Primers for phylogeny reconstruction in Bignonieae (Bignoniaceae) using herbarium samples

Abstract

• Premise of the study: New primers were developed for Bignonieae to enable phylogenetic studies within this clade using herbarium samples.• Methods and Results: Internal primers were designed based on available sequences of the plastid ndhF gene and the rpl32-trnL intergenic spacer region, and the nuclear gene PepC. The resulting primers were used to amplify DNA extracted from herbarium materials. High-quality data were obtained from herbarium samples up to 53 yr old.• Conclusions: The standardized methodology allows the inclusion of herbarium materials as alternative sources of DNA for phylogenetic studies in Bignonieae.

Phylogeny and biogeography of Tynanthus Miers (Bignonieae, Bignoniaceae)

“…This analysis used a relaxed uncorrelated lognormal clock and Yule process speciation prior to infer trees. A secondary calibration was applied, based on previous estimates derived from a comprehensive study of the whole tribe Bignonieae (Lohmann et al 2013). We used a normal prior with mean 13.4 and standard deviation of 2.0.…”

“…Three molecular markers were selected for this study: the plastid ndhF and rpl32-trnL and the nuclear pepC. Amplification primers and procedures followed Zuntini et al (2013). Amplification of all markers were conducted in 25 µl reactions containing 13.8 µl of water, 5 µl of 10X GoTaq buffer, 2.5 µl of 25 mM MgCl 2 , 1 µl of dNTP (10 µM), 0.5 µl of BSA, 0.5 µl of each primer (10 µM), 0.2 µl of Taq (Hot start, Promega) and 1 µl of template DNA.…”

“…Occurrences were categorized according to the four biogeographic areas adopted by Lohmann et al (2013), which reflect patterns of endemism in Neotropical Bignoniaceae as a whole, namely: (1) Eastern South America, (2) South American dry areas, (3) Lowland Amazonia and (4) Western South America and Central America.…”

Reestablishment of Mansoa ventricosa (Bignonieae, Bignoniaceae) based on molecular and morphological data

“…Extractions were conducted using the Invisorb Plant Mini Kit (Invitek, Berlin, Germany), following the manufacturer's protocol. We amplified the chloroplast marker ndhF (NADH dehydrogenase) following Zuntini et al (2013) and the nuclear marker PepC (Phosphoenolpyruvate carboxylase) using a nested PCR approach with the external primers (4F and 5R) from Lohmann (2006) for the first round, and internal primers (IV-119F and V-25R) from Zuntini et al (2013) for the second round. The first-round PCR contained 8.5 μL of H 2 O, 1 μL dimethyl sulfoxide (DMSO), 12.5 μL GoTaq Promega Master Mix, 1 μL 10mM each primer and 1 μL 10 ng of template DNA.…”

Revisão taxonômica, filogenia e evolução do nicho ecológico de Tynanthus Miers (Bignonieae, Bignoniaceae)

“…Three molecular markers were selected for this study: the plastid ndhF and rpl32-trnL and the nuclear pepC. Amplification primers and procedures followed Zuntini et al (2013). Amplification of all markers were conducted in 25 µl reactions containing 13.8 µl of water, 5 µl of 10X GoTaq buffer, 2.5 µl of 25 mM MgCl2, 1 µl of dNTP (10 µM), 0.5 µl of BSA, 0.5 µl of each primer (10 µM), 0.2 µl of Taq (Hot start, Promega) and 1 µl of template DNA.…”