#ERGAReads | Long-read sequencing for biodiversity analyses—A comprehensive guide 🧬
besjournals.onlinelibrary.wiley.com/doi/10.1111/...

@ilianabista.bsky.social @sgn.one @sangerinstitute.bsky.social
@britishecologicalsociety.org

#longreads #sequencing #guide #biodiversitygenomics #genomics

Cookbook for plant genome sequences - BMC Genomics BMC Genomics - Access to genome sequences is crucial to investigate and engineer traits in plants, explore biodiversity, and support phylogenetic studies. Over the last decade, affordable...

#ERGAReads | Cookbook for plant genome sequences 🌱 🌴 🌵 🌿 🌾 🌿 🍀
link.springer.com/article/10.1...

@bpucker.bsky.social @unibonn.bsky.social @puckerlab.bsky.social 🌱 🖥️

#Plant #genomes

Validate User

#ERGAReads | On the path to reference genomes for all biodiversity: laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life 🌳 🧬

academic.oup.com/gigascience/...

@sangerinstitute.bsky.social @gigascience.bsky.social
#genomes #biodiversitygenomics

FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life - Communications Biology FANTASIA, a protein language model-based tool, enables large-scale functional annotation across ~1000 animal proteomes, revealing novel gene functions in both model and non-model organisms beyond…

#ERGAReads | FANTASIA leverages language models to decode the functional dark proteome across the animal tree of life
www.nature.com/articles/s42...

@rosafernandez.bsky.social @commsbio.nature.com @csic.es @ibe-barcelona.bsky.social

#LLM #proteome #functional #annotation #genomes

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#ERGAReads | Genome size estimation from long read overlaps 🧑‍💻 🧬
🔗 academic.oup.com/bioinformati...

#bioinformatics #genomesize #Longreads

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and…

#ERGAReads | Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model 🧬
www.nature.com/articles/s41...
#GenomeAnnotation #Helixer @natmethods.nature.com

Ocean Genomes: reference genome resources for marine vertebrates - npj Biodiversity npj Biodiversity - Ocean Genomes: reference genome resources for marine vertebrates

#ERGAReads | 🐚 🌊 🧬 Ocean Genomes: reference genome resources for marine vertebrates
rdcu.be/e25OP

#ERGAReads | Identifying Key Biodiversity Areas Based on Distinct Genetic Diversity
🔗 onlinelibrary.wiley.com/share/ET4N3X... @unitrier.bsky.social @ipna.csic.es

A Beginner's Guide to Structural Variants in Eco‐Evolutionary Population Genomics Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence.…

#ERGAReads | A Beginner's Guide to Structural Variants in Eco-Evolutionary Population Genomics 🧬
🔗 onlinelibrary.wiley.com/doi/10.1111/...
#MolecularEcology #structuralvariants #genomics #PopulationGenomics @rebekahoomen.bsky.social @clairemerot.bsky.social

#ERGAReads | IChromosome-scale Genomes Show Rapid Diversification and Ancient Gene Flow Among Bear Species 🐻
🔗 doi.org/10.1093/gbe/...
@genomebiolevol.bsky.social

On the path to reference genomes for all biodiversity: laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life Abstract. Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally resolved refere

#ERGAReads | On the path to reference genomes for all biodiversity: laboratory protocols & lessons learned from processing over 2,000 species in the Sanger Tree of Life
🔗 academic.oup.com/gigascience/... @sangerinstitute.bsky.social @ebpgenome.bsky.social

The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity Abstract. Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we

#ERGAReads | The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity 🌈🧬
🔗 academic.oup.com/gbe/article/...

@genomebiolevol.bsky.social @unil.bsky.social @embl.org @mpi-bio-fml.bsky.social @univie.ac.at @uab.cat
#genomics #genomicdiversity

Integrative phylogenomics positions sponges at the root of the animal tree Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by…

#ERGAReads | Integrative #phylogenomics positions sponges at the root of the animal tree
🔗 www.science.org/doi/10.1126/... 🧬

#porifera #sponges #phylogenomics

Project Psyche: reference genomes for all Lepidoptera in Europe Project Psyche is a transnational initiative to generate and study chromosome-level reference genomes of all ~11 000 species of Lepidoptera (butterflies and moths) found in Europe. Here, we describe…

#ERGAReads | We start the year by highlighting our partner Project Psyche: reference genomes for all Lepidoptera in Europe! 🦋 🌍 🧬 @projectpsyche.bsky.social

🔗 www.cell.com/trends/ecolo...

