Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, and easy-to-share pipelines. While documentation for such tools is available, there are only a few freely accessible examples that teach the underlying concepts focused on CADD, especially addressing users new to the field. Here, we present TeachOpenCADD, a teaching platform developed by students for students, using open source compound and protein data as well as basic and CADD-related Python packages. We provide interactive Jupyter notebooks for central CADD topics, integrating theoretical background and practical code. TeachOpenCADD is freely available on GitHub: https://github.com/volkamerlab/TeachOpenCADD .
Hybridization between sea turtle species occurs with particularly high frequency at two adjacent nesting areas in northeastern Brazil. To understand the outcomes of hybridization and their consequences for sea turtle conservation, we need to evaluate the extent of hybridization occurrence and possible deleterious effects in the hybrid progeny. Thus, we investigated the hypothesis of the existence of a new hybrid spot offshore of Brazil’s northeastern coast. The Abrolhos Archipelago is surrounded by the largest and richest coral reefs in the South Atlantic and is known to be a nesting site for loggerhead turtles (Carettacaretta). In this study, we performed a multidisciplinary investigation into levels of hybridization in sea turtles and their reproductive output in the Abrolhos beaches. Genetic data from mitochondrial DNA (mtDNA) and six autosomal markers showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelysimbricata) and loggerhead females, and backcrossed hatchlings from both parental species. The type and extent of hybridization were characterized using genomic data obtained with the 3RAD method, which confirmed backcrossing between F1 hybrids and loggerhead turtles. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.
Reduced representation libraries present an opportunity to perform large scale studies on non-model species without the need for a reference genome. Methods that use restriction enzymes and fragment size selection to help obtain the desired number of loci -such as ddRAD -are highly flexible and therefore suitable to different types of studies. However, a number of technical issues are not approachable without a reference genome, such as size selection reproducibility across samples and coverage across fragment lengths. Moreover, identity thresholds are usually chosen arbitrarily in order to maximize the number of SNPs considering arbitrary parameters. We have developed a strategy to identify de novo a set of reduced-representation single-copy orthologs (R2SCOs). Our approach is based on overlapping reads that recreate original fragments and add information about coverage per fragment size. A further in silico digestion step limits the data to well covered fragment sizes, increasing the chance of covering the majority of loci across different individuals. By using full sequences as putative alleles, we estimate optimal identity thresholds from pairwise comparisons. We have demonstrated our full workflow with data from five sea turtle species. Locus numbers were similar across all species, even at increasing phylogenetics distances. Our results indicated that sea turtles have in general very low levels of heterozygosity. Our approach produced a high-quality set of reference loci, eliminating a series of biological and experimental biases that can strongly affect downstream analysis, and allowed us to explore the genetic variability within and across sea turtle species.
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