Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Daniel J Macqueen; Craig R Primmer; Ross D Houston; Barbara F Nowak; Louis Bernatchez; Steinar Bergseth; William S Davidson; Cristian Gallardo-Escarate; Tom Goldammer; Yann Guiguen; Patricia Iturra; James W Kijas; Ben F Koop; Sigbjorn  Lien; Alejandro Maass; Samuel A.M. Martin; Philip McGinnity; Martin Montecino; Kerry A Naish; Krista M Nichols; Kristinn Olafsson; Stig W Omholt; Yniv Palti; Graham S Plastow; Caird E Rexroa; Matthew L Rise; Rachael J Ritchie; Simen R Sandve; Patricia M Schulte; Alfredo Tello; Rodrigo Vidal; Jon Olav Vik; Anna Wargelius; Jose Manuel Yanez; The FAASG Consortium

doi:10.1186/s12864-017-3862-8

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Daniel J Macqueen, Craig R Primmer, Ross D Houston, Barbara F Nowak, Louis Bernatchez, Steinar Bergseth, William S Davidson, Cristian Gallardo-Escarate, Tom Goldammer, Yann Guiguen, Patricia Iturra, James W Kijas, Ben F Koop, Sigbjorn Lien, Alejandro Maass, Samuel A.M. Martin, Philip McGinnity, Martin Montecino, Kerry A Naish, Krista M NicholsKristinn Olafsson, Stig W Omholt, Yniv Palti, Graham S Plastow, Caird E Rexroa, Matthew L Rise, Rachael J Ritchie, Simen R Sandve, Patricia M Schulte, Alfredo Tello, Rodrigo Vidal, Jon Olav Vik, Anna Wargelius, Jose Manuel Yanez, The FAASG Consortium

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Abstract

We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

Original language	English
Article number	484
Journal	BMC Genomics
Volume	18
DOIs	https://doi.org/10.1186/s12864-017-3862-8
Publication status	Published - 27 Jun 2017

Bibliographical note

The first FAASG meeting (June 2016, https://www.faasg.org/publications/torontoworkshop-report) and the second meeting (January 2017, https://www.faasg.org/workshops/san-diego-workshop-january-2017) were organized and supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada)), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8.

Keywords

salmonid fish
genome biology
functional annotation
comparative biology
standardized data and metadata
data sharing
aquaculture
whole genome duplication
evolution
phenotyping

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Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture
© The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Final published version, 570 KBLicence: CC BY

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Macqueen, D. J., Primmer, C. R., Houston, R. D., Nowak, B. F., Bernatchez, L., Bergseth, S., Davidson, W. S., Gallardo-Escarate, C., Goldammer, T., Guiguen, Y., Iturra, P., Kijas, J. W., Koop, B. F., Lien, S., Maass, A., Martin, S. A. M., McGinnity, P., Montecino, M., Naish, K. A., ... The FAASG Consortium (2017). Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics, 18, Article 484. https://doi.org/10.1186/s12864-017-3862-8

Macqueen, DJ, Primmer, CR, Houston, RD, Nowak, BF, Bernatchez, L, Bergseth, S, Davidson, WS, Gallardo-Escarate, C, Goldammer, T, Guiguen, Y, Iturra, P, Kijas, JW, Koop, BF, Lien, S, Maass, A, Martin, SAM, McGinnity, P, Montecino, M, Naish, KA, Nichols, KM, Olafsson, K, Omholt, SW, Palti, Y, Plastow, GS, Rexroa, CE, Rise, ML, Ritchie, RJ, Sandve, SR, Schulte, PM, Tello, A, Vidal, R, Vik, JO, Wargelius, A, Yanez, JM & The FAASG Consortium 2017, 'Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture', BMC Genomics, vol. 18, 484. https://doi.org/10.1186/s12864-017-3862-8

