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Standards recommendations for the Earth BioGenome Project

https://doi.org/10.1073/pnas.2115639118
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1038/35048692openalex-snapshot
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/387s005openalex-snapshot
The Yeast Genome Directory
inferredcites →https://doi.org/10.1038/nature01262openalex-snapshot
Initial sequencing and comparative analysis of the mouse genome
inferredcites →https://doi.org/10.1038/s41586-021-03451-0openalex-snapshot
Towards complete and error-free genome assemblies of all vertebrate species
inferredcites →https://doi.org/10.1038/sdata.2016.18openalex-snapshot
The FAIR Guiding Principles for scientific data management and stewardship
inferredcites →https://doi.org/10.1073/pnas.1720115115openalex-snapshot
Earth BioGenome Project: Sequencing life for the future of life
inferredcites →https://doi.org/10.1073/pnas.2115635118openalex-snapshot
The Earth BioGenome Project 2020: Starting the clock
inferredcites →https://doi.org/10.1073/pnas.2115859119openalex-snapshot
Ethical, legal, and social issues in the Earth BioGenome Project
inferredcites →https://doi.org/10.1093/database/baw093openalex-snapshot
The Ensembl gene annotation system
inferredcites →https://doi.org/10.1093/gigascience/giaa153openalex-snapshot
Significantly improving the quality of genome assemblies through curation
inferredcites →https://doi.org/10.1093/molbev/msx319openalex-snapshot
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
inferredcites →https://doi.org/10.1093/nar/gkaa967openalex-snapshot
The international nucleotide sequence database collaboration
inferredcites →https://doi.org/10.1093/nar/gkr1006openalex-snapshot
The International Nucleotide Sequence Database Collaboration
inferredcites →https://doi.org/10.1093/nar/gkt1114openalex-snapshot
RefSeq: an update on mammalian reference sequences
inferredcites →https://doi.org/10.1093/nar/gky730openalex-snapshot
Assessing genome assembly quality using the LTR Assembly Index (LAI)
inferredcites →https://doi.org/10.1111/ahg.12364openalex-snapshot
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads
inferredcites →https://doi.org/10.1126/science.282.5396.2012openalex-snapshot
Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
inferredcites →https://doi.org/10.1126/science.287.5461.2185openalex-snapshot
The Genome Sequence of Drosophila melanogaster
inferredcites →https://doi.org/10.1126/science.355.6328.894openalex-snapshot
Sequencing all life captivates biologists
inferredcites →https://doi.org/10.3390/genes10010062openalex-snapshot
A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4513120openalex-extracted
Spatiotemporal Transcriptomic Atlas of Rhizome Formation in Oryza Longistaminata
inferred← citeshttps://doi.org/10.1002/edn3.432openalex-snapshot
Toward a national eDNA strategy for the United States
inferred← citeshttps://doi.org/10.1007/s40415-024-01064-1openalex-snapshot
Revisiting the cytogenetics of Vellozia Vand.: immunolocalization of KNL1 elucidates the chromosome number for the genus
inferred← citeshttps://doi.org/10.1016/b978-0-12-824112-7.00005-4openalex-snapshot
Possible solutions for the conservation of benthic habitats and organisms
inferred← citeshttps://doi.org/10.1016/j.cois.2022.100902openalex-snapshot
Exploring new genomic territories with emerging model insects
inferred← citeshttps://doi.org/10.1016/j.dci.2024.105207openalex-snapshot
Characterisation of defensins across the marsupial family tree
inferred← citeshttps://doi.org/10.1016/j.tree.2025.10.007openalex-snapshot
Project Psyche: reference genomes for all Lepidoptera in Europe
inferred← citeshttps://doi.org/10.1016/j.xgen.2024.100678openalex-snapshot
Leveraging genomes to support conservation and bioeconomy policies in a megadiverse country
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.5c01442openalex-snapshot
Whole Genome Assembly and Full-Length Transcriptome Sequencing of the Uncaria rhynchophylla Provides Insights into Genetic Control of Bioactive Alkaloid Biosynthesis
inferred← citeshttps://doi.org/10.1038/s41467-025-56329-4openalex-snapshot
Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors
inferred← citeshttps://doi.org/10.1038/s41477-023-01489-8openalex-snapshot
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
inferred← citeshttps://doi.org/10.1038/s41576-024-00691-4openalex-snapshot
Plant pangenomes for crop improvement, biodiversity and evolution
inferred← citeshttps://doi.org/10.1038/s41576-024-00718-wopenalex-snapshot
