An anchored chromosome?scale genome assembly of spinach improves annotation and reveals extensive gene rearrangements in euasterids

Spinach (Spinacia oleracea L.) is a member of the Caryophyllales family, basal eudicot asterid that consists sugar beet (Beta vulgaris L. subsp. vulgaris), quinoa (Chenopodium Willd.), and amaranth (Amaranthus hypochondriacus L.). With introduction baby leaf types, spinach has become staple food in many homes. Production issues focus on yield, nitrogen-use efficiency resistance to downy mildew (Peronospora effusa). Although genomes are available for above species, chromosome-level assembly exists only quinoa, allowing proper annotation structural analyses enhance crop improvement. We independently assembled annotated cultivar Viroflay using short-read strategy (Illumina) long-read strategies (Pacific Biosciences) develop chromosome-level, genetically anchored spinach. Scaffold N50 Illumina was 389 kb, whereas Pacific BioSciences 4.43 Mb, representing 911 Mb (93% genome) 221 scaffolds, 80% which oriented sequence-based genetic map, also described within this work. The two assemblies were 99.5% collinear. Independent with same comprehensive transcriptome dataset show quality directly affects significantly more genes predicted (26,862 vs. 34,877) assembly. Analysis confirms bias resistant gene motifs typical monocots. Evolutionary analysis indicates Spinacia paleohexaploid whole-genome triplication followed by extensive rearrangements identified Diversity 75 lines indicate variation ample hypothesis-driven, genomic-assisted breeding enabled