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title = "Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture",

abstract = "We describe an emerging initiative - the {\textquoteleft}Functional Annotation of All Salmonid Genomes{\textquoteright} (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.",

keywords = "salmonid fish, genome biology, functional annotation, comparative biology, standardized data and metadata, data sharing, aquaculture, whole genome duplication, evolution, phenotyping",

author = "Macqueen, {Daniel J} and Primmer, {Craig R} and Houston, {Ross D} and Nowak, {Barbara F} and Louis Bernatchez and Steinar Bergseth and Davidson, {William S} and Cristian Gallardo-Escarate and Tom Goldammer and Yann Guiguen and Patricia Iturra and Kijas, {James W} and Koop, {Ben F} and Sigbjorn Lien and Alejandro Maass and Martin, {Samuel A.M.} and Philip McGinnity and Martin Montecino and Naish, {Kerry A} and Nichols, {Krista M} and Kristinn Olafsson and Omholt, {Stig W} and Yniv Palti and Plastow, {Graham S} and Rexroa, {Caird E} and Rise, {Matthew L} and Ritchie, {Rachael J} and Sandve, {Simen R} and Schulte, {Patricia M} and Alfredo Tello and Rodrigo Vidal and Vik, {Jon Olav} and Anna Wargelius and Yanez, {Jose Manuel} and {The FAASG Consortium}",

note = "The first FAASG meeting (June 2016, https://www.faasg.org/publications/torontoworkshop-report) and the second meeting (January 2017, https://www.faasg.org/workshops/san-diego-workshop-january-2017) were organized and supported by the International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG), funded by: The Research Council of Norway (RCN), The Norwegian Seafood Research Fund (FHF), Genome British Columbia (GBC, Canada)), The Chilean Economic Development Agency (CORFO) and the Innova Chile Committee (InnovaChile). FAASG has also received support from the Biotechnology and Biological Sciences Research Council (UK) (ref: BB/P02582X/1). Initial FAASG pilot studies (currently in process) are being funded by the ICSASG and the U.S. Department of Agriculture (USDA), through NIFA National Research Support Project 8.",

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doi = "10.1186/s12864-017-3862-8",

language = "English",

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journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

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T1 - Functional Annotation of All Salmonid Genomes (FAASG)

T2 - an international initiative supporting future salmonid research, conservation and aquaculture

AU - Macqueen, Daniel J

AU - Primmer, Craig R

AU - Houston, Ross D

AU - Nowak, Barbara F

AU - Bernatchez, Louis

AU - Bergseth, Steinar

AU - Davidson, William S

AU - Gallardo-Escarate, Cristian

AU - Goldammer, Tom

AU - Guiguen, Yann

AU - Iturra, Patricia

AU - Kijas, James W

AU - Koop, Ben F

AU - Lien, Sigbjorn

AU - Maass, Alejandro

AU - Martin, Samuel A.M.

AU - McGinnity, Philip

AU - Montecino, Martin

AU - Naish, Kerry A

AU - Nichols, Krista M

AU - Olafsson, Kristinn

AU - Omholt, Stig W

AU - Palti, Yniv

AU - Plastow, Graham S

AU - Rexroa, Caird E

AU - Rise, Matthew L

AU - Ritchie, Rachael J

AU - Sandve, Simen R

AU - Schulte, Patricia M

AU - Tello, Alfredo

AU - Vidal, Rodrigo

AU - Vik, Jon Olav

AU - Wargelius, Anna

AU - Yanez, Jose Manuel

AU - The FAASG Consortium

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PY - 2017/6/27

Y1 - 2017/6/27

N2 - We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

AB - We describe an emerging initiative - the ‘Functional Annotation of All Salmonid Genomes’ (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.

KW - salmonid fish

KW - genome biology

KW - functional annotation

KW - comparative biology

KW - standardized data and metadata

KW - data sharing

KW - aquaculture

KW - whole genome duplication

KW - evolution

KW - phenotyping

U2 - 10.1186/s12864-017-3862-8

DO - 10.1186/s12864-017-3862-8

M3 - Editorial

C2 - 28655320

SN - 1471-2164

VL - 18

JO - BMC Genomics

JF - BMC Genomics

M1 - 484

ER -

Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture

Abstract

Bibliographical note

Keywords

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