TY - JOUR
T1 - An improved reference genome and first organelle genomes of Quercus suber
AU - Usié, Ana
AU - Serra, Octávio
AU - Barros, Pedro M.
AU - Barbosa, Pedro
AU - Leão, Célia
AU - Capote, Tiago
AU - Almeida, Tânia
AU - Rodrigues, Leandra
AU - Carrasquinho, Isabel
AU - Guimarães, Joana B.
AU - Mendoça, Diogo
AU - Nóbrega, Filomena
AU - Egas, Conceição
AU - Chaves, Inês
AU - Abreu, Isabel A.
AU - Saibo, Nelson J.M.
AU - Marum, Liliana
AU - Varela, Maria Carolina
AU - Matos, José
AU - Simões, Fernanda
AU - Miguel, Célia M.
AU - Oliveira, M. Margarida
AU - Ricardo, Cândido P.
AU - Gonçalves, Sónia
AU - Ramos, António Marcos
N1 - Funding Information:
The authors would like to thank Fundação João Lopes Fernandes for providing all plant materials.
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/12
Y1 - 2023/12
N2 - 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.
AB - 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.
KW - Chloroplast genome
KW - Cork oak
KW - Genome annotation
KW - Genome assembly
KW - Mitochondrial genome
KW - Phylogenetic analysis
UR - http://www.scopus.com/inward/record.url?scp=85176963626&partnerID=8YFLogxK
U2 - 10.1007/s11295-023-01624-8
DO - 10.1007/s11295-023-01624-8
M3 - Article
AN - SCOPUS:85176963626
SN - 1614-2942
VL - 19
JO - Tree Genetics and Genomes
JF - Tree Genetics and Genomes
IS - 6
M1 - 54
ER -