A recent report in the scientific journal Nature Genetics 49: 904–12 (May 2017), doi:10.1038/ng.3862, disclosed the results of genomic DNA sequencing and analysis of Betula pendula, the silver birch tree.
The report, entitled "Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch," was the result of a multinational effort* indicative of the importance of this species. B. pendula is a "pioneer boreal tree," and boreal forests comprise 30% of total global forest area. Recently these forests are undergoing "extensive climate change," including increases of 1.5 °C/year, a trend expected to reach an estimated 4-11 °C increase by 2100. As a consequence, climate zones will shift faster than the trees can migrate, an eventuality that could have commercially important consequences for fiber and biomass production. Silver birch are also attractive targets for forest biotechnology, having a relatively small (440 Mbp) genome and a rapid lifecycle (that can be induced to flower within 1 year).
The scientists sequenced 150 individual birch trees (80 from B. pendula) and assembled a 435 Mbp genomic map. Ancestor species to silver birch were known to have undergone a paleohexaploid event in its evolutionary history, but as a species there has been an absence of whole genome duplication events since. Comparisons of individuals sequenced across 12 sites from Western Norway to Siberia showed that the "effective population size" had crashed at "major points of climatic upheaval" (the Cretaceous–Paleogene boundary, where populations fell to less than 10,000; the Eocene-Oligocene, the mid-Miocene, and the Pleistocene), and these population crashes were also correlated with known speciation events. Further regarding these results on birch tree populations, the researchers showed Finland to be the source of genetic mixing between European and Asian varieties, and that Irish samples showed extensive genetic admixing between related species.
Using SNP analysis as the basis for the genetic map, the report identifies 14 chromosomal linkage groups and 3.4 million markers. These researchers also sequenced and annotated organellar genomes (mitochondria and chloroplasts), which were discussed primarily on the Suppplementary materials. By various means 16,906 - 18,951 transcripts were detected with an average length of 1,683 bp; genetic analysis yielded 17,746 genes based on almost full-length transcriptome evidence. Outside the protein-encoding portions of the silver birch genome, 49.23% of birch genomic DNA was transposable elements and 30.6% of it retrotransposons.
Assessing families of retrotransposons, Gypsy and Copia "superfamily" members were less common (8.5% and 2.3%, respectively), and had fewer evolutionarily "younger" (<50,000 y.o.) members compared with plant genomes having similar size and complexity. "Nonautonomous" element group TRIM elements were more abundant, at 6.4% compared with pear, for example (1.26%).
Comparing birch genome by syntenic alignment with grapevine and other eudicots, no evidence was found for whole genome duplications post-divergence from these other species; the only internally duplicated blocks of sequence stem from the ancient gamma hexaploidy event found at the base of the eudicot evolutionary tree.
The report also discloses two pools of duplications, which are known generally to be sources of functional novelty in eukaryotes: "duplicate genes deriving from the ancient hexaploidy event, and those stemming from ongoing tandem (segmental) duplications." Transcription factor genes were overrepresented in these duplications, which the authors interpreted as "biased retention of highly interconnected genes following the duplication of entire functional modules." Also, tandemly duplicated genes in silver birch were found to be enriched for secondary metabolism, bacterial defense, hormonal response, and hormone and nutrient transport. "These results suggest that whereas polyploid duplicates tend to diversify core processes in developmental and physiological regulation, tandem duplicates enhance the diversity of a plant's environmental response capacity, which is in concurrence with previous studies," the authors concluded.
Also found was genetic evidence of interspecies admixture, following genomic sequencing of "five other diploid birch species (Betula nana, Betula platyphylla, Betula populifolia, Betula occidentalis, and Betula lenta), the tetraploid birch Betula pubescens, two alder species from the related genus Alnus (Alnus incana and Alnus glutinosa), and B. pendula individuals originating from 12 populations native to Ireland, Norway, Finland, and Russia." The authors note that these comparisons are consistent with "allopatric division during the last Ice Age, followed by subsequent admixture when the two populations rejoined after ice-sheet retreat, as has been suggested on the basis of chloroplast DNA evidence."
The report shows the results of studies using resequenced individuals to detect regions of selective sweeps, where natural selection acting on a locus sweeps away variation across a genomic region surrounding the locus; these were found to have acted mostly on genes dating from the ancient gamma hexaploidy event. In these sweep regions 913 genetic loci were identified, including three that were 'significantly enriched: transmembrane receptor protein tyrosine kinase signaling pathway genes (23 genes including BAM3 (leaf shape, size and symmetry), PXC2, PXC3 (secondary cell wall formation in developing wood), MOL1 (cambrium homeostasis), MIK1 (stem vascular development), and MDIS1 (recognition of female chemoattractant); peptidyl-histidine phosphorylation genes, including phytochrome genes PHYA, PHYB, and PHYC (involved in red and far-red light response) and genes encoding histidine kinases such as cytokinin receptors AHK2, AHK3, and AHK4 (CRE1), osmosensor AHK1, and ethylene receptors ERS1 and ETR2, involved in acclimation to abiotic stress, shoot and root vascular development, flowering time, and longevity; and genes involved in longitudinal axis specification, including MONOPTEROS and GNL1 (embryo and vascular development), two homologs of TOADSTOOL 2 (meristem maintenance), and two homologs of WRKY2 (polen development and zygote polarization).
