How genomics can help biodiversity conservation

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

doi:10.1016/j.tig.2023.01.005

How genomics can help biodiversity conservation

Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, José A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Simona Secomandi, Hannes SvardalConstantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklós Bálint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Höglund^* (Corresponding Author), The European Reference Genome Atlas Consortium

^*Corresponding author for this work

Aberdeen Centre For Environmental Sustainability

Research output: Contribution to journal › Article › peer-review

Abstract

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Original language	English
Number of pages	15
Journal	Trends in Genetics
Early online date	16 Feb 2023
DOIs	https://doi.org/10.1016/j.tig.2023.01.005
Publication status	E-pub ahead of print - 16 Feb 2023

Keywords

Anthropocene
biodiversity genomics
genomic toolbox
reference genomes
conservation applications
European Reference Genome Atlas (ERGA)

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Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., Jentoft, S., Malukiewicz, J., Mouton, A., Oomen, R. A., Paez, S., Palsbøll, P. J., Pampoulie, C., Ruiz-López, M. J., Secomandi, S., ... The European Reference Genome Atlas Consortium (2023). How genomics can help biodiversity conservation. Trends in Genetics. https://doi.org/10.1016/j.tig.2023.01.005

Theissinger, K, Fernandes, C, Formenti, G, Bista, I, Berg, PR, Bleidorn, C, Bombarely, A, Crottini, A, Gallo, GR, Godoy, JA, Jentoft, S, Malukiewicz, J, Mouton, A, Oomen, RA, Paez, S, Palsbøll, PJ, Pampoulie, C, Ruiz-López, MJ, Secomandi, S, Svardal, H, Theofanopoulou, C, de Vries, J, Waldvogel, A-M, Zhang, G, Jarvis, ED, Bálint, M, Ciofi, C, Waterhouse, RM, Mazzoni, CJ, Höglund, J & The European Reference Genome Atlas Consortium 2023, 'How genomics can help biodiversity conservation', Trends in Genetics. https://doi.org/10.1016/j.tig.2023.01.005

@article{f469442cec724d45926d60b34e756433,

title = "How genomics can help biodiversity conservation",

abstract = "The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.",

keywords = "Anthropocene, biodiversity genomics, genomic toolbox, reference genomes, conservation applications, European Reference Genome Atlas (ERGA)",

author = "Kathrin Theissinger and Carlos Fernandes and Giulio Formenti and Iliana Bista and Berg, {Paul R.} and Christoph Bleidorn and Aureliano Bombarely and Angelica Crottini and Gallo, {Guido R.} and Godoy, {Jos{\'e} A.} and Sissel Jentoft and Joanna Malukiewicz and Alice Mouton and Oomen, {Rebekah A.} and Sadye Paez and Palsb{\o}ll, {Per J.} and Christophe Pampoulie and Ruiz-L{\'o}pez, {Mar{\'i}a J.} and Simona Secomandi and Hannes Svardal and Constantina Theofanopoulou and {de Vries}, Jan and Ann-Marie Waldvogel and Guojie Zhang and Jarvis, {Erich D.} and Mikl{\'o}s B{\'a}lint and Claudio Ciofi and Waterhouse, {Robert M.} and Mazzoni, {Camila J.} and Jacob H{\"o}glund and {The European Reference Genome Atlas Consortium} and Kara Layton",

note = "Acknowledgments We thank Cecilia Helmerson, Antonio Rivas, Nelson Lauzon, and Sally Leys, for the pictures of the Atlantic cod, the Iberian lynx, the European beech, and the freshwater sponge, respectively. We also thank Fabien Condamine, Love Dal{\'e}n, Richard Durbin, Bruno Fosso, Roderic Guig{\'o}, Marc Hanikenne, Alberto Pallavicini, Olga Vinnere Pettersson, Xavier Turon, and Detlef Weigel for their contributions to the manuscript, as well as the whole ERGA community for making this possible.",

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doi = "10.1016/j.tig.2023.01.005",

language = "English",

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T1 - How genomics can help biodiversity conservation

AU - Theissinger, Kathrin

AU - Fernandes, Carlos

AU - Formenti, Giulio

AU - Bista, Iliana

AU - Berg, Paul R.

AU - Bleidorn, Christoph

AU - Bombarely, Aureliano

AU - Crottini, Angelica

AU - Gallo, Guido R.

AU - Godoy, José A.

AU - Jentoft, Sissel

AU - Malukiewicz, Joanna

AU - Mouton, Alice

AU - Oomen, Rebekah A.

AU - Paez, Sadye

AU - Palsbøll, Per J.

AU - Pampoulie, Christophe

AU - Ruiz-López, María J.

AU - Secomandi, Simona

AU - Svardal, Hannes

AU - Theofanopoulou, Constantina

AU - de Vries, Jan

AU - Waldvogel, Ann-Marie

AU - Zhang, Guojie

AU - Jarvis, Erich D.

AU - Bálint, Miklós

AU - Ciofi, Claudio

AU - Waterhouse, Robert M.

AU - Mazzoni, Camila J.

AU - Höglund, Jacob

AU - The European Reference Genome Atlas Consortium

AU - Layton, Kara

N1 - Acknowledgments We thank Cecilia Helmerson, Antonio Rivas, Nelson Lauzon, and Sally Leys, for the pictures of the Atlantic cod, the Iberian lynx, the European beech, and the freshwater sponge, respectively. We also thank Fabien Condamine, Love Dalén, Richard Durbin, Bruno Fosso, Roderic Guigó, Marc Hanikenne, Alberto Pallavicini, Olga Vinnere Pettersson, Xavier Turon, and Detlef Weigel for their contributions to the manuscript, as well as the whole ERGA community for making this possible.

PY - 2023/2/16

Y1 - 2023/2/16

N2 - The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

AB - The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

KW - Anthropocene

KW - biodiversity genomics

KW - genomic toolbox

KW - reference genomes

KW - conservation applications

KW - European Reference Genome Atlas (ERGA)

U2 - 10.1016/j.tig.2023.01.005

DO - 10.1016/j.tig.2023.01.005

M3 - Article

JO - Trends in Genetics

JF - Trends in Genetics

SN - 0168-9525

ER -

How genomics can help biodiversity conservation

Abstract

Keywords

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