Publishing Data [Workshop]

Context: This short workshop was held on September 05 2023 in the context of the 115th Annual meeting of the German Zoological Society (DZG) in Kassel as part of the satellite workshop "Unlocking the rhythms of life with multiscale clocks", organized by the research training group "multiscale clocks" (https://www.uni-kassel.de/forschung/multiscale-clocks/welcome). Description: This short workshop specifically considers three questions that were raised in the preceding workshop part. During the working time with data and data visualizations, the participants were asked to reflect on the following: „Would you know how to obtain the underlying data?“, „Are you allowed to do with the data what you want?“, „What data/info would you require to check your hypothesis?“. The workshop consequently revolves around data publication. Designed to give a general overview, it covers access, locations and usage rights of published data from a user perspective; as a last part, the generation of reusable data is highlighted from the creator's perspective. Covered topics are open access requirements and colors; publication as supplement, in data journals, or in repositories; copyright and creative commons; research data management, life cycle, and the FAIR principles. The meaning of the FAIR principles was explored with the help of the FAIR Card Deck (unpubl.). Learning Goals: Be aware of research data management topics around data publication Understand the importance of labelling and documentation Know the FAIR principles Duration: 60 min Target Audience: Researchers (Students, PhD candidates, PostDocs) Anyone interested Prerequisites: none (participation in the preceding workshop was expected, but not absolutely necessary) Tools: For the presenter: FAIR Card Deck Mentimeter set up as "Open ended" statement collection for the take home messages from participants Upload Content: Itemized Upload Content File Description 2023-08-30_DZG-Clocks-DataPublication.key Slide deck in editable .key format 2023-08-30_DZG-Clocks-DataPublication.pptx Slide deck in editable .pptx format 2023-08-30_DZG-Clocks-DataPublication.pdf Slide deck as .pdf 2023-08-30_DataPubl_Script.xlsx Presenter's script in editable .xlsx format 2023-08-30_DataPubl_Script.pdf Presenter's script as .pdf Notes: Three FAIR Card Decks were used, with only the cards 9-5 from each deck

Protein-Coding Gene Repertoires : Annotation, Characterization, and Variability in Holometabola

Three previously unavailable prerequisites for gene repertoire analyses are established and used within this thesis: (1) a new tool (COGNATE, written in Perl) was developed and used that records all gene structure parameters instead of relying on summary metrics; (2) it was ensured that automatically generated gene models are suitable for gene structure analyses; and (3) a unique species sample was employed, which representatively covers a younger radiation and allows the comparison of holometabolous and hemimetabolous. Goal of this thesis was to describe and analyze the variation of gene structures within and between repertoires of the species-rich and diverse insects as a step towards understanding and explaining the mechanisms and driving factors of insect genome evolution. COGNATE was employed to evaluate the magnitude of changes in predicted structural properties of protein-coding genes due to manual curation by comparing annotated gene sets from seven insect species sequenced by the i5k initiative. The properties of automatically generated gene models and their manually curated replacements do not differ extensively, and major correlative trends regarding gene structures can be recovered from both sets. From these results I conclude that gene models yielded from unsupervised annotation procedures are a suitable data basis to characterize structural gene features of a whole repertoire. The gene repertoires of twelve Hymenoptera were structurally characterized using COGNATE. The two focal species, non-apocritan "symphytans", possess small genomes and gene repertoires, but a strikingly high GC content of more than 41 %. Striking features are highlighted and lead to the conclusion that structural analyses of gene structure parameters can be used to direct efforts of detailed investigations, for example focused on here discovered miniature introns of ants. The established analysis approach was used to assess the variability in protein-coding gene repertoires in a characterization of the repertoires of a large, unique species sample. Previous research suggested universal patterns of conservation within a gene repertoire in relation to others by which it could be partitioned: highly conserved genes, genes moderately conserved and unevenly distributed across taxa, and lineage- or species-specific genes. My results show that considerable differences exist in gene structural parameters between and within these gene sets beyond previously described patterns. This work provides a solid baseline of expectations on insect gene structure variation as well as manifold investigative leads prompting further research

Repertoire-wide gene structure analyses : a case study comparing automatically predicted and manually annotated gene models

Background The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Results Our results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. Conclusions In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative

Pirate Illustrations for Research Data Management Training

This collection of icons and comics was created to illustrate a workshop on Data Management Plans (https://doi.org/10.5281/zenodo.5575920). It is provided here to allow further reuse, for example to illustrate presentations. The theme of this collection is revolving around pirates, their accessories, and maritime items in general. Created by Jeanne Wilbrandt

