Genome Sequence and RAD Tags For Birch (Betula) Ecological Genomics

The plant genus Betula (birch) comprises 30-60 species found in a variety of environments from sub-arctic scrub to sub-tropical forest. The members of the genus show a range of growth habits including tall single-stemmed trees, multi-stemmed trees, and woody shrubs. Hybridisation and polyploidy are common in the genus, and little is known about the genomic basis of its adaptations. As a foundation for ecological genomic research, we present the first genome sequence for the genus with a de novo reference genome sequence assembled from 66× short read coverage, of Betula nana (dwarf birch). This diploid species is the keystone woody species of sub-arctic scrub communities but of conservation concern in Britain. We also present restriction-site associated DNA (RAD) tags for B. nana and closely related Betula tree species. Assembly of RAD tags in 15 individuals by alignment to the reference B. nana genome yielded 44k-86k RAD loci per individual, whereas de novo RAD assembly yielded 64k-121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species-specific alleles.