Genome assembly in the telomere-to-telomere era
inferred← citeshttps://doi.org/10.1038/s41576-025-00828-zopenalex-snapshot
Transcriptomics in the era of long-read sequencing
inferred← citeshttps://doi.org/10.1038/s41586-024-08187-1openalex-snapshot
Structural variation in the pangenome of wild and domesticated barley
inferred← citeshttps://doi.org/10.1038/s41586-025-09270-xopenalex-snapshot
A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
inferred← citeshttps://doi.org/10.1038/s41587-024-02147-wopenalex-snapshot
Quality assessment of gene repertoire annotations with OMArk
inferred← citeshttps://doi.org/10.1038/s41592-022-01512-4openalex-snapshot
A complete, telomere-to-telomere human genome sequence presents new opportunities for evolutionary genomics
inferred← citeshttps://doi.org/10.1038/s41597-023-02593-2openalex-snapshot
Chromosome-scale genomes of five Hongmu species in Leguminosae
inferred← citeshttps://doi.org/10.1038/s41597-024-03628-yopenalex-snapshot
Improved high quality sand fly assemblies enabled by ultra low input long read sequencing
inferred← citeshttps://doi.org/10.1038/s41597-025-04776-5openalex-snapshot
Chromosome-scale genomes of wild and cultivated Morinda officinalis
inferred← citeshttps://doi.org/10.1038/s41597-025-05306-zopenalex-snapshot
Annotation of protein-coding genes in 49 diatom genomes from the Bacillariophyta clade
inferred← citeshttps://doi.org/10.1038/s44185-023-00013-7openalex-snapshot
Indigenous peoples and local communities as partners in the sequencing of global eukaryotic biodiversity
inferred← citeshttps://doi.org/10.1038/s44185-024-00054-6openalex-snapshot
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics
inferred← citeshttps://doi.org/10.1073/pnas.2115643118openalex-snapshot
Threatened Species Initiative: Empowering conservation action using genomic resources
inferred← citeshttps://doi.org/10.1073/pnas.2519345123openalex-snapshot
Nine changes needed to deliver a radical transformation in biodiversity measurement
inferred← citeshttps://doi.org/10.1080/00218839.2025.2455852openalex-snapshot
Standard methods and good practices in Apis honey bee omics research
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf238openalex-snapshot
FastGA: fast genome alignment
inferred← citeshttps://doi.org/10.1093/bioadv/vbaf326openalex-snapshot
Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae685openalex-snapshot
Tiberius: end-to-end deep learning with an HMM for gene prediction
inferred← citeshttps://doi.org/10.1093/g3journal/jkad040openalex-snapshot
Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella , a global pest of cotton
inferred← citeshttps://doi.org/10.1093/g3journal/jkad119openalex-snapshot
Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator
inferred← citeshttps://doi.org/10.1093/g3journal/jkad203openalex-snapshot
Genome-wide methylation patterns from canine nanopore assemblies
inferred← citeshttps://doi.org/10.1093/g3journal/jkae160openalex-snapshot
Chromosome-scale genome assembly of the hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest
inferred← citeshttps://doi.org/10.1093/g3journal/jkaf286openalex-snapshot
A trio-binning approach for genome assembly reveals extensive structural variation between two Cannabis cultivars: Punto Rojo and Cherry Pie
inferred← citeshttps://doi.org/10.1093/g3journal/jkag105openalex-snapshot
Chromosome-level genome assembly of the Erythrina gall wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae)
inferred← citeshttps://doi.org/10.1093/gbe/evac131openalex-snapshot
A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein
inferred← citeshttps://doi.org/10.1093/gbe/evag179openalex-snapshot
A T2T Genome of the Lobed-Lip Iguazu Joana ( Crenicichla tuca ) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes
inferred← citeshttps://doi.org/10.1093/genetics/iyag172openalex-snapshot
Toward standardization in arthropod and biodiversity genome projects
inferred← citeshttps://doi.org/10.1093/gigascience/giaf079openalex-snapshot
A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes
inferred← citeshttps://doi.org/10.1093/gigascience/giaf085openalex-snapshot
A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps
inferred← citeshttps://doi.org/10.1093/gigascience/giaf097openalex-snapshot
First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata)
inferred← citeshttps://doi.org/10.1093/gigascience/giag036openalex-snapshot
MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes
inferred← citeshttps://doi.org/10.1093/hr/uhad183openalex-snapshot
A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis inChaenomeles speciosa
