Highlights from the 16th International Society for Computational Biology Student Council Symposium 2020.

In this meeting overview, we summarise the scientific program and organisation of the 16th International Society for Computational Biology Student Council Symposium in 2020 (ISCB SCS2020). This symposium was the first virtual edition in an uninterrupted series of symposia that has been going on for 15 years, aiming to unite computational biology students and early career researchers across the globe. [Abstract copyright: Copyright: © 2021 Cuypers WL et al.

A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage

Abstract: Background: Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans. Results: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage. Conclusions: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy

ISCB Student Council Symposium 2021, a virtual global venue : challenges and lessons learned

Since 2004, the ISCB Student Council has been organizing different symposia worldwide, gathering together the community of young computational biologists. Due to the coronavirus disease 2019 (COVID-19) pandemic situation, the world scientific community was forced to cancel in-person meetings for almost two years, imposing the adoption of virtual formats instead. After the successful editions of our continental symposia in 2020 in the USA, Latin America, and Europe, we organized our flagship global event, the Student Council Symposium (SCS) 2021, trying to apply all previous lessons learned and to exploit the advantages that virtuality has to offer

FAIR+E pathogen data for surveillance and research: lessons from COVID-19

The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research

Global network of computational biology communities: ISCB's regional student groups breaking barriers [version 1; peer review: Not peer reviewed]

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: “Nurture the new generation of computational biologists”.Fil: Shome, Sayane. University of Iowa; Estados UnidosFil: Parra, Rodrigo Gonzalo. European Molecular Biology Laboratory; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Fatima, Nazeefa. Uppsala Universitet; SueciaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Cuypers, Bart. Universiteit Antwerp; BélgicaFil: Moosa, Yumna. University of KwaZulu Natal; SudáfricaFil: Da Rocha Coimbra, Nilson. Universidade Federal de Minas Gerais; BrasilFil: Assis, Juliana. Universidade Federal de Minas Gerais; BrasilFil: Giner Delgado, Carla. Universitat Autònoma de Barcelona; EspañaFil: Dönertaş, Handan Melike. European Molecular Biology Laboratory. European Bioinformatics Institute; Reino UnidoFil: Cuesta Astroz, Yesid. Universidad de Antioquia; Colombia. Universidad Ces. Facultad de Medicina.; ColombiaFil: Saarunya, Geetha. University of South Carolina; Estados UnidosFil: Allali, Imane. Universite Mohammed V. Rabat; Otros paises de África. University of Cape Town; SudáfricaFil: Gupta, Shruti. Jawaharlal Nehru University; IndiaFil: Srivastava, Ambuj. Indian Institute of Technology Madras; IndiaFil: Kalsan, Manisha. Jawaharlal Nehru University; IndiaFil: Valdivia, Catalina. Universidad Andrés Bello; ChileFil: Olguín Orellana, Gabriel José. Universidad de Talca; ChileFil: Papadimitriou, Sofia. Vrije Unviversiteit Brussel; Bélgica. Université Libre de Bruxelles; BélgicaFil: Parisi, Daniele. Katholikie Universiteit Leuven; BélgicaFil: Kristensen, Nikolaj Pagh. Technical University of Denmark; DinamarcaFil: Rib, Leonor. Universidad de Copenhagen; DinamarcaFil: Guebila, Marouen Ben. University of Luxembourg; LuxemburgoFil: Bauer, Eugen. University of Luxembourg; LuxemburgoFil: Zaffaroni, Gaia. University of Luxembourg; LuxemburgoFil: Bekkar, Amel. Universite de Lausanne; SuizaFil: Ashano, Efejiro. APIN Public Health Initiatives; NigeriaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Moreyra, Nicolás Nahuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Ecología, Genética y Evolución de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Ecología, Genética y Evolución de Buenos Aires; Argentin

