title: Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.
abstract: Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family.
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.|IBIS Bioscience, Carlsbad, CA, USA.
authors.forename: Todd P
authors.initials: TP
authors.lastname: Michael
authors.affiliation: IBIS Bioscience, Carlsbad, CA, USA.|Donald Danforth Center for Plant Science, St. Louis, MO, USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Bryant
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Gutierrez
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Nikolai
authors.initials: N
authors.lastname: Borisjuk
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Philomena
authors.initials: P
authors.lastname: Chu
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Hanzhong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, China.|Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Xia
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, China.
authors.forename: Junfei
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Peng
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
authors.forename: Moaine
authors.initials: M
authors.lastname: El Baidouri
authors.affiliation: BioNano Genomics, San Diego, CA, USA.
authors.forename: Boudewijn
authors.initials: B
authors.lastname: Ten Hallers
authors.affiliation: BioNano Genomics, San Diego, CA, USA.
authors.forename: Alex R
authors.initials: AR
authors.lastname: Hastie
authors.affiliation: BioNano Genomics, San Diego, CA, USA.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Liang
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Acosta
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Gilbert
authors.affiliation: IBIS Bioscience, Carlsbad, CA, USA.
authors.forename: Connor
authors.initials: C
authors.lastname: McEntee
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Donald Danforth Center for Plant Science, St. Louis, MO, USA.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.affiliation: Institute for Systems Biology, Jianghan University, Wuhan, China.|Department of Computer Science and Engineering, Washington University, St. Louis, MO, USA.
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Lam
mesh_terms: D029064:Araceae / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D019175:DNA Methylation; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D010940:Plant Proteins
keywords: 
  Spirodela polyrhiza
  ; BioNano Genomics; duckweed; methylome; next-generation sequencing; rDNA repeats; structure variation