It's more than stamp collecting: how genome sequencing can unify biological research

Richards, Stephen

doi:10.1016/j.tig.2015.04.007

Cited by 42 publications

(31 citation statements)

References 101 publications

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“…A conceptual argument for sequencing eukaryotic life was made by Stephen Richards in 2015 (11). Richards (11) argued that current technology would permit sequencing a vast number of species and that a phylogenetic approach to stratifying samples for sequencing would accelerate scientific discovery.…”

Section: Sequencing All Eukaryotic Life: Why Nowmentioning

confidence: 99%

Earth BioGenome Project: Sequencing life for the future of life

Lewin

Robinson

Kress

et al. 2018

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

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Increasing our understanding of Earth's biodiversity and responsibly stewarding its resources are among the most crucial scientific and social challenges of the new millennium. These challenges require fundamental new knowledge of the organization, evolution, functions, and interactions among millions of the planet's organisms. Herein, we present a perspective on the Earth BioGenome Project (EBP), a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth's eukaryotic biodiversity over a period of 10 years. The outcomes of the EBP will inform a broad range of major issues facing humanity, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. We describe hurdles that the project faces, including data-sharing policies that ensure a permanent, freely available resource for future scientific discovery while respecting access and benefit sharing guidelines of the Nagoya Protocol. We also describe scientific and organizational challenges in executing such an ambitious project, and the structure proposed to achieve the project's goals. The far-reaching potential benefits of creating an open digital repository of genomic information for life on Earth can be realized only by a coordinated international effort.

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Section: Sequencing All Eukaryotic Life: Why Nowmentioning

confidence: 99%

Earth BioGenome Project: Sequencing life for the future of life

Lewin

Robinson

Kress

et al. 2018

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

Self Cite

768

593

View full text Add to dashboard Cite

show abstract

“…Although single genes can influence behavior (Fischman et al , 2011), social behavior is often multifaceted and can reflect a complex genetic architecture (Walling et al , 2008; Mikheyev and Linksvayer, 2015) including influences from epigenetic mechanisms (Cardoso et al , 2015). Genomes in particular are useful resources for evolutionary questions of social behavior because they grant access to both broad scale and fine scale details and mechanisms (Richards, 2015). For social behavior, while there are multiple Hymenopteran genomes available to investigate fine scale detail, we lack sufficiently distantly related species to address broader patterns.…”

Section: Introductionmentioning

confidence: 99%

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

Cunningham

Wiberg

et al. 2015

Preprint

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22Testing for conserved and novel mechanisms underlying phenotypic evolution requires a diversity of 23 genomes available for comparison spanning multiple independent lineages. For example, complex social 24 behavior in insects has been investigated primarily with eusocial lineages, nearly all of which are 25 Hymenoptera. If conserved genomic influences on sociality do exist, we need data from a wider range of taxa 26 that also vary in their levels of sociality. Here we present information on the genome of the subsocial beetle 27 Nicrophorus vespilloides, a species long used to investigate evolutionary questions of complex social 28 behavior. We used this genome to address two questions. First, does life history predict overlap in gene 29 models more strongly than phylogenetic groupings? Second, like other insects with highly developed social 30 behavior but unlike other beetles, does N. vespilloides have DNA methylation? We found the overlap in gene 31 models was similar between N. vespilloides and all other insect groups regardless of life history. Unlike 32 previous studies of beetles, we found strong evidence of DNA methylation, which allows this species to be 33 used to address questions about the potential role of methylation in social behavior. The addition of this 34 genome adds a coleopteran resource to answer questions about the evolution and mechanistic basis of 35 sociality. 36 37 Introduction 38Understanding phenotypic evolution necessitates investigating both the ultimate and proximate influences on 39 traits; however, these investigations require the appropriate tools. Social behavior is a particularly thorny 40 phenotype to study because of its complexity, variation, and its multi-level integration across an organism 41 (Boake et al., 2002). In addition, social behavior also often displays unusual evolutionary dynamics arising 42 from the genetic influences on interactions required for sociality (McGlothlin et al., 2010). Although single 43 genes can influence behavior (Fischman et al., 2011), social behavior is often multifaceted and can reflect a 44 complex genetic architecture (Walling et al., 2008; Mikheyev and Linksvayer, 2015) including influences 45 from epigenetic mechanisms (Cardoso et al., 2015). Genomes in particular are useful resources for 46 evolutionary questions of social behavior because they grant access to both broad scale and fine scale details 47 and mechanisms (Richards, 2015). For social behavior, while there are multiple Hymenopteran genomes 48 available to investigate fine scale detail, we lack sufficiently distantly related species to address broader 49 patterns. It is therefore important to develop genomic resources for organisms that are particularly 50 phenotypic models of social behavior but where genomic information is lacking. 51The genomes of several social insect are now available, including eusocial species such as honey 52 bees (Elsik et al., 2014), stingless bees (Kapheim et al., 2015), several ant species (Gadau et al., 2012), a 53 termite (Terrapon et al., 2...

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“…Understanding which elements are associated with "climate change tolerant" coral species will present opportunities for management strategies aiming to preserve the resilience of coral reef regions. Generation of holobiont genome reference data is not an end (Richards, 2015), but rather the foundational necessity for research targeting resilience and adaptability of coral holobionts. As such, it substantiates, rather than replaces, other efforts of coral reef research.…”

Section: Case Study: Genomic Approaches To Assess Adaptability Of Cormentioning

confidence: 99%

The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change

et al. 2015

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It's more than stamp collecting: how genome sequencing can unify biological research

Cited by 42 publications

References 101 publications

Earth BioGenome Project: Sequencing life for the future of life

Earth BioGenome Project: Sequencing life for the future of life

TheNicrophorus vespilloidesgenome and methylome, a beetle with complex social behavior

The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change

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