisis citogenéticos indican un número cromosómico básico de x=21, similar a las otras especies basales del Neotrópico.

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Section: Methodsmentioning

confidence: 99%

From Cuba to most of the neotropic: habenaria bicornis (orchidaceae) is widespread from Mexico to southeastern Brazil

Batista¹,

Proite²,

Carvalho³

et al. 2014

Lankesteriana

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“…(b) PCR amplification and DNA sequencing A total of 1230 aligned nucleotide positions across the ITS and ETS (Baldwin et al 1995;Baldwin & Markos 1998) were amplified using primers 17SE and 26SE (Sun et al 1994) and Hel1 and 18S ETS (Baldwin & Markos 1998), respectively. Standard automated sequencing protocols ( Jousselin et al 2003) were used except that DMSO was added to all reactions.…”

Section: Methodsmentioning

confidence: 99%

60 million years of co-divergence in the fig–wasp symbiosis

et al. 2005

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Figs (Ficus; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant-pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant-insect co-divergence over a geological time frame spanning at least 60 million years.

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“…For the trnL intron amplification we used the two universal primers C (forward) and D (reverse) (Taberlet et al, 1991), and PCR conditions consisting of 3 min denaturing step at 94°C, 40 cycles of 1 min at 94°C (denaturation), 30 s at 50°C (annealing), 1 min at 72°C (extension), and further extension for 10 min at 72°C. For the nuclear ribosomal ITS/5.8S region we used the amplification primers 17SE and 26SE (Sun et al, 1994) and the sequencing primers ITS 92 (Desfeux and Lejeune, 1996) and ITS 04 (White et al, 1990). The ITS/5.8S region was amplified using a run program with a 3 min denaturing step at 94°C, followed by 28-30 cycles of 1 min at 94°C (denaturation); 1 min at 50-52°C (annealing); 2:30 min at 72°C (extension) and further extension for 7 min at 72°C.…”

Section: Dna Amplification and Sequencingmentioning

confidence: 99%

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

Queiroz

São-Mateus

Delgado‐Salinas

et al. 2017

Molecular Phylogenetics and Evolution

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. E-mail address: luciano.paganucci@gmail.com (L.P. de Queiroz). ABSTRACTThe papilionoid legume tribe Brongniartieae comprises a collection of 13 genera with disparate morphologies that were previously positioned in at least three remotely related tribes. The Brongniartieae displays a wide geographical disjunction between Australia and the New World and previous phylogenetic studies had provided conflicting results about the relationships between the American and Australian genera. We carry out phylogenetic analyses of (1) a plastid matK dataset extensively sampled across legumes to solve the enigmatic relationship of the Cuban-endemic monospecific genus Behaimia; and (2) multilocus datasets with focus on all genera ever referred toBrongniartieae. These analyses resulted in a well-resolved and strongly-supported phylogenetic tree of the Brongniartieae. Increased molecular sampling in papilionoid legume phylogeny has dramatically changed our understanding of the evolution and taxonomic classification in this species rich lineage of economically and ecologically important legumes (family Leguminosae).The prevailing traditional hypotheses of generic relationships assumed that the papilionate flower would be a signature of the most "derived" groups, whereas the more caesalpinioid and mimosoid-like floral organizations, involving undifferentiated petals and free stamens, marked mostly the "primitive" tribes within the subfamily Papilionoideae (Polhill, 1981a). Hence, such an evolutionary perspective has largely influenced the way in which the modern subfamily, tribe, and even genus-level classification of legumes was built (LPWG, 2013(LPWG, , 2017. In the past 15 years, molecular phylogenetic studies have underpinned dramatic taxonomic changes after revealing unexpected relationships, suggesting that floral architecture is relatively labile in the early-branching papilionoid lineages (e.g. Pennington et al., 2001;Wojciechowski et al., 2004; Cardoso et al., 2012aCardoso et al., , 2013aCardoso et al., , 2015Ramos et al., 2016).The recent examples of broad phylogenetic re-alignments that were unexpectedly revealed in the early-branching genera of Papilionoideae (Cardoso et al., 2012a(Cardoso et al., , 2012b(Cardoso et al., , 2012c(Cardoso et al., , 2013a(Cardoso et al., , 2017Ramos et al., 2016; Castellanos et al., in press) are not an exception across legumes. For example, dramatic shuffling in the placement of genera has also been necessary within the species-rich canavanine-accumulating clade (Wojciechowski et al., 2004;Silva et al., 2012;Sirichamorn et al., ...

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Phylogenetic analysis of Sorghum and related taxa using internal transcribed spacers of nuclear ribosomal DNA

Cited by 717 publications

References 25 publications

From Cuba to most of the neotropic: habenaria bicornis (orchidaceae) is widespread from Mexico to southeastern Brazil

From Cuba to most of the neotropic: habenaria bicornis (orchidaceae) is widespread from Mexico to southeastern Brazil

60 million years of co-divergence in the fig–wasp symbiosis

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

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