The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio

• Published in: BMC genetics 2024-06, Vol.25 (1), p.64-5, Article 64
• Main Authors: Bianco, Luca, Fontana, Paolo, Marchesini, Alexis, Torre, Sara, Moser, Mirko, Piazza, Stefano, Alessandri, Sara, Pavese, Vera, Pollegioni, Paola, Vernesi, Cristiano, Malnoy, Mickael, Torello Marinoni, Daniela, Murolo, Sergio, Dondini, Luca, Mattioni, Claudia, Botta, Roberto, Sebastiani, Federico, Micheletti, Diego, Palmieri, Luisa
• Format: Article
• Language: English
• Subjects: Analysis; Archives & records; Bioinformatics; Castanea sativa; Chestnut; Chromosome-scale; Chromosomes; Chromosomes, Plant - genetics; Data Note; Economic aspects; European chestnut; Fagaceae - genetics; Genes; Genetic aspects; Genome sequence assembly; Genome, Plant - genetics; Genomes; Genomics; Genotype; Growth; Haplotypes; Haplotypes - genetics; Hardwoods; Indigenous species; MicroRNAs; Molecular Sequence Annotation; Nucleotide sequence
• ISSN: 2730-6844; 2730-6844; 1471-2156
• DOI: 10.1186/s12863-024-01245-7

The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.