inferred← citeshttps://doi.org/10.1093/jhered/esae042openalex-snapshot
A chromosome-level genome assembly of the common eider, Somateria mollissima (Linnaeus, 1758)
inferred← citeshttps://doi.org/10.1093/jxb/erae085openalex-snapshot
Hi-C techniques: from genome assemblies to transcription regulation
inferred← citeshttps://doi.org/10.1093/nargab/lqae075openalex-snapshot
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics
inferred← citeshttps://doi.org/10.1101/2022.06.14.496215openalex-snapshot
AuCoMe: inferring and comparing metabolisms across heterogeneous sets of annotated genomes
inferred← citeshttps://doi.org/10.1101/2022.09.13.507768openalex-snapshot
Genomic erosion in the assessment of species’ extinction risk and recovery potential
inferred← citeshttps://doi.org/10.1101/2022.11.25.517970openalex-snapshot
Multifaceted quality assessment of gene repertoire annotation with OMArk
inferred← citeshttps://doi.org/10.1101/2022.12.30.521993openalex-snapshot
A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
inferred← citeshttps://doi.org/10.1101/2023.09.25.559365openalex-snapshot
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics
inferred← citeshttps://doi.org/10.1101/2024.02.14.580266openalex-snapshot
Adaptive diversification through structural variation in barley
inferred← citeshttps://doi.org/10.1101/2024.05.29.594498openalex-snapshot
First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri
inferred← citeshttps://doi.org/10.1101/2024.09.10.612026openalex-snapshot
Revisiting the cytogenetics of Vellozia Vand.: immunolocalization of KLN1 elucidates the chromosome number for the genus
inferred← citeshttps://doi.org/10.1101/gr.277118.122openalex-snapshot
Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
inferred← citeshttps://doi.org/10.1101/gr.279865.124openalex-snapshot
Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
inferred← citeshttps://doi.org/10.1111/1744-7917.70085openalex-snapshot
New tsetse ( Glossina fuscipes fuscipes ) genomes generated from wild and laboratory‐reared specimens
inferred← citeshttps://doi.org/10.1111/1755-0998.13893openalex-snapshot
Genomics and conservation: Guidance from training to analyses and applications
inferred← citeshttps://doi.org/10.1111/1755-0998.14025openalex-snapshot
Comparative analysis of amphibian genomes: An emerging resource for basic and applied research
inferred← citeshttps://doi.org/10.1111/acv.12971openalex-snapshot
The future is here: an easy‐to‐use toolkit for integrating genetics into conservation management
inferred← citeshttps://doi.org/10.1111/mec.70001openalex-snapshot
Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation
inferred← citeshttps://doi.org/10.1111/mec.70085openalex-snapshot
Whole Genome Sequencing Reveals How Plasticity and Genetic Differentiation Underlie Sympatric Morphs of Arctic Charr
inferred← citeshttps://doi.org/10.1111/pbi.14294openalex-snapshot
Spatiotemporal transcriptomic atlas of rhizome formation in Oryza longistaminata
inferred← citeshttps://doi.org/10.1111/raq.70073openalex-snapshot
Single‐Cell Sequencing: A Sharp Sword for Deciphering Biological Innovations and Evolutionary Adaptations in Lower Vertebrates and Invertebrates
inferred← citeshttps://doi.org/10.1111/tpj.70390openalex-snapshot
Assembling genomes of non‐model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)
inferred← citeshttps://doi.org/10.1128/mbio.01770-25openalex-snapshot
Rethinking large-scale phylogenomics with EukPhylo v.1.0, a flexible toolkit to enable phylogeny-informed data curation and analyses of diverse eukaryotic lineages
inferred← citeshttps://doi.org/10.1186/s12859-023-05449-zopenalex-snapshot
Galba: genome annotation with miniprot and AUGUSTUS
inferred← citeshttps://doi.org/10.1186/s12862-025-02443-2openalex-snapshot
Genomic insights into the population structure and adaptive variation of Mullus barbatus in the Mediterranean Sea
inferred← citeshttps://doi.org/10.1186/s12864-025-11247-zopenalex-snapshot
Advancing genetic improvement in the omics era: status and priorities for United States aquaculture
inferred← citeshttps://doi.org/10.1186/s12983-025-00561-7openalex-snapshot
Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide
inferred← citeshttps://doi.org/10.1186/s13059-026-04128-5openalex-snapshot
MGA: a tool for haplotype-mixed assembly of long and accurate reads
inferred← citeshttps://doi.org/10.12688/f1000research.161461.1openalex-snapshot
The genome sequence of Tethysbaena scabra (Pretus, 1991), the first known in the peracarid crustacean order Thermosbaenacea.
