A reference genome sequence for the european silver fir (abies alba mill.): a community-generated genomic resource

Mosca, Elena; Cruz, Fernando; Gómez-Garrido, Jèssica; Gut, Marta; Alioto, Tyler; Neale, David D.

doi:http://dx.doi.org/10.1534/g3.119.400083

A reference genome sequence for the european silver fir (abies alba mill.): a community-generated genomic resource

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Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S et al. A reference genome sequence for the european silver fir (abies alba mill.): a community-generated genomic resource. G3 (Bethesda). 2019;9(7):2039-49. DOI: 10.1534/g3.119.400083

Abstract

Silver fir (Abies alba Mill.) is a keystone conifer of European montane forest ecosystems that has experienced large fluctuations in population size during during the Quaternary and, more recently, due to land-use change. To forecast the species' future distribution and survival, it is important to investigate the genetic basis of adaptation to environmental change, notably to extreme events. For this purpose, we here provide a first draft genome assembly and annotation of the silver fir genome, established through a community-based initiative. DNA obtained from haploid megagametophyte and diploid needle tissue was used to construct and sequence Illumina paired-end and mate-pair 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 open the gate for new research and more precise genetic monitoring of European silver fir forests.