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

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Salojärvi , J , Smolander , O-P , Nieminen , K , Rajaraman , S , Safronov , O , Safdari , P , Lamminmäki , A , Immanen , J , Lan , T , Tanskanen , J , Rastas , P , Amiryousefi , A , Jayaprakash , B , Kammonen , J I , Hagqvist , R , Eswaran , G , Ahonen , V H , Serra , J A , Asiegbu , F O , Barajas-Lopez , J D D , Blande , D , Blokhina , O , Blomster , T , Broholm , S , Brosche , M , Cui , F , Dardick , C , Ehonen , S E , Elomaa , P , Escamez , S , Fagerstedt , K V , Fujii , H , Gauthier , A , Gollan , P J , Halimaa , P , Heino , P I , Himanen , K , Hollender , C , Kangasjarvi , S , Kauppinen , L , Kelleher , C T , Kontunen-Soppela , S , Koskinen , J P , Kovalchuk , A , Karenlampi , S O , Kärkönen , A K , Lim , K-J , Leppälä , J , Macpherson , L , Mikola , J , Mouhu , K , Mähönen , A P , Niinemets , U , Oksanen , E , Overmyer , K , Palva , E T , Pazouki , L , Pennanen , V , Puhakainen , T , Poczai , P , Possen , B J H M , Punkkinen , M , Rahikainen , M M , Rousi , M , Ruonala , R , van der Schoot , C , Shapiguzov , A , Sierla , M , Sipilä , T P , Sutela , S , Teeri , T H , Tervahauta , A I , Vaattovaara , A , Vahala , J , Vetchinnikova , L , Welling , A , Wrzaczek , M , Xu , E , Paulin , L G , Schulman , A H , Lascoux , M , Albert , V A , Auvinen , P , Helariutta , Y & Kangasjarvi , J 2017 , ' Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch ' , Nature Genetics , vol. 49 , no. 6 , pp. 904-912 . https://doi.org/10.1038/ng.3862

Title: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
Author: 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; Kangasjarvi, Saijaliisa; Kauppinen, Leila; Kelleher, Colin T.; Kontunen-Soppela, Sari; Koskinen, J. Patrik; Kovalchuk, Andriy; Karenlampi, Sirpa O.; Kärkönen, Anna K.; Lim, Kean-Jin; Leppälä, Johanna; Macpherson, Lee; Mikola, Juha; Mouhu, Katriina; Mähönen, Ari Pekka; Niinemets, Ulo; 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; Kangasjarvi, Jaakko
Contributor: University of Helsinki, Biosciences
University of Helsinki, Institute of Biotechnology
University of Helsinki, Bioinformatics for Molecular Biology and Genomics (BMBG)
University of Helsinki, Bioinformatics for Molecular Biology and Genomics (BMBG)
University of Helsinki, Bioinformatics for Molecular Biology and Genomics (BMBG)
University of Helsinki, Plant ROS-Signalling
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, University of Cambridge
University of Helsinki, Bioinformatics for Molecular Biology and Genomics (BMBG)
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Forest Sciences
University of Helsinki, Biosciences
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Pekka Heino / Principal Investigator
University of Helsinki, Biosciences
University of Helsinki, University of Turku
University of Helsinki, Biosciences
University of Helsinki, Institute of Biotechnology
University of Helsinki, Department of Forest Sciences
University of Helsinki, Viikki Plant Science Centre (ViPS)
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Plant Biology
University of Helsinki, Environmental Sciences
University of Helsinki, Asteraceae developmental biology and secondary metabolism
University of Helsinki, Institute of Biotechnology
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Finnish Museum of Natural History
University of Helsinki, University of Turku
University of Helsinki, Institute of Biotechnology
University of Helsinki, Plant Biology
University of Helsinki, Plant Biology
University of Helsinki, Biosciences
University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Bioinformatics for Molecular Biology and Genomics (BMBG)
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Biosciences
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Institute of Biotechnology
University of Helsinki, Viikki Plant Science Centre (ViPS)
University of Helsinki, Biosciences
Date: 2017-05-08
Language: eng
Number of pages: 12
Belongs to series: Nature Genetics
ISSN: 1061-4036
URI: http://hdl.handle.net/10138/231474
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.
Subject: ARABIDOPSIS-THALIANA
TRANSCRIPTION FACTOR
BETULA-PUBESCENS
CAMBIAL ACTIVITY
FLOWERING TIME
PHYTOCHROME-C
CYTOKININ
SIZE
EVOLUTION
PLANTS
1184 Genetics, developmental biology, physiology
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