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

Author
item SALOJARVI, JARKKO - University Of Helsinki
item SMOLANDER, OLLI-PEKKA - University Of Helsinki
item NIEMINEN, KAISA - Natural Resources Institute Finland (LUKE)
item RAJARAMAN, SITARAM - University Of Helsinki
item MOHAMMADI, OMID - University Of Helsinki
item SAFDARI, PEZHMAN - University Of Helsinki
item LAMMINMAKI, AIRI - University Of Helsinki
item IMMANEN, JUHA - University Of Helsinki
item LAN, TIANYING - University Of Buffalo
item TANSKANEN, JAAKKO - University Of Helsinki
item RASTAS, PASI - University Of Cambridge
item AMIRYOUSEFI, ALI - University Of Helsinki
item JAYAPRAKASH, BALAMURALIKRISH - National Institute For Health And Welfare (HELSINKI)
item KAMMONEN, JUHANA - University Of Helsinki
item HAGQVIST, RISTO - Natural Resources Institute Finland (LUKE)
item ESWARAN, GUGAN - University Of Helsinki
item AHONEN, VIIVI - University Of Eastern Finland
item ALONSO-SERRA, JUAN - University Of Helsinki
item ASIEGBU, FRED - University Of Helsinki
item BARAJAS-LOPEZ, JUAN DE DIOS - University Of Turku
item BLANDE, DANIEL - University Of Eastern Finland
item BLOKHINA, OLGA - University Of Helsinki
item BLOMSTER, TIINA - University Of Helsinki
item BROHOLM, SUVI - University Of Helsinki
item BROSCHE, MIKAEL - University Of Tartu
item CUI, FUQIANG - University Of Helsinki
item Dardick, Christopher - Chris
item EHONEN, SANNA - University Of Helsinki
item ELOMAA, PAULA - University Of Helsinki
item ESCAMEZ, SACHA - University Of Umea
item FAGERSTEDT, KURT - University Of Helsinki
item FUJII, HIROAKI - University Of Turku
item GAUTHIER, ADRIEN - University Of Helsinki
item GOLLAN, PETER - University Of Turku
item HALIMAA, PAULILNA - University Of Eastern Finland
item HEINO, PEKKA - University Of Helsinki
item HIMANEN, KRISTIINA - University Of Helsinki
item Hollender, Courtney
item KANGASJARVI, SAIJALIISA - University Of Turku
item KAUPPIENEN, LEILA - University Of Helsinki
item KELLEHER, COLIN - Botanic Garden
item KONTUNEN-SOPPELA, SARI - University Of Eastern Finland
item KOSKINEN, PATRIK - University Of Helsinki
item KOVALCHUK, ANDRIY - University Of Helsinki
item KARENIAMPI, SIRPA - University Of Eastern Finland
item KARKONEN, ANNA - University Of Helsinki
item LIM, KEAN-JIN - University Of Helsinki
item LEPPALA, JOHANNA - University Of Helsinki
item MACPHERSON, LEE - King'S College
item MIKOLA, JULIA - University Of Helsinki
item MOUHU, KATRIINA - University Of Helsinki
item NIINEMETS, YLO - Estonian University Of Life Sciences
item OKSANEN, ELINA - University Of Eastern Finland
item OVERMEYER, KIRK - University Of Helsinki
item PALVA, TAPIO - University Of Helsinki
item PAZOUKI, LEILA - Estonian University Of Life Sciences
item PENNANEN, VILLE - University Of Helsinki
item PUHAKAINEN, TUULA - University Of Helsinki
item POCZAI, PETER - University Of Helsinki
item POSSEN, BOY - Royal Botanical Gardens
item PUNKKINEN, MATLEENA - University Of Turku
item RAHIKAINEN, MOONA - University Of Turku
item ROUSI, MATTI - Natural Resources Institute Finland (LUKE)
item RUONALA, RAILI - University Of Helsinki
item VAN DER SCHOOT, CHRISTIAAN - Norwegian University Of Life Sciences
item SHAPIGUZOV, ALEXEY - Russian Academy Of Sciences
item SIERIA, MAIJA - University Of Helsinki
item TEERI, TEEMU - University Of Helsinki
item TERVAHAUTA, ARJA - University Of Eastern Finland
item VAATTOVAARA, ALEKSIA - University Of Helsinki
item VAHALA, JORMA - University Of Helsinki
item VETCHINNIKOVA, LIDIA - Russian Academy Of Sciences
item WELLING, ANNIKKI - Finnish Food Safety Authority
item WRZACZEK, MICHAEL - University Of Helsinki
item XU, ENJUN - University Of Helsinki
item PAULIN, LARS - University Of Helsinki
item SCHULMAN, ALAN - Natural Resources Institute Finland (LUKE)
item LASCOUX, MARTIN - Uppsala University
item ALBERT, VICTOR - University Of Buffalo
item AUVINEN, PETRI - University Of Helsinki
item HELARIUTTA, YKA - University Of Cambridge
item KANGASJARVI, JAAKKO - King Saud University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/12/2017
Publication Date: 5/8/2017
Citation: Salojarvi, J., Smolander, O., Nieminen, K., Rajaraman, S., Mohammadi, O., Safdari, P., Lamminmaki, A., Immanen, J., Lan, T., Tanskanen, J., Rastas, P., Amiryousefi, A., Jayaprakash, B., Kammonen, J., Hagqvist, R., Eswaran, G., Ahonen, V., Alonso-Serra, J., Asiegbu, F., Barajas-Lopez, J., Blande, D., Blokhina, O., Blomster, T., Broholm, S., Brosche, M., Cui, F., Dardick, C.D., Ehonen, S., Elomaa, P., Escamez, S., Fagerstedt, K., Fujii, H., Gauthier, A., Gollan, P., Halimaa, P., Heino, P., Himanen, K., Hollender, C.A., Kangasjarvi, S., Kauppienen, L., Kelleher, C., Kontunen-Soppela, S., Koskinen, P., Kovalchuk, A., Kareniampi, S., Karkonen, A., Lim, K., Leppala, J., Macpherson, L., Mikola, J., Mouhu, K., Niinemets, Y., Oksanen, E., Overmeyer, K., Palva, T., Pazouki, L., Pennanen, V., Puhakainen, T., Poczai, P., Possen, B., Punkkinen, M., Rahikainen, M., Rousi, M., Ruonala, R., Van Der Schoot, C., Shapiguzov, A., Sieria, M., Teeri, T., Tervahauta, A., Vaattovaara, A., Vahala, J., Vetchinnikova, L., Welling, A., Wrzaczek, M., Xu, E., Paulin, L., Schulman, A., Lascoux, M., Albert, V., Auvinen, P., Helariutta, Y., Kangasjarvi, J. 2017. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nature Genetics. 49(6):904-915.

