NEW YORK (GenomeWeb) – A University of Helsinki-led team of researchers has sequenced the genome of the silver birch tree.
Silver birch, a pioneer boreal tree, is found across Europe, from Finland and Ireland to Germany and Siberia. As the Helsinki-led team reported today in Nature Genetics, it sequenced silver birches from all over Europe to uncover selective sweeps that appear to have helped it adapt to local environments.
"What makes a birch tree hardy in different environments? A tree in Finland may die if you plant it in Siberia because plants have local adaptations — specific genetic mutations — that help them survive where they are found," Helsinki's Ykä Helariutta said in a statement. "An understanding of these natural adaptations can facilitate genetic engineering and artificial selection. That's why our research could be very useful for forest biotechnology."
To generate the silver birch, Betula pendula, genome, Helariutta and his colleagues sequenced 150 inbred trees.
The researchers relied on a combination of sequencing approaches to assemble and chromosomally anchor its genome. Namely, they constructed a hybrid nuclear genome assembly based on 9x coverage generated on the Roche 454 platform that they polished with Illumina paired-end reads. With the addition of mate-pair libraries sequenced via both the Illumina and SOLiD platforms and additional coverage from Pacific Biosciences' RSII platform, they yielded a 435-megabase genome that they assembled into 3,474 superscaffolds.
As the researchers noted, much of the B. pendula genome is made up of transposable elements and transposons. An ancient hexaploidy event contributed to some duplicated regions, while others were due to ongoing tandem duplications. Transcription factors were overrepresented among the polyploidy duplicates, while the tandem duplicated genes were enriched for gene families involved in secondary metabolism, bacterial defense, and hormone response, the researchers said.
Helariutta and his colleagues also sequenced other members of the Betula genus to find evidence of admixture between birch species. Additionally, they noted weak population structure among B. pendula that separated them broadly into two groups, eastern and western, which the researchers suspected was due to allopatric division during the last Ice Age. They also noted population crashes that corresponded with times of climatic disturbance.
In an analysis of 60 silver birches hailing from different parts of Europe, the researchers identified 913 genes that appeared to have been under recent selection. These genes were enriched for involvement in transmembrane receptor protein tyrosine kinase signaling, peptidyl-histidine phosphorylation, and longitudinal axis specification.
About half these genes were also associated with environmental conditions like latitude, longitude, temperature, and precipitation, including a gene that encodes a sugar homeostasis protein and one associated with cell wall phenotypes in Arabidopsis.
Additionally, two other genes involved in red and far-red light sensing — PHYC and FRS10 — contained variations that correlated with latitude, longitude, and temperature. PHYC also varied with precipitation, which suggested to the researchers that these changes might be due to environmental adaptations.
"The selective sweeps we identified may be the basis for local adaptation for different populations of birch," Helsinki's Jarkko Salojärvi said. "Trees in Siberia are under different selective pressure from trees in Finland, so genes are being tweaked in different ways in these two places to allow these plants to better adjust to their environment."
Such differences, Helsinki's Petri Auvinen added, might also be of relevance to forest biotechnology efforts.