A genome sequence resource for the European chestnut (Castanea sativa Mill.) and the development of genic microsatellite markers

European chestnut (Castanea sativa Mill.), commonly referred to as sweet chestnut, is one of the four cultivated members of the Eucastanon section of the Castanea genus and the tree is valuable for both nut and timber production. C. sativa nuts are recognized as the highest quality chestnuts. C. sativa has significant economic importance in Europe and has spread by human activity to all geographical regions that are within the species’ ecological limits. The present work describes a C. sativa genome assembly of the cultivar Sarı Aşılama, which is the most widely cultivated chestnut in Anatolia. The assembly represents 83.4% of the chestnut genome with a gene completeness estimate of 90.2%. The repetitive DNA content of the assembly was identified as 47% and was predominated by LTR (long terminal repeat) retrotransposons. 20,161 annotated protein coding gene models were identified in the assembly and genome-based miRNA (micro RNA) identification analysis with a machine-learned classifier proved successful in identifying 1489 putative loci. Protein coding gene models were scanned for microsatellites for the development of genic markers and cross-species transferability was assessed, resulting in 1600 consensus genic markers for the European and Asian chestnut genomes. The markers tested on a collection of chestnut genotypes proved successful in discriminating C. sativa cultivars and hybrids. The European chestnut genome assembly and, data from genome characterization and marker development analyses are anticipated to make a useful and significant contribution to genomic research in the Castanea genus.