Phylogeny and diversification history of the large Neotropical genus <i>Philodendron</i> (Araceae): Accelerated speciation in a lineage dominated by epiphytes

Canal, Dubán; Köster, Nils; Jones, K.; Korotkova, Nadja; Croat, Thomas B.; Borsch, Thomas

doi:10.1002/ajb2.1111

Cited by 15 publications

(7 citation statements)

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“…Moreover, annonex2embl has been employed by several molecular phylogenetic investigations to facilitate their sequence submissions to ENA. Specifically, the software has so far been used in Roy et al (2017), Korotkova et al (2018), Canal et al (2018), Borsch et al (2018), andFalcon-Hidalgo et al (2019) to submit DNA sequence data via the Webin submission portal.…”

Section: Resultsmentioning

confidence: 99%

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA

Gruenstaeudl

2020

Bioinformatics

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Motivation The submission of annotated sequence data to public sequence databases constitutes a central pillar in biological research. The surge of novel DNA sequences awaiting database submission due to the application of next-generation sequencing has increased the need for software tools that facilitate bulk submissions. This need has yet to be met with the concurrent development of tools to automate the preparatory work preceding such submissions. Results The author introduce annonex2embl, a Python package that automates the preparation of complete sequence flatfiles for large-scale sequence submissions to the European Nucleotide Archive. The tool enables the conversion of DNA sequence alignments that are co-supplied with sequence annotations and metadata to submission-ready flatfiles. Among other features, the software automatically accounts for length differences among the input sequences while maintaining correct annotations, automatically interlaces metadata to each record and displays a design suitable for easy integration into bioinformatic workflows. As proof of its utility, annonex2embl is employed in preparing a dataset of more than 1500 fungal DNA sequences for database submission. Availability and implementation annonex2embl is freely available via the Python package index at http://pypi.python.org/pypi/annonex2embl. Supplementary information Supplementary data are available at Bioinformatics online.

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Section: Resultsmentioning

confidence: 99%

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA

Gruenstaeudl

2020

Bioinformatics

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“…These subgenera are phylogenetically supported (e.g. monophyletic) but details of their interrelationships are yet unresolved (Canal et al 2018;Sakuragui et al 2018). Consequently, the subgenus Meconostigma has been recognized as the new genus Thaumatophyllum Schott by some authors (Sakuragui et al 2018) but not by others (Canal et al 2018;Boyce and Croat 2020).…”

Section: Introductionmentioning

confidence: 99%

“…monophyletic) but details of their interrelationships are yet unresolved (Canal et al 2018;Sakuragui et al 2018). Consequently, the subgenus Meconostigma has been recognized as the new genus Thaumatophyllum Schott by some authors (Sakuragui et al 2018) but not by others (Canal et al 2018;Boyce and Croat 2020). Whatever the taxonomic status, all the studies on the reproductive ecology of Philodendron have demonstrated that pollination occurs at dusk or early evening and is exclusively attributed to cyclocephaline scarab beetles (Melolonthidae, Dynastinae, Cyclocephalini) (Moore et al 2013;Gibernau et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Chemical diversity of floral scents in 9 species of Philodendron (Araceae) from French Guiana

Gibernau

Gonçalves²,

Navarro

et al. 2022

Botany Letters

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We provide a characterization of the floral scent chemistry of nine species of Philodendron present in French Guiana. The scent samples were obtained by dynamic headspace, in situ in French Guiana, or from plants in the living aroid collection at the Botanical Garden of the University of Brasilia. Overall, we identified 43 volatile organic compounds (VOCs) belonging to the compound classes of monoterpenes, sesquiterpenes, irregular terpenes, benzenoids, aliphatics, jasmone derivatives, and nitrogen-containing compounds. Five of these floral VOCS are new reports for Philodendron. Interestingly, the floral blends in the investigated species were comprised of 3 -22 VOCs; but when considering only major VOCs (≥ 5%), each fragrant blend could be summarized into one up to four constituents. Except for P. acutatum and P. billietiae, whose floral scents were largely dominated (≥ 93%) by 4-vinylanisole, fragrances of the investigated species were dominated (≥ 62%) each by a different VOC (i.e., dehydrojasmone, dihydro-β-ionone, (E)-4,8-dimethylnona-1,3,7-trien-5-yl acetate, methyl benzoate, 1,3,5-trimethoxybenzene, dihydrobovolide, or (Z)-jasmone). Consequently, all floral scent compositions significantly differed from one other. We compare our results to published data to provide an insight into the floral scent chemistry within the genus Philodendron. We further discuss the diversity of VOCs in cyclocephaline scarab-pollinated aroids.

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“…Specifically, EMBL2checklists was employed for the preparation of hundreds of DNA 291 sequences used in two plant phylogenetic and one fungal metagenomic 292 investigation [46][47][48]. The two plant phylogenetic investigations utilized common plant 293 DNA barcoding markers to infer the phylogenetic history of select plant lineages [46,47]. 294 The fungal metagenomic investigation utilized nrDNA barcodes to characterize 295 arbuscular mycorrhizal soil fungi [48].…”

mentioning

confidence: 99%

“…Upon 382 processing with EMBL2checklists, the user receives a checklist that can be directly 383 uploaded to ENA or further edited with a common spreadsheet editor. The utility of 384 EMBL2checklists is best illustrated by its application during the submission preparation 385 of hundreds of DNA sequences submitted to ENA during the publication process of 386 several recent investigations [46][47][48]. With the development of EMBL2checklists, we 387 hope to provide a useful software tool to plant biologists and bioinformaticians alike, 388 increase the amount of sequence data deposited to public sequence databases [7] and 389 advance the idea of publicly-shared research data [9,10].…”

mentioning

confidence: 99%

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

Gruenstaeudl

Hartmaring

2018

Preprint

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Background. The submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant DNA barcoding. Methods. A Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called "checklists") for a subsequent upload to the public sequence database of the European Nucleotide Archive (ENA). The software tool, titled "EMBL2checklists", automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates output that can be uploaded via the interactive Webin submission system of ENA.Results. EMBL2checklists provides a simple, platform-independent tool that automates the conversion of common plant DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in the submission of DNA sequences of two recent plant phylogenetic investigations and one fungal metagenomic study. Discussion. EMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant biologists without bioinformatics expertise to generate submission-ready checklists from common plant DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing. October 4, 2018 1/18 1 Only a few software tools assist in the preparation of DNA sequence data for submission 2 to public sequence databases, despite the centrality of this process for generating and 3 disseminating novel biological data. Contemporary biological research depends on the 4 preservation, curation, and reproducibility of the data under study [1, 2], and the 5 submission of analyzed data to publicly accessible databases constitutes one of the most 6 important best-practices in biology [3, 4], particularly in the era of big data [5]. DNA 7 sequences generated to identify and characterize novel organisms or un...

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Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes

Cited by 15 publications

References 93 publications

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA

Chemical diversity of floral scents in 9 species of Philodendron (Araceae) from French Guiana

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

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Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes

Cited by 15 publications

References 93 publications

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA

Chemical diversity of floral scents in 9 species of Philodendron (Araceae) from French Guiana

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant DNA barcoding sequences to ENA

Contact Info

Product

Resources

About

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA

`annonex2embl`: automatic preparation of annotated DNA sequences for bulk submissions to ENA