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

Authors: Amanda M Hulse-Kemp, Hamed Bostan, Shiyu Chen, Hamid Ashrafi, Kevin Stoffel, Walter Sanseverino, Linzhou Li, Shifeng Cheng, Michael C. Schatz, Tyler Garvin, Lindsey J. du Toit, Elizabeth Tseng, Jason Chin, Massimo Iorizzo, Allen Van Deynze

Institutions:

Department of Plant Sciences, University of California, Davis, CA, USA
Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
Department of Horticulture, North Carolina State University, Raleigh, NC, USA
Sequentia Biotech, Barcelona, Spain
BGI-Shenzhen, Shenzhen, China
Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building 1121, Cold Spring Harbor, NY, 11724 USA
Washington State University, SU Mount Vernon Northwestern Washington Research & Extension Center (NWREC), Mount Vernon, WA, 98273 USA
Pacific Biosciences, Menlo Park, CA, USA

Publication: The Plant Genome

Date: June 2021

Full paper: https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20101

Abstract:

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