The Earth BioGenome Project 2020: Starting the clock

Lewin, Harris A.; Richards, Stephen; Aiden, E; Allende, Miguel L.; Archibald, John M.; Bálint, Miklós; Barker, Katharine; Baumgartner, Bridget L.; Belov, Katherine; Bertorelle, Giorgio; Blaxter, Mark; Cai, Jing; Caperello, Nicolette; Carlson, Keith; Castilla‐Rubio, Juan Carlos; Chaw, Shu‐Miaw; Chen, Lei; Childers, Anna K.; Coddington, Jonathan A.; Conde, Dalia Amor; Corominas, Montserrat; Crandall, Keith A.; Crawford, Andrew J.; Di-Palma, Federica; Durbin, Richard; Ebenezer, ThankGod Echezona; Edwards, Scott V.; Fédrigo, Olivier; Flicek, Paul; Formenti, Giulio; Gibbs, Richard A.; Gilbert, M. Thomas P.; Goldstein, Melissa M.; Graves, Jennifer A. Marshall; Greely, Henry T.; Grigoriev, Igor V.; Hackett, Kevin J.; Hall, Neil; Haussler, David; Helgen, Kristofer M.; Hogg, Carolyn J.; Isobe, Sachiko; Jakobsen, Kjetill Sigurd; Janke, Axel; Jarvis, Erich D.; Johnson, Warren E.; Jones, Steven J.M.; Karlsson, Elinor K.; Kersey, Paul J.; Kim, Jin-Hyoung; Kress, W. John; Kuraku, Shigehiro; Lawniczak, Mara K. N.; Leebens‐Mack, James H.; Li, Xueyan; Lindblad‐Toh, Kerstin; Liu, Xin; Lopez, Jose V.; Marquès‐Bonet, Tomàs; Mazard, Sophie; Mazet, Jonna A. K.; Mazzoni, Camila J.; Myers, Eugene W.; O’Neill, Rachel J.; Paez, Sadye; Park, Hyun; Robinson, Gene E.; Roquet, Cristina; Ryder, Oliver A.; Sabir, Jamal S. M.; Shaffer, H. Bradley; Shank, Timothy M.; Sherkow, Jacob S.; Soltis, Pamela S.; Tang, Boping; Tedersoo, Leho; Uliano-Silva, Marcela; Wang, Kun; Wei, Xiaofeng; Wetzer, Regina; Wilson, Julia L.; Xu, Xun; Yang, Huanming; Yoder, Anne D.; Zhang, Guojie

doi:10.1073/pnas.2115635118

Cited by 206 publications

(129 citation statements)

References 28 publications

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“…As technology expands and genome sequence representation increases across the Tree of Life, we envision a future in which the concept of DNA barcodes extends to a much larger interpretation of genome space. DNA barcoding continues to evolve with methodological and technological advances in conjunction with the increasing accessibility to high-throughput sequencing and the growing database of whole genome sequences fostered through international consortia, such as the Earth BioGenome Project [37,38]. A diversity of genetic tools is especially needed in clades, such as green plants, with highly complex genomes that require significant resources to assemble [205].…”

Section: Discussionmentioning

confidence: 99%

“…One of these, the Global Genome Biodiversity Network (GGBN, https://www.ggbn.org/ggbn_portal/, accessed on 26 January 2022 [36]) represents a network of well-curated tissue collections that seeks to develop standards, share collection information, and facilitate biodiversity genomics research. More recently, the Earth BioGenome Project (EBP; https: //www.earthbiogenome.org/, accessed on 26 January 2022) was launched [37] as a "moonshot" [38] for biology that aims to sequence whole genomes of all eukaryotic species on Earth in ten years. Although not specifically aimed at DNA barcode loci, EBP will indirectly provide a wealth of sequence data for the major DNA barcode loci of plants, animals, and fungi.…”

Section: National and International Sequencing Consortiamentioning

confidence: 99%

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The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Gostel

Kress

2022

Diversity

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DNA barcoding has transformed the fields of ecology, evolution, and conservation by providing a rapid and effective tool for species identification. The growth of DNA barcodes as a resource for biologists has followed advances in computational and sequencing technology that have enabled high-throughput barcoding applications. The global DNA barcode database is expanding to represent the diversity of species on Earth thanks to efforts by international consortia and expanding biological collections. Today, DNA barcoding is instrumental in advancing our understanding of how species evolve, how they interact, and how we can slow down their extirpation and extinction. This review focuses on current applications of DNA barcode sequences to address fundamental lines of research, as well as new and expanding applications of which DNA barcoding will play a central role.

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Section: Discussionmentioning

confidence: 99%

Section: National and International Sequencing Consortiamentioning

confidence: 99%

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

Gostel

Kress

2022

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“…PacBio CCS sequencing leverages PacBio’s continuous long read technology to create a consensus sequence by sequencing a read repeatedly to produce a read pool with higher consensus accuracy than traditional long read technology and lengths that far exceed Illumina reads [ 1 ]. This technology has been used to sequence and assemble the breadth of eukaryotes, and is the preferred method used by various sequencing initiatives such as the Earth BioGenome Project [ 2 , 3 ], the Vertebrate Genome Project [ 4 ], the i5K Initiative [ 5 ], the Ag100Pest Initiative [ 6 ], among others to generate data supporting highly contiguous and highly accurate contig assemblies that meet the criteria for reference-quality assemblies [ 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

et al. 2022

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Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

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“…The Earth BioGenome Project (EBP) aims to sequence and characterize reference genomes for each known eukaryotic species ( 1 , 2 ). The project initiated from early discussions including a working group in 2017 ( 3 ), and formally launched at the Wellcome foundation EBP/Vertebrate Genomes Project (VGP) workshop in London on November first, 2018.…”

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confidence: 99%

“…The project initiated from early discussions including a working group in 2017 ( 3 ), and formally launched at the Wellcome foundation EBP/Vertebrate Genomes Project (VGP) workshop in London on November first, 2018. This ambitious vision builds on previous successes, starting with sequencing the human genome ( 4 ) and those of associated model organisms ( 5 – 9 ), through projects completing tens and more recently hundreds of genome sequences ( 1 ). A major positive outcome of these efforts—especially those of the VGP—has been a renewed focus on producing high-quality reference genomes, suitable for use as long-term resources faithfully representing the DNA sequence of each species in chromosomal scaffolds with few gaps.…”

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confidence: 99%

Standards recommendations for the Earth BioGenome Project

Lawniczak

Durbin

Flicek

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

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The Earth BioGenome Project 2020: Starting the clock

Cited by 206 publications

References 28 publications

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Standards recommendations for the Earth BioGenome Project

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