University of Oulu

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

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Author: Salojärvi, Jarkko1,2; Smolander, Olli-Pekka3; Nieminen, Kaisa4;
Rajaraman, Sitaram1,2; Safronov, Omid1,2; Safdari, Pezhman1,2; Lamminmäki, Airi1,2; Immanen, Juha1,2,3; Lan, Tianying5; Tanskanen, Jaakko2,3,4; Rastas, Pasi6,7; Amiryousefi, Ali1,2; Jayaprakash, Balamuralikrishna3,7,8; Kammonen, Juhana I.3; Hagqvist, Risto9; Eswaran, Gugan1,2,3; Ahonen, Viivi Helena10,7,11; Serra, Juan Alonso1,2,3; Asiegbu, Fred O.2,12; Barajas-Lopez, Juan de Dios; Blande, Daniel10; Blokhina, Olga1; Blomster, Tiina1,2,3; Broholm, Suvi1,2,3,13,7; Brosche, Mikael1,2,14; Cui, Fuqiang1,2,7,15; Dardick, Chris16; Ehonen, Sanna E.1,2; Elomaa, Paula2,13; Escamez, Sacha17; Fagerstedt, Kurt V.1,2; Fujii, Hiroaki18; Gauthier, Adrien1,2,7,19; Gollan, Peter J.18; Halimaa, Pauliina; Heino, Pekka I.2,20; Himanen, Kristiina2,13; Hollender, Courtney16; Kangasjärvi, Saijaliisa18; Kauppinen, Leila21; Kelleher, Colin T.22; Kontunen-Soppela, Sari23; Koskinen, J. Patrik3,7,24; Kovalchuk, Andriy2,12; Kärenlampi, Sirpa O.10; Kärkönen, Anna K.2,4,13,7; Lim, Kean-Jin2,13; Leppälä, Johanna1,2; Macpherson, Lee25; Mikola, Juha26; Mouhu, Katriina2,13; Mähönen, Ari Pekka1,2,3; Niinemets, Ülo27; Oksanen, Elina23; Overmyer, Kirk1,2; Palva, E. Tapio2,20; Pazouki, Leila27; Pennanen, Ville2,20; Puhakainen, Tuula20,7,28; Poczai, Peter29; Possen, Boy J. H. M.30,7,31; Punkkinen, Matleena18; Rahikainen, Moona M.18; Rousi, Matti30; Ruonala, Raili3,32,7; van der Schoot, Christiaan33; Shapiguzov, Alexey1,2,34; Sierla, Maija1,2; Sipilä, Timo P.1,2; Sutela, Suvi35; Teeri, Teemu H.2,13; Tervahauta, Arja I.10; Vaattovaara, Aleksia1,2; Vahala, Jorma1,2; Vetchinnikova, Lidia36; Welling, Annikki1,7,37; Wrzaczek, Michael1; Xu, Enjun1,2,7,38; Paulin, Lars G.3; Schulman, Alan H.2,3,4; Lascoux, Martin39,40; Albert, Victor A.5; Auvinen, Petri3; Helariutta, Ykä1,2,3,32; Kangasjärvi, Jaakko1,2
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: Nature Publishing Group, 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.

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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:
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/.
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