Interpretive Summary: The nuclear genome of the silver birch tree, Betula pendula, was sequenced and assembled. Additionally, the evolutionary history of other birch species was assessed based on the sequencing of 80 individual trees. The work described here lays the foundation for future genetic improvement of this agronomically important timber species. It also provides insight into the genetic contributions associated with the evolution of forest trees in response to climate change.

Technical Abstract: Silver birch, Betula pendula, is a common pioneer tree species in boreal forests across Eurasia. In contrast to most other trees, which have generation times from several years to decades, birch can be induced to flower within one year. This, together with a small 440 Mb genome and advanced breeding material, makes birch an attractive target for modern genomics-based biotechnology. We assembled the nuclear genome sequence of a fourth-generation, self-pollinated individual and anchored it by genetic linkage to chromosomes. Deep-time coding sequence evolution was analyzed by partitioning duplicate genes based on their evolutionary origins. Polyploid duplicates, dating back to the pan-core-eudicot paleohexaploid event, were enriched for transcription factor activities, whereas, tandem duplicates were over-represented with environmental response and secondary metabolic functions. Population genomic analyses based on 80 resequenced individuals representing most of the geographic species range showed effective population size crashes at well-known points of climatic upheaval during geologic history. Selective sweeps, shallow-time adaptive events, were enriched for genes originating from the ancient polyploidy event, and included genes involved in receptor kinase signaling, cytokinin and light perception, and sexual reproduction. Several candidates showed signatures of recent natural selection correlating with environmental variables. For example, selective sweeps in PHYC and FRS10, two tightly linked genes encoding light-response proteins, correlated with latitude/longitude and temperature, and in the case of PHYC, also with precipitation. Similar associations were detected for ARR1, which acts in growth-promoting cytokinin perception, and for KAK and MED5A, which are involved in wood development. Overall, swept genes were enriched for key developmental or physiological triggering functions, suggesting that at least in birch, selection has acted by tuning the timing and crosstalk between fundamental plant processes.