The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland

Background Lake Þingvallavatn in Iceland, a part of the river Ölfusá drainage basin, was presumably populated by brown trout soon after it formed at the end of the last Ice Age. The genetic relatedness of the brown trout in Þingvallavatn to other populations in the Ölfusá drainage basin is unknown. After the building of a dam at the outlet of the lake in 1959 brown trout catches declined, though numbers have now increased. The aim of this study was to assess effects of geographic isolation and potential downstream gene flow on the genetic structure and diversity in brown trout sampled in several locations in the western side of the watershed of River Ölfusá. We hypothesized that brown trout in Lake Þingvallavatn constituted several local spawning populations connected by occasional gene flow before the damming of the lake. We also estimated the effective population size (NE) of some of these populations and tested for signs of a recent population bottleneck in Lake Þingvallavatn. Methods We sampled brown trout inhabiting four lakes and 12 rivers within and near the watershed of River Ölfusá by means of electro- and net- fishing. After stringent data filtering, 2,597 polymorphic loci obtained from ddRADseq data from 317 individuals were ascertained as putative neutral markers. Results Overall, the genetic relatedness of brown trout in the Ölfusá watershed reflected the connectivity and topography of the waterways. Ancestry proportion analyses and a phylogenetic tree revealed seven distinct clusters, some of which corresponded to small populations with reduced genetic diversity. There was no evidence of downstream gene flow from Lake Þingvallavatn, although gene flow was observed from much smaller mountain populations. Most locations showed low NE values (i.e., ~14.6 on average) while the putative anadromous trout from River Sog and the spawning population from River Öxará, that flows into Lake Þingvallavatn, showed notably higher NE values (i.e., 71.2 and 56.5, respectively). No signals of recent population bottlenecks were detected in the brown trout of Lake Þingvallavatn. Discussion This is the first time that the genetic structure and diversity of brown trout in the watershed of River Ölfusá have been assessed. Our results point towards the presence of a metapopulation in the watershed of Lake Þingvallavatn, which has been influenced by restoration efforts and is now dominated by a genetic component originated in River Öxará. Many of the locations studied represent different populations. Those that are isolated in headwater streams and lakes are genetically distinct presenting low genetic diversity, yet they can be important in increasing the genetic variation in downstream populations. These populations should be considered for conservation and direct management

Microsatellites in Common whelk

Genepop format, five loci: bu67, bu119, bu122, bu145, bu151. Populations: Britain (BR), Faeroe Islnds (FE), Greenland (GR1-4), Canada (CA), Iceland: Faxafloi (FA), Hempill (HE), Hruteyjar (HR), Oddbjarnarsker (OD), Hunafloi (HF

Data from: Divergence and molecular variation in common whelk Buccinum undatum (Buccinidae) in Iceland: a trans-Atlantic comparison

The dispersal and history of species affects their genetic population structure at both small and large geographical scales. The common whelk, Buccinum undatum, is a widespread subtidal gastropod in the North Atlantic that has no planktonic larvae and has thus limited dispersal capacity. The snail, which has been harvested by humans for centuries, is highly variable in morphology. To evaluate the population structure in the rich fishing grounds in western Iceland and its divergence from samples across the Atlantic, genetic patterns based on sequence variation in two mtDNA genes (COI and 16S) and five microsatellites were studied and compared to variation in populations from both sides of the Atlantic. Significant differences in allele and haplotype frequencies were found among samples separated by short distances along the coast of Iceland. Partition of the variation showed larger variance among samples obtained from distant regions than from neighbouring sites and genetic distances were correlated with geographical distance among populations in Europe. Phylogeographic patterns in mtDNA reveal different monophyletic lineages on both sides of the Atlantic, which predate the onset of the Ice-age and which may constitute cryptic species. Similar micro- and macrogeographic patterns were observed for the mtDNA and microsatellite markers despite high frequencies of null alleles. Bayesian skyline reconstructions of the demographic history and mismatch distributions suggest that while sizes of some populations were unaffected by Ice Age glaciations others show signs of expansion after the last glacial maximum. These phylogeographic patterns are consistent with patterns expected for low dispersal species that have survived in allopatric glacial refugial populations on both sides of the Atlantic and in deep-sea refugia within each continent. The observed genetic structure has implications for conservation and sustainable management of the harvested populations

Investigation of the effects of estrogen on skeletal gene expression during zebrafish larval head development

