SRA

Here we sequenced 150 birch individuals and assembled a B. pendula reference genome from a fourth-generation inbred line, resulting in a high-quality assembly of 435 Mb that was linked to chromosomes using a dense genetic map. We analyzed SNPs in the genomes of 80 birch individuals spanning most of the geographic range of B. pendula, as well as seven other members of Betulaceae. Population genomic analyses of these data provide insights into the deep-time evolution of the birch family and on recent natural selection acting on silver birch. We constructed a hybrid nuclear genome assembly starting from 9× sequence coverage with Roche 454 technology. Assembled contigs were polished with Illumina paired-end data and connected and ordered using mate-pair libraries sequenced on both Illumina and SOLiD platforms, followed by further scaffolding and gap filling with 30× coverage of PacBio reads longer than 6,000 bp. This resulted in a first assembly consisting of 5,642 scaffolds with an N50 of 240 kb Further scaffolding with additional PacBio reads resulted in 3,474 (super)scaffolds with N50 value of 527.7 kb. A total of 391 Mb of scaffolds (89% of the estimated 440-Mb genome) was assembled into 14 chromosomal linkage groups via an ultra-high-density genomic linkage map consisting of 3.4 million markers. In addition to the nuclear genome, organellar genomes were assembled and annotated. Evidence for birch gene models was obtained by sequencing EST libraries from 12 different birch tissues or growth conditions, providing 18,951 transcripts with an average length of 1,683 bp, and by carrying out de novo assembly of RNA-seq reads, yielding 16,906 transcripts. We annotated the nuclear genome in two stages. After initial automated gene prediction, 3,192 genes were manually annotated and used to train gene predictors for a second round, yielding 28,153 high-quality gene models, of which 17,746 were supported by nearly full-length transcriptomic evidence. The GFF annotation and assembled pseudochromosomes are available by contacting the authors of the related article.