Journal Article
An improved reference genome and first organelle genomes of Quercus suber
Ana Usié; Octávio Serra; Pedro M. Barros; Pedro Barbosa; Célia Leão; Tiago Capote; Tânia Almeida; Leandra Rodrigues; Isabel Carrasquinho; Joana B. Guimarães; Diogo Mendoça; Filomena Nóbrega; Conceição Egas; Inês Chaves; Isabel A. Abreu; Nelson J. M. Saibo; Liliana Marum; Maria Carolina Varela; José Matos; Fernanda Simões; Célia M. Miguel; M. Margarida Oliveira; Cândido P. Ricardo; Sónia Gonçalves; António Marcos Ramos
Tree Genetics & Genomes · Vol. 19, Issue 6 · 2023
Abstract
Cork oak ( Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean region and widespread in southwest Europe and northwest Africa. An improved genome assembly of cork oak using a combination of Illumina and PacBio sequencing is presented in this study. The assembled genome contains 2351 scaffolds longer than 1000 bp, accounting for 765.7 Mbp of genome size, L90 of 755, and a N50 of 1.0 Mbp, with 40,131 annotated genes. The repetitive sequences constitute 53.6% of the genome. The genome sequences of chloroplast and mitochondrion were determined for the first time, with a genome size of 161,179 bp and 531,858 bp, respectively. Phylogenetic analysis based on complete chloroplast genome sequence showed that Q. suber is closely related to Quercus variabilis , two cork-producing species with commercial use. All data generated are available through the public databases, being ready to be used without restrictions. This study provides an improved nuclear genome assembly together with the organelle genomes of cork oak. These resources will be useful for further breeding strategies and conservation programs and for comparative genomic studies in oak species.