An annotated haplotype-resolved genome sequence assembly of diploid German chamomile, Matricaria chamomilla

Matricaria chamomilla L. (chamomile) is a medicinal plant that is widely used for treating skin infections and respiratory ailments. Chamomile belongs to the Asteraceae family of flowering plants and is a primarily outcrossing species with a heterozygous genome. Despite its extensive use, no reference genome has been available for chamomile until now. We present a chromosome-level genome sequence for chamomile which was assembled with TRITEX pipeline from PacBio accurate long reads and chromosome conformation capture sequencing data. The assembled pseudo-haploid genome has a total size of 2.75 Gb, organized into 9 chromosomes with a scaffold N50 of 285 Mb. This high-quality reference genome has a BUSCO value of 98.8% and includes 47,820 functional genes. Additionally, we assembled a haplotype-resolved genome, taking advantage of the high heterozygosity of chamomile. The haplotype assemblies have total sizes of 2.28 Gb and 2.34 Gb and cover 87.6% and 89.8% of the pseudo-haploid reference genome, respectively. Our assemblies provide a valuable resource for genetics and genomics works for chamomile and related members of the Asteraceae.