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

Autor: Hulse-Kemp AM; Department of Plant Sciences, University of California, Davis, CA, USA.; USDA, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Raleigh, NC, USA.; Department of Crop and Soil Science, North Carolina State University, Raleigh, NC, USA., Bostan H; Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA., Chen S; Department of Plant Sciences, University of California, Davis, CA, USA., Ashrafi H; Department of Horticulture, North Carolina State University, Raleigh, NC, USA., Stoffel K; Department of Plant Sciences, University of California, Davis, CA, USA., Sanseverino W; Sequentia Biotech SL, Barcelona, Catalonia, Spain., Li L; BGI-Shenzhen, Shenzhen, China., Cheng S; BGI-Shenzhen, Shenzhen, China.; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518060, P. R. China., Schatz MC; Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building 1121, Cold Spring Harbor, NY, 11724, USA.; Departments of Computer Science and Biology, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA., Garvin T; Cold Spring Harbor Laboratory, One Bungtown Road, Koch Building 1121, Cold Spring Harbor, NY, 11724, USA., du Toit LJ; Washington State University, SU Mount Vernon Northwestern Washington Research & Extension Center (NWREC), Mount Vernon, WA, 98273, USA., Tseng E; Pacific Biosciences, Menlo Park, CA, USA., Chin J; Pacific Biosciences, Menlo Park, CA, USA.; DNAnexus Inc, 1975 W El Camino Real #204, Mountain View, CA, 94040, USA., Iorizzo M; Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA.; Department of Horticulture, North Carolina State University, Raleigh, NC, USA., Van Deynze A; Department of Plant Sciences, University of California, Davis, CA, USA.
Jazyk: angličtina
Zdroj: The plant genome [Plant Genome] 2021 Jul; Vol. 14 (2), pp. e20101. Date of Electronic Publication: 2021 Jun 10.
DOI: 10.1002/tpg2.20101
Abstrakt: 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.
(© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)
Databáze: MEDLINE
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