How genomics can help biodiversity conservation

Theissinger, Kathrin; Fernandes, Carina; Formenti, Giulio; Bista, Iliana; Berg, Paul R.; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido Roberto; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A.; Paez, Sadye; Palsbøll, Per; Pampoulie, Christophe; Ruiz‐López, María José; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; Vries, Jan de; Waldvogel, Ann‐Marie; Jarvis, Erich D.; Bálint, Miklós; Ciofi, Claudio; Waterhouse, Robert M.; Mazzoni, Camila J.; Höglund, Jacob

doi:10.1016/j.tig.2023.01.005

Cited by 73 publications

(49 citation statements)

References 148 publications

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“…Numerous studies have established the importance of genomic data to understand the evolutionary history of a species and to develop appropriate conservation and management strategies (Kenny et al, 2020; Kleinman-Ruiz et al, 2017; Nong et al, 2021; Pfenninger et al, 2021; Saremi et al, 2019). Whole-genome sequencing (WGS) leads to a better understanding of the biology of a species and provides insights into fundamental processes that shape their evolution (Ryder, 2005), and its application can provide important and accurate information about its demographic history, admixture, introgression, recombination, linkage disequilibrium, genomic regions evolving under selective pressures and other evolutionary processes (Theissinger et al, 2023). For critically endangered species like the brown-headed spider monkey, genomic approaches are even more valuable due to the scarcity of samples for genetic studies; therefore, WGS maximizes the information that researchers can harness from each sample.…”

Section: Resultsmentioning

confidence: 99%

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

Pozo,

Quintana,

Larreátegui

et al. 2023

Preprint

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The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference genome which until now was unavailable forA. f. fusciceps. The present study reports the first whole genome sequence and assembly ofA. f. fuscicepsgenerated using Oxford Nanopore long reads. DNA was extracted from a subadult male and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable to other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.

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Section: Resultsmentioning

confidence: 99%

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

Pozo,

Quintana,

Larreátegui

et al. 2023

Preprint

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“…As genomic sequencing has become increasingly cost effective and the platforms and computational algorithms become more technically efficient, many biodiversity genomics tools have become available to expedite the investigation of both known and unknown species e.g., DNA barcoding, genome skimming, reduced representation sequencing, transcriptome sequencing, and whole genome sequencing for reference genome production 10 . Reference genomes ( see glossary) are one such tool that offer an unparalleled, scalable, and increasingly cost-effective high resolution insight into species, and their accessibility has made the construction of a planetary-wide genomic database of all eukaryotic life a more realistic endeavor 11 .…”

Section: Reference Genomes As a Key Biodiversity Genomics Toolmentioning

confidence: 99%

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

Mc Cartney,

Formenti,

Mouton

et al. 2023

Preprint

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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.

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“…the Vertebrate Genomes Project (Rhie et al, 2021), the Earth BioGenome Project (Lawniczak et al, 2022) As genome assembly is both a time-consuming and computationally intensive endeavour, an often-used alternative strategy involves aligning sequence reads to a previously assembled genome of the same, or closely related, species. This approach, commonly called 'read mapping', is much faster than de novo assembly, but has the drawback that structural variation between the sequenced sample and the reference genome (being mapped to) will be difficult to discern (Theissinger et al, 2023). Yet, for many biological questions, read mapping offers a quick and sufficient alternative to de novo assembly.…”

Section: Recent Advances In Genome Sequencing and Assemblymentioning

confidence: 99%

Genomics and conservation: Guidance from training to analyses and applications

Schiebelhut,

Guillaume,

Kuhn

et al. 2023

Molecular Ecology Resources

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Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

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How genomics can help biodiversity conservation

Cited by 73 publications

References 148 publications

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

Genome Report: First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

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

Genomics and conservation: Guidance from training to analyses and applications

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