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

Abstract

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...

Supplementary material 4 from: Silakadze N, Mosulishvili M, Borsch T, Kilian N (2024) The polyphyletic Caucasus-centred Campanula subg. Scapiflorae (Campanulaceae) revisited with a newly circumscribed C. sect. Tridentatae for its core clade. PhytoKeys 243: 149-184. https://doi.org/10.3897/phytokeys.243.120908

“…Indels were coded as binary characters using the Simple Indel Coding approach (Simmons and Ochoterena 2000) as implemented in SeqState version 1.4.1 (Müller 2005). Consensus DNA sequences were submitted to ENA (European Nucleotide Archive) (www.ebi.ac.uk/ena/), using the software tool EMBL2checklists (Gruenstaeudl and Hartmaring 2019).…”

The polyphyletic Caucasus-centred Campanula subg. Scapiflorae (Campanulaceae) revisited with a newly circumscribed C. sect. Tridentatae for its core clade

“…Indels were coded as binary characters using the Simple Indel Coding approach (Simmons and Ochoterena 2000) as implemented in SeqState version 1.4.1 (Müller 2005). Consensus DNA sequences were submitted to ENA (European Nucleotide Archive) (www.ebi.ac.uk/ena/), using the software tool EMBL2checklists (Gruenstaeudl and Hartmaring 2019).…”

Figure 1 from: Silakadze N, Mosulishvili M, Borsch T, Kilian N (2024) The polyphyletic Caucasus-centred Campanula subg. Scapiflorae (Campanulaceae) revisited with a newly circumscribed C. sect. Tridentatae for its core clade. PhytoKeys 243: 149-184. https://doi.org/10.3897/phytokeys.243.120908

“…Indels were coded as binary characters using the Simple Indel Coding approach (Simmons and Ochoterena 2000) as implemented in SeqState version 1.4.1 (Müller 2005). Consensus DNA sequences were submitted to ENA (European Nucleotide Archive) (www.ebi.ac.uk/ena/), using the software tool EMBL2checklists (Gruenstaeudl and Hartmaring 2019).…”