Whole genome sequencing of safflower A2 using PacBio HiFi reads, Optical mapping, HiC and Illumina paired-end reads
Safflower or Carthamus tinctorius L a member of the family Asteraceae is an annual diploid oilseed crop that can grow under low moisture and high saline conditions Compared to other vegetable oils safflower oil has higher amounts of mono and polyunsaturated fatty acids namely oleic and linoleic acid which make it suitable for various uses in food and industry Despite its utility as an oilseed and a source of pharmacologically important compounds the cultivation of safflower is replete with its own set of challenges such as spinyness susceptibility to biotic and abiotic stresses and scarcity of genotypescultivars with high oil content Therefore a consolidated research effort is required to generate genomic resources in safflower to aid breeding efforts A contiguous and a richly annotated genome sequence is the foundation for discovery of the genetrait discovery evolutionary and phylogenetic studies genome dynamics as well as deciphering the link between genotypes and the phenotypes This study presents a de novo complete accurate and contiguous chromosomelevel genome assembly of SafflowerA2 accession rich in oleic acid and oil content representing an American regional gene pool Genome assembly was constructed with integration of PacBio HiFi reads Bionano optical mapping HiC and Illumina paired end reads Initially long Pacbio HiFi reads were assembled into the contigs using Hifiasm with default parameters Using optical maps and contigs assembly hybrid scaffolding was performed using Bionano solve Finally pseudochromosomes were constructed from the scaffold level assembly using pairedend HiC reads through SALSA and pretext viewer