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

Jarkko SalojärviOlli-Pekka SmolanderKaisa NieminenSitaram RajaramanOmid SafronovPezhman SafdariAiri LamminmäkiJuha ImmanenTianying LanJaakko TanskanenPasi RastasAli AmiryousefiBalamuralikrishna JayaprakashJuhana I KammonenRisto HagqvistGugan EswaranViivi Helena AhonenJuan Alonso SerraFred O AsiegbuJuan de Dios Barajas-LopezDaniel BlandeOlga BlokhinaTiina BlomsterSuvi BroholmMikael BroschéFuqiang CuiChris DardickSanna E EhonenPaula ElomaaSacha EscamezKurt V FagerstedtHiroaki FujiiAdrien GauthierPeter J GollanPauliina HalimaaPekka I HeinoKristiina HimanenCourtney HollenderSaijaliisa KangasjärviLeila KauppinenColin T KelleherSari Kontunen-SoppelaJ Patrik KoskinenAndriy KovalchukSirpa O KärenlampiAnna K KärkönenKean-Jin LimJohanna LeppäläLee MacphersonJuha MikolaKatriina MouhuAri Pekka MähönenÜlo NiinemetsElina OksanenKirk OvermyerE Tapio PalvaLeila PazoukiVille PennanenTuula PuhakainenPéter PoczaiBoy J H M PossenMatleena PunkkinenMoona M RahikainenMatti RousiRaili RuonalaChristiaan van der SchootAlexey ShapiguzovMaija SierlaTimo P SipiläSuvi SutelaTeemu H TeeriArja I TervahautaAleksia VaattovaaraJorma VahalaLidia VetchinnikovaAnnikki WellingMichael WrzaczekEnjun XuLars G PaulinAlan H SchulmanMartin LascouxVictor A AlbertPetri AuvinenYkä HelariuttaJaakko Kangasjärvi
Published in: Nature genetics (2017)
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.
Keyphrases
  • genome wide
  • life cycle
  • gold nanoparticles
  • genome wide identification
  • copy number
  • dna methylation
  • climate change
  • single cell
  • transcription factor
  • silver nanoparticles
  • genome wide analysis
  • oxidative stress