#butterflies #moths #genomes

#ERGAReads | The #VGP @genomeark team built rdeval, a tool to quickly compute, store & visualise sequencing read stats. From FASTQ to snapshot files & visual reports, speeding up data quality checks at scale.
🔗 academic.oup.com/bioinformati... @giulio_formenti @erichjarvis

#ERGAReads 🌍 Amphibians & reptiles face global change but many regions lack the genomic data needed to guide conservation. This review maps genomic “coldspots,” revealing gaps in adaptive potential studies & calling for stronger global collaborations.
onlinelibrary.wiley.com/doi/10.1111/...

#ERGAReads | A new statistic (IDrisk) to quantify how long runs of homozygosity (ROHs) and heterozygosity in non-ROH regions can be used to predict the risk of inbreeding depression in a population.
🔗 www.cell.com/trends/ecolo...

#conservation #genomics #inbreeding @sandiegozoo.bsky.social

#ERGAReads | Clitellates - terrestrial & freshwater annelids - underwent dramatic #genome reshuffling, losing synteny with their marine relatives. This rare burst of genomic change reshaped chromosome structure in the group
🔗 rdcu.be/euNbT
#genomics #evolution #Annelida @rosafernandez.bsky.social

#ERGAReads | To unlock the full power of #genomics in biodiversity conservation, we need harmonised standards for genome-wide analyses. A new @ergabiodiv.bsky.social review calls for stakeholder-informed best practices to guide future efforts.

🔗 onlinelibrary.wiley.com/doi/10.1111/...

#ERGAReads | Amphibians are among the most threatened vertebrates 🐸 The Amphibian Genomics Consortium unites 280+ scientists to advance genomic resources and conservation efforts for this vital, understudied group.
🔗https://doi.org/10.1186/s12864-024-10899-7
#genomics #amphibians #conservation

#ERGAReads | Can sex chromosomes reveal what autosomes miss?
This study on red deer 🦌 compares autosomal vs. X-chromosome data from 144 genomes, uncovering contrasting population histories. The X chromosome better preserves signals from Late Glacial isolation.

🔗 doi.org/10.1093/molb...
#Genomics

#ERGAReads | 13 new high-quality cetacean genomes produced by the Cetacean Genomes Project offer key insights into the group's ancestry and adaptation 🐬🐋🧬

🔗 www.frontiersin.org/journals/mar...

#genomics #conservation #cetaceans @ebpgenome.bsky.social @vertebrategenomes.bsky.social @noaa.gov

#ERGAReads | Over 10,000 species are listed as Critically Endangered by the IUCN. This review highlights global patterns, threats & actions needed, calling for urgent investment to prevent extinctions 🌍🦎🌿

🔗 rdcu.be/euM65

#ERGAReads | Comparative analysis of 163 ant genomes uncovers how #genome rearrangements, gene family expansions and selection shaped the evolution of caste systems and social complexity in ants 🐜🧬

🔗 www.cell.com/cell/fulltex...

@cellpress.bsky.social
#ants #evolution #socialevolution

#ERGAReads | Analysis of 3 pentaploid dogrose genomes provide insights into their unique reproductive strategies & advance our understanding of genome #evolution and meiotic mechanisms in organisms with asymmetrical inheritance systems 🏵️
🔗 www.nature.com/articles/s41...
@sgn.one @ceplas.bsky.social

#ERGAReads | The Arthropoda Assembly Assessment Catalogue offers an automated, interactive overview of #genome assembly quality across arthropods using #BUSCOs🪲🦟🐛
A tool for tracking coverage & guiding future sequencing efforts.
🔗 doi.org/10.1093/giga...

#Genomics #Arthropoda #BUSCO

#ERGAReads | The California Conservation Genomics Project (CCGP) is setting a new benchmark in large-scale landscape #genomics for #conservation. 🌿🌊 #CCGP aims to map genomic diversity, connectivity and climate resilience across California’s ecosystems.

🔗 doi.org/10.1093/jher...

#ERGAReads | This week, we highlight Squalomix, our newest associated partner 🦈🧬 #Squalomix tackles key challenges in #elasmobranch genomics through advanced cytological techniques and high-fidelity long-read sequencing.
🔗 f1000research.com/articles/11-...

@kurakulabmsm.bsky.social #sharks #rays

#ERGAReads | @ebpgenome.bsky.social aims to generate high-quality reference #genomes across the tree of life 🌍
This new paper outlines evolving standards for sample acquisition & processing and key challenges for the future of the project.
🔗 doi.org/10.1093/giga... #bestpractices #samplecollection

#ERGAReads | Scientific #data analysis should be scalable, transparent, and shareable - yet computational #workflows are often fragmented and hard to find. #WorkflowHub tackles this with a unified registry that promotes reproducibility, and #FAIRdata:

🔗 www.nature.com/articles/s41...