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 organization: Biosciences
Viikki Plant Science Centre (ViPS)
Institute of Biotechnology
Bioinformatics for Molecular Biology and Genomics (BMBG)
Plant-Fungal Interactions Group
Plant ROS-Signalling
Department of Forest Sciences
Frederick Asiegbu / Principal Investigator
Forest Ecology and Management
Department of Agricultural Sciences
Plant stress and natural variation
Plant Biology
Ecosystem processes (INAR Forest Sciences)
Asteraceae developmental biology and secondary metabolism
Plant Production Sciences
Pekka Heino / Principal Investigator
Tapio Palva Research Group
Genetics
Environmental Sciences
Terrestrial Interactions Research Group
Ari Pekka Mähönen / Principal Investigator
Finnish Museum of Natural History
Botany
Embryophylo
Teemu Teeri / Principal Investigator
Receptor-Ligand Signaling Group
Alan Schulman / Principal Investigator
DNA Sequencing and Genomics
Yrjö Helariutta / Principal Investigator
Date: 2017-05-08
Language: eng
Number of pages: 12
Belongs to series: Nature Genetics
ISSN: 1061-4036
DOI: https://doi.org/10.1038/ng.3862
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
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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