COGNATE: comparative gene annotation characterizer

Abstract Background The comparison of gene and genome structures across species has the potential to reveal major trends of genome evolution. However, such a comparative approach is currently hampered by a lack of standardization (e.g., Elliott TA, Gregory TR, Philos Trans Royal Soc B: Biol Sci 370:20140331, 2015). For example, testing the hypothesis that the total amount of coding sequences is a reliable measure of potential proteome diversity (Wang M, Kurland CG, Caetano-Anollés G, PNAS 108:11954, 2011) requires the application of standardized definitions of coding sequence and genes to create both comparable and comprehensive data sets and corresponding summary statistics. However, such standard definitions either do not exist or are not consistently applied. These circumstances call for a standard at the descriptive level using a minimum of parameters as well as an undeviating use of standardized terms, and for software that infers the required data under these strict definitions. The acquisition of a comprehensive, descriptive, and standardized set of parameters and summary statistics for genome publications and further analyses can thus greatly benefit from the availability of an easy to use standard tool. Results We developed a new open-source command-line tool, COGNATE (Comparative Gene Annotation Characterizer), which uses a given genome assembly and its annotation of protein-coding genes for a detailed description of the respective gene and genome structure parameters. Additionally, we revised the standard definitions of gene and genome structures and provide the definitions used by COGNATE as a working draft suggestion for further reference. Complete parameter lists and summary statistics are inferred using this set of definitions to allow down-stream analyses and to provide an overview of the genome and gene repertoire characteristics. COGNATE is written in Perl and freely available at the ZFMK homepage ( https://www.zfmk.de/en/COGNATE ) and on github ( https://github.com/ZFMK/COGNATE ). Conclusion The tool COGNATE allows comparing genome assemblies and structural elements on multiples levels (e.g., scaffold or contig sequence, gene). It clearly enhances comparability between analyses. Thus, COGNATE can provide the important standardization of both genome and gene structure parameter disclosure as well as data acquisition for future comparative analyses. With the establishment of comprehensive descriptive standards and the extensive availability of genomes, an encompassing database will become possible

A first integrative study of the identity and origins of the British Dwarf Pill Millipede populations, Trachysphaera cf. lobata (Diplopoda, Glomerida, Glomeridae)

Three populations of the pill millipede genus Trachysphaera Heller 1858 are present in Great Britain, one on the Isle of Wight, one in South Wales and one in mid-Wales. To identify and characterize the British Trachysphaera populations, the intraspecific and interspecific variation of the populations in South Wales and on the Isle of Wight were studied and evaluated in a first integrative study of members of Trachysphaera, utilizing barcoding and SEM. DNA was extracted from 28 British Trachysphaera and 10 French T. lobata (Ribaut 1954) specimens, one each of French T. cf. drescoi (Conde and Demange 1961) and T. pyrenaica (Ribaut 1908), and one of Spanish T. cf. rousseti (Demange 1959); the barcoding fragment of the COI gene was amplified and their genetic intra- and interpopulation distances compared with one another using two Italian T. spp. and one Croatian T. schmidti Heller 1858 specimens as near outgroups. To compare the genetic distances with the morphological characters, 15 characters of a total of 13 British Trachysphaera, together with two specimens of T. pyrenaica, two T. cf. drescoi and one of T. cf. rousseti were imaged, using the same individuals utilized for DNA extraction. Albeit both British populations are genetically distant, they are closely related (1.9–2.5% p-distance) to French T. lobata, corroborating results of earlier studies. Between different Trachysphaera species, genetic distance was high (16.7–18.8%). The morphological study showed the non-reliability of key taxonomic characters in Trachysphaera, with genetically identical individuals exhibiting morphological variation, especially on the telopods. The only observed morphological characters constant within and different between species were the number of rows of sclerotized bacilli on the tergites, as well as the shape of the male and female anal shield. Both, barcoding and the morphological study identify the British Trachysphaera populations as T. lobata

Additional file 4: of COGNATE: comparative gene annotation characterizer

The COGNATE package. This archive file contains the COGNATE package, including Perl scripts, Additional file 1: Parameter table, Readme, example data and output, and the GAL library. (ZIP 566 kb

Additional file 3: of COGNATE: comparative gene annotation characterizer

Result table. COGNATE results of analyzing exon and intron lengths of Apis mellifera. This data sheet contains the mean and median lengths of exons and introns, which are part of the 10,733 transcripts analyzed by COGNATE (default run, i.e., using the longest of each gene’s alternative transcripts). In total, 76,276 exons and 65,543 introns were taken into account. The data is visualized in Fig. 2. (XLSX 225 kb

Intrasexual cuticular hydrocarbon dimorphism in a wasp sheds light on hydrocarbon biosynthesis genes in Hymenoptera

Cuticular hydrocarbons (CHCs) cover the cuticle of insects and serve as desiccation barrier and as semiochemicals. While the main enzymatic steps of CHC biosynthesis are well understood, few of the underlying genes have been identified. Here we show how exploitation of intrasexual CHC dimorphism in a mason wasp, Odynerus spinipes, in combination with whole-genome sequencing and comparative transcriptomics facilitated identification of such genes. RNAi-mediated knockdown of twelve candidate gene orthologs in the honey bee, Apis mellifera, confirmed nine genes impacting CHC profile composition. Most of them have predicted functions consistent with current knowledge of CHC metabolism. However, we found first-time evidence for a fatty acid amide hydrolase also influencing CHC profile composition. In situ hybridization experiments furthermore suggest trophocytes participating in CHC biosynthesis. Our results set the base for experimental CHC profile manipulation in Hymenoptera and imply that the evolutionary origin of CHC biosynthesis predates the arthropods’ colonization of land.SCOPUS: ar.jinfo:eu-repo/semantics/publishe