Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Salojärvi, Jarkko; Smolander, Olli-Pekka; Nieminen, Kaisa; Rajaraman, Sitaram; Safronov, Omid; Safdari, Pezhman; Lamminmäki, Airi; Immanen, Juha; Lan, Tianying; Tanskanen, Jaakko; Rastas, Pasi; Amiryousefi, Ali; Jayaprakash, Balamuralikrishna; Kammonen, Juhana I.; Hagqvist, Risto; Eswaran, Gugan; Ahonen, Viivi Helena; Serra, Juan Alonso; Asiegbu, Fred O.; Barajas-Lopez, Juan de Dios; Blande, Daniel; Blokhina, Olga; Blomster, Tiina; Broholm, Suvi; Brosche, Mikael; Cui, Fuqiang; Dardick, Chris; Ehonen, Sanna E.; Elomaa, Paula; Escamez, Sacha; Fagerstedt, Kurt V.; Fujii, Hiroaki; Gauthier, Adrien; Gollan, Peter J.; Halimaa, Pauliina; Heino, Pekka I.; Himanen, Kristiina; Hollender, Courtney; Kangasjärvi, Saijaliisa; Kauppinen, Leila; Kelleher, Colin T.; Kontunen-Soppela, Sari; Koskinen, J. Patrik; Kovalchuk, Andriy; Kärenlampi, Sirpa O.; Kärkönen, Anna K.; Lim, Kean-Jin; Leppälä, Johanna; Macpherson, Lee; Mikola, Juha; Mouhu, Katriina; Mähönen, Ari Pekka; Niinemets, Ülo; Oksanen, Elina; Overmyer, Kirk; Palva, E. Tapio; Pazouki, Leila; Pennanen, Ville; Puhakainen, Tuula; Poczai, Peter; Possen, Boy J. H. M.; Punkkinen, Matleena; Rahikainen, Moona M.; Rousi, Matti; Ruonala, Raili; van der Schoot, Christiaan; Shapiguzov, Alexey; Sierla, Maija; Sipilä, Timo P.; Sutela, Suvi; Teeri, Teemu H.; Tervahauta, Arja I.; Vaattovaara, Aleksia; Vahala, Jorma; Vetchinnikova, Lidia; Welling, Annikki; Wrzaczek, Michael; Xu, Enjun; Paulin, Lars G.; Schulman, Alan H.; Lascoux, Martin; Albert, Victor A.; Auvinen, Petri; Helariutta, Ykä; Kangasjärvi, Jaakko

JultikaUniversity of Oulu repository

	Salojärvi, J., et al. (2017) Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics, 49 (6), 904-912. doi:10.1038/ng.3862 Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch Saved in:
Author:	Salojärvi, Jarkko^1,2; Smolander, Olli-Pekka³; Nieminen, Kaisa⁴; Rajaraman, Sitaram^1,2; Safronov, Omid^1,2; Safdari, Pezhman^1,2; Lamminmäki, Airi^1,2; Immanen, Juha^1,2,3; Lan, Tianying⁵; Tanskanen, Jaakko^2,3,4; Rastas, Pasi^6,7; Amiryousefi, Ali^1,2; Jayaprakash, Balamuralikrishna^3,7,8; Kammonen, Juhana I.³; Hagqvist, Risto⁹; Eswaran, Gugan^1,2,3; Ahonen, Viivi Helena^10,7,11; Serra, Juan Alonso^1,2,3; Asiegbu, Fred O.^2,12; Barajas-Lopez, Juan de Dios; Blande, Daniel¹⁰; Blokhina, Olga¹; Blomster, Tiina^1,2,3; Broholm, Suvi^1,2,3,13,7; Brosche, Mikael^1,2,14; Cui, Fuqiang^1,2,7,15; Dardick, Chris¹⁶; Ehonen, Sanna E.^1,2; Elomaa, Paula^2,13; Escamez, Sacha¹⁷; Fagerstedt, Kurt V.^1,2; Fujii, Hiroaki¹⁸; Gauthier, Adrien^1,2,7,19; Gollan, Peter J.¹⁸; Halimaa, Pauliina; Heino, Pekka I.^2,20; Himanen, Kristiina^2,13; Hollender, Courtney¹⁶; Kangasjärvi, Saijaliisa¹⁸; Kauppinen, Leila²¹; Kelleher, Colin T.