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

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Salojärvi, J., Smolander, O., 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, de Dios Barajas-Lopez, J., Blande, D., Blokhina, O., Blomster, T., Broholm, S., Brosché, 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., Kangasjärvi, S., Kauppinen, L., Kelleher, C. T, Kontunen-Soppela, S., Koskinen, J P., Kovalchuk, A., Kärenlampi, S. O, Kärkönen, A. K, Lim, K., Leppälä, J., Macpherson, L., Mikola, J., Mouhu, K., Mähönen, A. P., Niinemets, Ü., 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., & Kangasjärvi, J. Nature Genetics, 49(6):904–912, June, 2017.

Paper doi abstract bibtex

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 .

@article{salojarvi_genome_2017,
	title = {Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch},
	volume = {49},
	issn = {1061-4036, 1546-1718},
	url = {http://www.nature.com/articles/ng.3862},
	doi = {10/f96grj},
	abstract = {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
              .},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Genetics},
	author = {Salojärvi, Jarkko and Smolander, Olli-Pekka and Nieminen, Kaisa and Rajaraman, Sitaram and Safronov, Omid and Safdari, Pezhman and Lamminmäki, Airi and Immanen, Juha and Lan, Tianying and Tanskanen, Jaakko and Rastas, Pasi and Amiryousefi, Ali and Jayaprakash, Balamuralikrishna and Kammonen, Juhana I and Hagqvist, Risto and Eswaran, Gugan and Ahonen, Viivi Helena and Serra, Juan Alonso and Asiegbu, Fred O and de Dios Barajas-Lopez, Juan and Blande, Daniel and Blokhina, Olga and Blomster, Tiina and Broholm, Suvi and Brosché, Mikael and Cui, Fuqiang and Dardick, Chris and Ehonen, Sanna E and Elomaa, Paula and Escamez, Sacha and Fagerstedt, Kurt V and Fujii, Hiroaki and Gauthier, Adrien and Gollan, Peter J and Halimaa, Pauliina and Heino, Pekka I and Himanen, Kristiina and Hollender, Courtney and Kangasjärvi, Saijaliisa and Kauppinen, Leila and Kelleher, Colin T and Kontunen-Soppela, Sari and Koskinen, J Patrik and Kovalchuk, Andriy and Kärenlampi, Sirpa O and Kärkönen, Anna K and Lim, Kean-Jin and Leppälä, Johanna and Macpherson, Lee and Mikola, Juha and Mouhu, Katriina and Mähönen, Ari Pekka and Niinemets, Ülo and Oksanen, Elina and Overmyer, Kirk and Palva, E Tapio and Pazouki, Leila and Pennanen, Ville and Puhakainen, Tuula and Poczai, Péter and Possen, Boy J H M and Punkkinen, Matleena and Rahikainen, Moona M and Rousi, Matti and Ruonala, Raili and van der Schoot, Christiaan and Shapiguzov, Alexey and Sierla, Maija and Sipilä, Timo P and Sutela, Suvi and Teeri, Teemu H and Tervahauta, Arja I and Vaattovaara, Aleksia and Vahala, Jorma and Vetchinnikova, Lidia and Welling, Annikki and Wrzaczek, Michael and Xu, Enjun and Paulin, Lars G and Schulman, Alan H and Lascoux, Martin and Albert, Victor A and Auvinen, Petri and Helariutta, Ykä and Kangasjärvi, Jaakko},
	month = jun,
	year = {2017},
	pages = {904--912},
}

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