Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study

Abstract

Background: GenBank is a public repository that houses millions of nucleotide sequences. Several software have been developed to extract information stored in GenBank. However, none of them are useful to extract and organize GenBank accession based on metadata. We developed a new script called Datataxa, which works to mine GenBank information. The checklist of the Flora del Bajío y de Regiones Adyacentes (FBRA) was used as a case study to apply our script.Questions: How many species occurring in the FBRA have records in GenBank? What percentage of those records have been used for phylogenetic, phylogeographic, phylogenomic, barcoding, genetic diversity, and biogeographic studies?Methods: Datataxa was written in AutoIt Scripting Language in order to facilitate the extraction of information from GenBank. This information was classified in six study categories. A checklist of species published fascicles of FBRA was used as study case to apply our new script, and the previous categories were applied to the FBRA species list.Results: The script allowed us to search for meta information, like publication titles, for 2,558 species that were included in the FBRA. Of these, 1,575 had a least one record in GenBank. A total of 1,322 species were used in phylogenetic studies, followed by barcoding studies (326) and biogeographic studies (298). Phylogenomic (41), phylogeographic (34), and diversity studies (34) were the least represented.Conclusions: Datataxa was useful for mining metadata sequence information from GenBank and can be used with any list of species to get the GenBank accessions’ metadata.

Biogeographical History of the Yucatan Peninsula Endemic Flora (Spermatophyta) from a Phylogenetic Perspective1

“…For the compilation of phylogenetic and biogeographical hypotheses, we performed a metasearch of evolutionary and biogeographical scientific publications based on molecular phylogenetic and/or morphological evidence of endemic and quasi-endemic taxa of the YPBP. First, we used the Datataxa script (Ruiz-Sánchez et al, 2019) to extract meta-information on articles from the Genbank database (Benson et al, 2018). The search categories were Phylogenetic studies (including the terms phylogen*, monop*, systemat*, sistemat*, relationsh*, relacio*), Phylogeographic studies (phylogeog*, filogeog*), Phylogenomic analysis (phylogenom*, genome-scale, “plastid genome”), Diversity studies (diver*, geneti*, pop*, pobl*) and Biogeography (biogeog*).…”

Biodiversity at the global scale: the synthesis continues

“…A question that may arise at this point is: What connection is there to specimens? Megaphylogenetic approaches, generally rooted primarily in GenBank resources, tend to anonymize the original data sources, but because (at least evaluated in terms of species coverage) most plant sequence data derives from molecular systematic or DNA barcoding studies (e.g., Ruiz-Sanchez et al, 2019), there usually are specimen links even if these are not reflected in inconsistently applied metadata fields (Chen and Sarkar, 2011;Tahsin et al, 2018;Troudet et al, 2018) or inconsistent voucher citation practices (Funk et al, 2018). Recent promising attempts have been made to discover and take advantage of linkages between molecular repositories and specimen metadata, which are particularly essential for studies conducted at the population level (Tahsin et al, 2016(Tahsin et al, , 2018Pelletier and Carstens, 2018), and other situations where sequence data without provenances are generally useless.…”