Whole-Genome Sequencing of two Swedish Individuals on PromethION

Background: Chromosomes can undergo various changes such as deletions, inversions, insertions, and/or translocations resulting in structural variation differences between individuals. Structural variants are a common source of variability in the human genome and have been known to be associated with common diseases such as autism, cancer, and rare human diseases [1, 2]. However, they have not yet been extensively studied at the higher resolution. SVs are complex genomic components partially due to being known to emerge in repetitive regions [3]. Alignment of short reads to repetitive regions can cause ambiguity and has, therefore, posed challenges in the past to detect SVs. New approaches for SV detection have been enabled by the recent improvements in sequencing technologies. In particular, the new long-read single-molecule sequencing instruments provided by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) produce a high yield in a short period while keeping a low cost for a library preparation. These instruments make it possible to generate high quality representations of whole genomes and enable reliable structural variant calling in human individuals [4, 5]. Objectives: A recent study performed on PacBio’s Single-Molecule Real-Time sequencing of two Swedish human genomes, Swe1 (male) and Swe2 (female), as part of the SweGen 1000 Genomes project (https://swefreq.nbis.se), uncovered over 17K SVs per individual as well as various other genomic components [6] that are otherwise not detectable in short reads. As a follow-up study, we have now generated data for the same two Swedish individuals on the ONT’s PromethION system, a new nanopore based sequencing instrument, that is known for its higher throughput as compared to the PacBio. Results and Conclusion: We present a pilot study that evaluates nanopore data derived from wholegenome sequencing (WGS) on PromethION in comparison to the Single-Molecule Real-Time (SMRT) reads obtained from the PacBio RS II platform. We performed comparative analyses of single- molecule long-read technologies in a context of mappability, and SV detection that resulted in an average of 17k and 24k variants across nanopore and SMRT datasets, respectively. The results will be useful for the large-scale SweGen project in a context of validation and comparison of SVs in Swedish individuals. In addition, the study serves as a bioinformatics pipeline for future long-read data analyses and sets a basis for what to consider when designing future PromethION experiments.Whole-Genome Sequencing of two Swedish Individuals on Oxford Nanopore PromethION Chromosomes can undergo various changes such as large deletions and/or insertions, resulting in structural variation differences between individuals. Structural variants (SVs) are a common source of variability in the human genome and are known to be associated with several diseases. SVs often involve complex genomic rearrangements that are difficult to resolve using short read sequencing technologies. New approaches enabled by the latest generation of long-read single-molecule sequencing instruments, provided by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), can produce a sufficient amount of data to enable SV detection across entire human genomes to a reasonable cost. Previously, we performed PacBio sequencing of two Swedish human genomes, as part of the SweGen 1000 Genomes project (https://swefreq.nbis.se) and uncovered over 17,000 SVs per individual (Ameur et al, 2018). A majority of these SVs were not detectable in short reads. As a follow-up, we have now generated data for the same individuals on ONT’s PromethION system, a new nanopore-based platform known for its higher throughput as compared to PacBio. We present a pilot study that evaluates nanopore data derived from whole-genome sequencing (WGS) on PromethION in comparison to the Single-Molecule Real-Time (SMRT) reads obtained from the PacBio RSII platform. We performed comparative analyses of single- molecule technologies in a context of mappability, and SV detection that resulted in an average of 17k and 24k variants across nanopore and SMRT datasets, respectively. The results will be useful for the large-scale SweGen project, while the study serves as a bioinformatics pipeline for future long-read data analyses and sets a basis for what to consider when designing future PromethION experiments. Master’s Degree Project in Bioinformatics 30 credits 2019 Department of Biology, Lund University Advisor: Adam Ameur National Genomics Infrastructure, Science for Life Laboratory, Uppsala, Swede

Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies

D3.3 (M18) - Report on curation in core ELIXIR registries (an ELIXIR Norway ELIXIR3 deliverable)

This report serves as an update on the progress of WP3 Task 3.4 in ELIXIR3, in support of curation efforts on content in repositories of metadata, datasets, tools, training, workflows, and other resources, in line with the ELIXIR Platforms. The report documents progress made, methods used, and plans for the near future as of month 18 of a 48-month timeline. ELIXIR Norway extends support to numerous internal and external service providers in Norway, in cases where the services have been accepted as ELIXIR Services. Being an ELIXIR Service comes with many advantages, from gaining exposure to a broader range of potential users to a raised profile throughout ELIXIR, that can help secure future funding, among other benefits. While these Services maintain specific operational responsibilities, ELIXIR Norway offers versatile infrastructure-related support. We provide a first-line helpdesk, potential Node e-infrastructure integration (where feasible), service monitoring, and metrics collection. Our technology hub further enriches this by imparting best practices and standards, and hosting workshops and conferences. The inception of Task 3.4 is based on observations that most ELIXIR Norway Services do not promote available resources sufficiently, including relevant ontologies, essential repositories like Bio.tools and FAIRsharing, and key Services from other ELIXIR Platforms. The primary objective of the Task is to assist service providers, task forces, and other Tasks and work packages in effectively using available resources for maximum benefit. The work in this Task has been aligned with, and partially builds up on the work performed in the European context in the H2020 project ELIXIR-CONVERGE (February 2020 - July 2023) (871074)