inferred← citeshttps://doi.org/10.12688/f1000research.161461.2openalex-snapshot
The genome sequence of Tethysbaena scabra (Pretus, 1991), the first known in the peracarid crustacean order Thermosbaenacea.
inferred← citeshttps://doi.org/10.12688/f1000research.161461.3openalex-snapshot
The genome sequence of Tethysbaena scabra (Pretus, 1991), the first known in the peracarid crustacean order Thermosbaenacea.
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.18658.1openalex-snapshot
Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.21143.1openalex-snapshot
A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project
inferred← citeshttps://doi.org/10.12688/wellcomeopenres.22949.1openalex-snapshot
Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases
inferred← citeshttps://doi.org/10.2144/btn-2022-0021openalex-snapshot
The Earth BioGenome Project: A Success Story for Whole-Genome Sequencing?
inferred← citeshttps://doi.org/10.24072/pcjournal.393openalex-snapshot
High quality genome assembly of the brown hare (Lepus europaeus) with chromosome-level scaffolding
inferred← citeshttps://doi.org/10.24072/pcjournal.514openalex-snapshot
Chromosome-level reference genome assembly for the mountain hare (Lepus timidus)
inferred← citeshttps://doi.org/10.3389/fbinf.2024.1462923openalex-snapshot
Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads
inferred← citeshttps://doi.org/10.3389/fevo.2022.943361openalex-snapshot
Predictors of sequence capture in a large-scale anchored phylogenomics project
inferred← citeshttps://doi.org/10.3389/fevo.2022.966605openalex-snapshot
Cross-sectional use of barcode of life data system and GenBank as DNA barcoding databases for the advancement of museomics
inferred← citeshttps://doi.org/10.3389/fpls.2023.1271305openalex-snapshot
Editorial: Bioinformatics, big data and agriculture: a challenge for the future
inferred← citeshttps://doi.org/10.3389/fpls.2025.1684559openalex-snapshot
Sensing a rainbow of colors: algal photoreceptors
inferred← citeshttps://doi.org/10.3389/fsci.2025.1514835openalex-snapshot
The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life
inferred← citeshttps://doi.org/10.3389/fvets.2023.1217135openalex-snapshot
Influence of genomic variations on glanders serodiagnostic antigens using integrative genomic and transcriptomic approaches
inferred← citeshttps://doi.org/10.3390/ijms23115869openalex-snapshot
Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani
inferred← citeshttps://doi.org/10.3390/ijpb16030109openalex-snapshot
Biotechnological and Genomic Applications in the Conservation of Native Blueberries in Natural Habitats
inferred← citeshttps://doi.org/10.3897/arphapreprints.e103105openalex-snapshot
Biodiversity biobanks: a landscape analysis
inferred← citeshttps://doi.org/10.4274/nkmj.galenos.2024.36002openalex-snapshot
Relationship Between Endometriosis, Borderline Adnexal Tumors and Malignant Tumors: A Retrospective Case Study
inferred← citeshttps://doi.org/10.48550/arxiv.2308.07877openalex-snapshot
Genome assembly in the telomere-to-telomere era
inferred← citeshttps://doi.org/10.6084/m9.figshare.24070220openalex-snapshot
Additional file 1 of Galba: genome annotation with miniprot and AUGUSTUS
inferred← citeshttps://doi.org/10.64898/2026.06.16.732382openalex-snapshot
SPA-C: an hybrid tool to accurately scaffold genomes using Hi-C and Deep-Learning
inferred← citeshttps://doi.org/10.64898/2026.07.31.742074openalex-snapshot
A chromosome-level genome of the franciscana dolphin, Pontoporia blainvillei
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