²²; Kontunen-Soppela, Sari²³; Koskinen, J. Patrik^3,7,24; Kovalchuk, Andriy^2,12; Kärenlampi, Sirpa O.¹⁰; Kärkönen, Anna K.^2,4,13,7; Lim, Kean-Jin^2,13; Leppälä, Johanna^1,2; Macpherson, Lee²⁵; Mikola, Juha²⁶; Mouhu, Katriina^2,13; Mähönen, Ari Pekka^1,2,3; Niinemets, Ülo²⁷; Oksanen, Elina²³; Overmyer, Kirk^1,2; Palva, E. Tapio^2,20; Pazouki, Leila²⁷; Pennanen, Ville^2,20; Puhakainen, Tuula^20,7,28; Poczai, Peter²⁹; Possen, Boy J. H. M.^30,7,31; Punkkinen, Matleena¹⁸; Rahikainen, Moona M.¹⁸; Rousi, Matti³⁰; Ruonala, Raili^3,32,7; van der Schoot, Christiaan³³; Shapiguzov, Alexey^1,2,34; Sierla, Maija^1,2; Sipilä, Timo P.^1,2; Sutela, Suvi³⁵; Teeri, Teemu H.^2,13; Tervahauta, Arja I.¹⁰; Vaattovaara, Aleksia^1,2; Vahala, Jorma^1,2; Vetchinnikova, Lidia³⁶; Welling, Annikki^1,7,37; Wrzaczek, Michael¹; Xu, Enjun^1,2,7,38; Paulin, Lars G.³; Schulman, Alan H.^2,3,4; Lascoux, Martin^39,40; Albert, Victor A.⁵; Auvinen, Petri³; Helariutta, Ykä^1,2,3,32; Kangasjärvi, Jaakko^1,2
Organizations:	¹Univ Helsinki, Dept Biosci, Div Plant Biol, Helsinki, Finland. ²Univ Helsinki, Viikki Plant Sci Ctr, Helsinki, Finland. ³Univ Helsinki, Inst Biotechnol, Helsinki, Finland. ⁴Nat Resources Inst Finland Luke, Green Technol, Helsinki, Finland. ⁵Univ Buffalo, Dept Biol Sci, Buffalo, NY USA. ⁶Univ Cambridge, Dept Zool, Cambridge, England. ⁷Univ Helsinki, Dept Biosci, Ecol Genet Res Unit, Helsinki, Finland. ⁸Natl Inst Hlth & Welf THL, Kuopio, Finland. ⁹Nat Resources Inst Finland Luke, Green Technol, Haapastensyrja, Layliainen, Finland. ¹⁰Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio, Finland. ¹¹Work Environm Labs, Finnish Inst Occupat Hlth, Kuopio, Finland. ¹²Univ Helsinki, Dept Forest Sci, Helsinki, Finland. ¹³Univ Helsinki, Dept Agr Sci, Helsinki, Finland. ¹⁴Univ Tartu, Inst Technol, Tartu, Estonia. ¹⁵Zhejiang Agr & Forestry Univ, Sch Forest Biotechnol, Hangzhou, Zhejiang, Peoples R China. ¹⁶USDA, Appalachian Fruit Res Stn, Agr Res Serv, Kearnysville, WV USA. ¹⁷Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, Umea, Sweden. ¹⁸Univ Turku, Dept Biochem, Mol Plant Biol, Turku, Finland. ¹⁹UniLaSalle, Unite AGRI TERR, Campus Rouen, Mont St Aignan, France. ²⁰Univ Helsinki, Dept Biosci, Div Genet, Helsinki, Finland. ²¹Univ Helsinki, Dept Biosci, Helsinki, Finland. ²²Natl Bot Gardens Ireland, DBN Plant Mol Lab, Dublin, Ireland. ²³Univ Eastern Finland, Dept Environm & Biol Sci, Joensuu, Finland. ²⁴Blueprint Genet, Helsinki, Finland. ²⁵Kings Coll London, Dept Haemato Oncol, London, England. ²⁶Univ Helsinki, Dept Environm Sci, Helsinki, Finland. ²⁷Estonian Univ Life Sci, Inst Agr & Environm Sci, Tartu, Estonia. ²⁸Sci Agr Soc Finland, Agr & Food