A reference genome sequence for the European silver fir (Abies alba Mill.): a community-generated genomic resource

Abstract

Silver fir (Abies alba Mill.) is widespread in Central, Eastern and Southern Europe. In Southern Europe, its distribution has increased overall during the 20th century due to land-use change and recolonization from refugial, over-logged populations. During recent decades, its distribution has decreased in most of its distributional range, mainly due to extreme temperature events, forest management practices and ungulate browsing. To forecast its future distribution and survival, it is important to investigate the genetic basis of its adaptation to environmental change, notably extreme events. Here, we provide a first draft genome assembly and annotation of the silver fir genome. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end (PE) and mate-pair (MP) libraries, respectively, to high depth. The assembled A. alba genome sequence accounted for over 37 million scaffolds corresponding to 18.16 Gb, with a scaffold N50 of 14,051 bp. Despite the fragmented nature of the assembly, a total of 50,757 full-length genes were functionally annotated in the nuclear genome. The chloroplast genome was also assembled into a single scaffold (120,908 bp) that shows a high collinearity with both the A. koreana and A. sibirica complete chloroplast genomes. This first genome assembly of silver fir is an important genomic resource that is now publicly available in support of a new generation of research. By genome-enabling this important conifer, this resource will be opening the gate for new experiments and more precise genetic monitoring of European silver fir forests.