In addition, 423 of the 913 genes had between 9% and 100% of the observed allelic variation explanable by population structure and general environmental variables such as temperature and precipitation. Six genes had significant associations and what the authors termed 'intriguing molecular functions." These genes were verified by phylogenetic analysis as orthologs of the A. thaliana genes SWEETIE (involved in sugar homeostasis, response to abiotic stresses such as cold and drought), KAKTUS (KAK) (a suppressor of endoreduplication associated with lower temperatures), ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1)(a cytokine signaling gene, important in wood formation in tree trunks), MED5A (encoding Mediator complex protein MED5A, also known as MED33A, involved in lignin formation, important for pulp and paper production), PHYTOCHROME C (PHYC), and FAR1-RELATED SEQUENCE 10 (FRS10)(genes that are genetically linked and together involved in red and far-red light sensing, shade avoidance, canopy density, temperature-dependent adaptation, and flowering time regulation).
As summarized by the authors, the significance of these findings is as follows:
Using the B. pendula reference genome and resequenced individuals spanning the geographic range of silver birch, we were able to characterize genomic adaptations at several levels. First, we detected enrichments of [transcription factor] functions that date to the core-eudicot crown radiation. Second, we uncovered a suite of gene duplicates involved in environmental responses that were not polyploidy derived but instead stem from ongoing tandem duplication processes. Such duplicates are generated by the same mechanisms as copy number variants (CNVs), which have come under intense recent study (particularly in animal genomes) as adaptive "tuning knobs" at the inter-population level.
In view of the ecological and commercial importance of the silver birch, its potential for biotechnological adaptation as an improved source of wood pulp, and its active selection by changing climate conditions, the results in this paper suggest the silver birch may be a fruitful model for how genetic adaptation in arboreal forests can be understood and responsibly exploited.
As has frequently the case, such genomic studies yield new insights into the genetic basis for well-known variations (see, for example, "Leg Length Variation in Dogs and its Relevance to Human Mutations"). In silver birch, the research reported here uncovered the basis for the "weeping" phenotype (B. pendula "Yoingii") in silver birch to be related to "an in-frame stop codon was found in the birch AtLAZY1 ortholog." The LAZY1 gene is known to be a member of the IGT protein family and regulates tiller orientation in rice and maize as well as inflorescence branch angle in Arabidopsis. It is also believed to "influence gravitropism through regulation of auxin transport and signaling." "Lateral organs in maize lazy1 mutants fail to grow vertically, giving rise to a phenotype similar to that observed in 'Youngii'," and thus the authors conclude that "[t]he stop codon in the birch LAZY1 ortholog could thus explain its weeping phenotype."
* A plurality of researchers were from various departments at the University of Helsinki; Department of Environmental and Biological Sciences, University of Eastern Finland; Genetics and Physiology Unit, University of Oulu; Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University; Finnish National Institute of Health and Welfare; Finnish Institute of Occupational Health, School of Forest Biotechnology; Green Technology, Natural Resources Institute Finland; Molecular Plant Biology, Department of Biochemistry, University of Turku, Finland; Agricultural and Food Science/Scientific Agricultural Society of Finland; Chemistry and Toxicology Research Unit, Finnish Food Safety Authority Evira; Department of Plant Sciences, Norwegian University of Life Sciences, Norway; Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden; Blueprint Genetics; Forest Research Institute Karelian Research Centre Russian Academy of Sciences and Institute of Plant Physiology, Russian Academy of Sciences, Russia; Institute of Botany, The Chinese Academy of Sciences and Zhejiang Agriculture and Forestry University, China; Unité AGRI′TERR, UniLaSalle, Campus de Rouen, France; Sainsbury Laboratory, University of Cambridge, and Department of Haemato-oncology, King's College London, UK; DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin; Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences and Institute of Technology, University of Tartu, Estonia; Royal Haskoning DHV, Netherlands; Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, West Virginia; and Department of Biological Sciences, University of Buffalo.
Image of Betula pendula, Inari wilderness, Finland, by Percita at Flickr, from the Wikipedia Commons under the Creative Commons Attribution-Share Alike 2.0 Generic license.