Sci, Lemu, Finland. ²⁹Univ Helsinki, Finnish Museum Nat Hist Botany, Helsinki, Finland. ³⁰Nat Resources Inst Finland Luke, Management & Prod Renewable Resources, Helsinki, Finland. ³¹Royal Haskoning DHV, Maastricht Airport, Beek, Netherlands. ³²Univ Cambridge, Sainsbury Lab, Cambridge, England. ³³Norwegian Univ Life Sci, Dept Plant Sci, As, Norway. ³⁴Russian Acad Sci, Inst Plant Physiol, Moscow, Russia. ³⁵Univ Oulu, Genet & Physiol Unit, Oulu, Finland. ³⁶Russian Acad Sci, Karelian Res Ctr, Forest Res Inst, Petrozavodsk, Russia. ³⁷Finnish Food Safety Author Evira, Chem & Toxicol Res Unit, Helsinki, Finland. ³⁸Chinese Acad Sci, Inst Bot, Beijing, Peoples R China. ³⁹Uppsala Univ, Dept Ecol & Genet, Evolutionary Biol Ctr, Uppsala, Sweden. ⁴⁰Uppsala Univ, Sci Life Lab, Uppsala, Sweden.
Format:	article
Version:	published version
Access:	open
Online Access:	PDF Full Text (PDF, 2.6 MB)
Persistent link:	http://urn.fi/urn:nbn:fi-fe201708228180
Language:	English
Published:	Springer Nature, 2017
Publish Date:	2017-08-22
Description:	Abstract Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A. see all 
Series:	Nature genetics
ISSN:	1061-4036
ISSN-E:	1546-1718
ISSN-L:	1061-4036
Volume:	49
Pages:	904 - 912
DOI:	10.1038/ng.3862
OADOI:	https://oadoi.org/10.1038/ng.3862
Type of Publication:	A1 Journal article – refereed
Field of Science:	1184 Genetics, developmental biology, physiology 1181 Ecology, evolutionary biology
Subjects:	Genomics Plant genetics Population genetics Article
Funding:	We thank A. Korpijaakko, A. Korpilahti, S. Koskela, K. Lipponen, P. Laamanen, H. Kangas, M. Rantanen, and E.-M. Turkki for excellent assistance, and L. Schulman and L. Junikka (University of Helsinki Botanical Gardens) for providing birch species samples. Birch sequencing was supported by a Finnish Technology Development Agency (TEKES) grant to J.K., Y.H., and P.A. J.K. and Y.H. were supported by the Finnish Centre of Excellence in Molecular Biology of Primary Producers (Academy of Finland CoE program 2014-2019, decision 271832). Y.H. was funded by the Gatsby Foundation and the European Research Council Advanced Investigator Grant SYMDEV. V.A.A. acknowledges support from the US National Science foundation (0922742 and 1442190). J.S. acknowledges a University of Helsinki 3-year grant. A.H.S. and J.T. acknowledge Academy of Finland decision (266430). EST libraries were created with TEKES funding to E.T.P.
Copyright information:	© The Author(s) 2017. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
	https://creativecommons.org/licenses/by/4.0/

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Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

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