DOI: 10.5061/dryad.vx0k6dk13
title: Sequence alignment of Stizophyllum for the markers: Ndhf, rpl32-trnl and pepc

description: The reconstruction of molecular phylogenies, such as those of the genus
 Stizophyllum (Bignonieae, Bignoniaceae), a group of Neotropical lianas,
 provides valuable insights into their evolutionary history. In this study,
 we analyzed both chloroplast markers (ndhF and rpl32-trnL) and a nuclear
 marker (pepC), individually and in combination, to enhance the systematic
 understanding of the genus. A total of 33 specimens, representing the
 three currently recognized species and two new combinations, were
 collected under legal guidelines with appropriate collection permits and
 included in the sequencing analysis. Our dataset comprises the alignments
 for each marker, the combined chloroplast markers (cpDNA), and the full
 dataset with all markers combined (combined All).
description: # Seq\_Aligment
 [https://doi.org/10.5061/dryad.vx0k6dk13](https://doi.org/10.5061/dryad.vx0k6dk13) ``` Sequence alignment for 3 markers: ndhF, rpl32-trnl and pepC of Stizophyllum Miers species (Bignonieae, Bignoniaceae). Extraction of leaf tissue, we pulverized 60 mg of plant material with TissueLyzer (Qiagen, Düsseldorf, Germany) and extracted DNA using the Invisorb Spin Plant Mini Kit (Invitek, Berlin, Germany) following the manufacturer’s instructions. For specimens with less than 60 mg of leaf tissue, the CTAB protocol of Doyle and Doyle (1987) was used. We amplified each sample using Sanger sequencing, for the chloroplast markers the protocol of Lohmann (2006), with adjustments suggested by Zuntini et al. (2013), was used and for the nuclear markers, we used the nested PCR strategy described by Francisco and Lohmann (2017). Contigs were assembled through manual inspection of chromatograms using Geneious 9.1.8 (Kearse et al., 2012) ``` ## Description of the data and file structure ``` File in Nexus format for Bayesian and ML analysis. Including the number of taxa, name of the specimens (taxlables) and then the alignment for each specimen ``` The data were obtained through DNA extraction from 60 mg of leaf material using a TissueLyzer (Qiagen, Düsseldorf, Germany), followed by DNA isolation with either the Invisorb Spin Plant Mini Kit (Invitek, Berlin, Germany) or the CTAB protocol of Doyle and Doyle (1987). For the amplification of chloroplast markers, we followed the protocol of Lohmann (2006), with modifications proposed by Zuntini et al. (2013). Nuclear markers were amplified using the nested PCR strategy described by Francisco and Lohmann (2017). All PCR products were purified and sequenced by Macrogen Inc. (Seoul, Korea). Forward and reverse sequences were obtained, and contigs were assembled through manual inspection of chromatograms using Geneious 9.1.8 (Kearse et al., 2012). Seq_alingment_ndhf -  Assembled sequences of 31 taxa: 29 from the Stizophyllum genus and 2 outgroups for the chloroplast marker ndhF Seq_alignment_rpl32 -  Assembled sequences of 24 taxa: 22 from the Stizophyllum genus and 2 outgroups for the chloroplast marker rpl32-trnL Seq_alignment_pepc -  Assembled sequences of 19 taxa: 17 from the Stizophyllum genus and 2 outgroups for the nuclear marker pepC Seq_alignment_Combined - the full dataset with all markers combined (combined All) Seq_alignment_cpDNA - the combined chloroplast markers (cpDNA)