The development of craniofacial skeletal structures requires well-orchestrated tissue interactions controlled by distinct molecular signals. Disruptions in normal function of these molecular signals have been associated with a wide range of craniofacial malformations. A pathway mediated by estrogens is one of those molecular signals that plays role in formation of bone and cartilage including craniofacial skeletogenesis. Studies in zebrafish have shown that while higher concentrations of 17-β estradiol (E2) cause severe craniofacial defects, treatment with lower concentrations result in subtle changes in head morphology characterized with shorter snouts and flatter faces. The molecular basis for these morphological changes, particularly the subtle skeletal effects mediated by lower E2 concentrations, remains unexplored. In the present study we address these effects at a molecular level by quantitative expression analysis of sets of candidate genes in developing heads of zebrafish larvae treated with two different E2 concentrations. To this end, we first validated three suitable reference genes, ppia2, rpl8 and tbp, to permit sensitive quantitative real-time PCR analysis. Next, we profiled the expression of 28 skeletogenesis-associated genes that potentially respond to estrogen signals and play role in craniofacial development. We found E2 mediated differential expression of genes involved in extracellular matrix (ECM) remodelling, mmp2/9/13, sparc and timp2a, as well as components of skeletogenic pathways, bmp2a, erf, ptch1/2, rankl, rarab and sfrp1a. Furthermore, we identified a co-expressed network of genes, including cpn1, dnajc3, esr1, lman1, rrbp1a, ssr1 and tram1 with a stronger inductive response to a lower dose of E2 during larval head development

Patterns of MiRNA Expression in Arctic Charr Development

<div><p>Micro-RNAs (miRNAs) are now recognized as a major class of developmental regulators. Sequences of many miRNAs are highly conserved, yet they often exhibit temporal and spatial heterogeneity in expression among species and have been proposed as an important reservoir for adaptive evolution and divergence. With this in mind we studied miRNA expression during embryonic development of offspring from two contrasting morphs of the highly polymorphic salmonid Arctic charr (<i>Salvelinus alpinus</i>), a small benthic morph from Lake Thingvallavatn (SB) and an aquaculture stock (AC). These morphs differ extensively in morphology and adult body size. We established offspring groups of the two morphs and sampled at several time points during development. Four time points (3 embryonic and one just before first feeding) were selected for high-throughput small-RNA sequencing. We identified a total of 326 conserved and 427 novel miRNA candidates in Arctic charr, of which 51 conserved and 6 novel miRNA candidates were differentially expressed among developmental stages. Furthermore, 53 known and 19 novel miRNAs showed significantly different levels of expression in the two contrasting morphs. Hierarchical clustering of the 53 conserved miRNAs revealed that the expression differences are confined to the embryonic stages, where miRNAs such as sal-miR-130, 30, 451, 133, 26 and 199a were highly expressed in AC, whereas sal-miR-146, 183, 206 and 196a were highly expressed in SB embryos. The majority of these miRNAs have previously been found to be involved in key developmental processes in other species such as development of brain and sensory epithelia, skeletogenesis and myogenesis. Four of the novel miRNA candidates were only detected in either AC or SB. miRNA candidates identified in this study will be combined with available mRNA expression data to identify potential targets and involvement in developmental regulation.</p></div

Comparison of expression of 8 selected miRNAs (miR-17, 26a, 30b, 140, 181a, 196a and 199a) at three developmental time-points for two contrasting Arctic charr morphs (AC and SB) quantified by small RNA-seq (upper panel) or qPCR (lower panel).

<p>Comparison of expression of 8 selected miRNAs (miR-17, 26a, 30b, 140, 181a, 196a and 199a) at three developmental time-points for two contrasting Arctic charr morphs (AC and SB) quantified by small RNA-seq (upper panel) or qPCR (lower panel).</p

Heat-map showing relative expression of the 53 miRNAs significantly differentially expressed between AC and SB morphs.

<p>Expression levels for each miRNA were normalized across samples using variance stabilizing transformation. Blue denotes high and white low relative expression. AC stands for Aquaculture charr and SB stands for Small benthic charr. Numbers 1, 2, 3 and 4 depict the four developmental points.</p

Two contrasting Arctic charr morphs differing in size, coloration and head morphology.

<p>Top: Arctic charr from aquaculture stock (AC) is large, silvery and has a pointed snout and long lower jaw, Bottom: Small benthic charr from Thingvallavatn (SB) is small, dark and has a sub-terminal mouth and rounded snout.</p