RNA-Seq Data Kuehdorf, Jetschke, Ballani, and Appenroth, 2013 . Wholegenome sequencing using different approaches and clones yielded two reference maps. Callus induction and regeneration in Spirodela and Lemna. Clipboard, Search History, and several other advanced features are temporarily unavailable. Zhu Y, Li X, Gao X, Sun J, Ji X, Feng G, Shen G, Xiang B, Wang Y. Biotechnol Biofuels. The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Zitteliana 48, 113128 (2009). Here we select Spirodela polyrhiza for whole-genome sequencing. Spirodela polyrhiza (Greater Duckweed) (The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype e Info Genome ID: Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Spirodela polyrhiza (great duckweed) genome assembly Spirodela_polyrhiza_v01 from Waksman Institute [GCA_000504445.1 ] 1. 11, 6999 (2005). Plant Biol (Stuttg). 2015 Jan;17 Suppl 1:10-5. doi: 10.1111/plb.12201. Spirodela polyrhiza is a fastgrowing aquatic monocot with highly reduced morphology, genome size and number of proteincoding genes. Genome Sequencing, Assembly, and Annotation. Greater Duckweed, Spirodela polyrhiza, has the smallest genome of the duckweed family at 158 Mb (Wang et al., 2011; Bog et al., 2015) and propagates asexually through budding from its reduced leaf-stem (frond) structure (Figure 1a). Advances in plant chromosome identification and cytogenetic techniques. Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). S.polyrhiza is an ideal system for biofuels, bioremediation, and carbon cycling due to its aspects of fast-growing, direct contact with media, and small genome size (~150 Mb). Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of. Status of duckweed genomics and transcriptomics. doi: 10.1093/gbe/evaa220. Privacy, Help The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. Epub 2018 Sep 28. An D, Zhou Y, Li C, Xiao Q, Wang T, Zhang Y, Wu Y, Li Y, Chao DY, Messing J, Wang W. Proc Natl Acad Sci U S A. ASM198140v1 - Genome - Assembly - NCBI. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Li J. et al. Using Oxford Nanopore sequencing combined with Hi-C scaffolding, we generated a highly contiguous, chromosome-scale assembly of S. polyrhiza line Sp7498 (Sp7498_HiC). Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Genome Biol Evol. We find that this geographically widespread and numerically abundant species has very low levels of genetic diversity. The Venn diagram illustrates shared and distinct cluster. Bethesda, MD 20894, Copyright Keywords: Genome Biol Evol. Epub 2017 Feb 3. To unleash the great potential of duckweed as a new model plant as well as facilitating its domestication Diversity at nonsynonymous sites relative to synonymous sites is high, suggesting that purifying selection is weak. Careers. Epub 2014 Mar 26. Hoang PTN, Rouillard JM, Macas J, Kubalov I, Schubert V, Schubert I. Chromosoma. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and Colour map ranges are 3050%, 030%, 070% and 01.5%, respectively. Members of the family Lemnaceae are tiny aquatic monocots that range in size from 1.5 cm long (Spirodela polyrhiza) to less than a millimeter (Wolffia globosa). of GC content within a sequence fragment (window) is shown as a function of the window size for several plants and a random nucleotide sequence. Status of duckweed genomics and transcriptomics. Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Figure 2. Duckweeds belong to the order Alismatales and. Plant Biol (Stuttg). Heatmap tracks illustrate from outer to inner circle GC content, gene, repeat and GAGA-repeat densities. Plant Cell Rep. 22, 457464 (2004). 2015 Jan;17 Suppl 1:10-5. doi: 10.1111/plb.12201. The Venn diagram illustrates shared and distinct cluster classes from an orthoMCL analysis of the plant proteomes of. The Mitochondrial Genome of an Aquatic Plant, Spirodela polyrhiza Wenqin Wang, Yongrui Wu, Joachim Messing* Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America Abstract Background: Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral The genome contains two rounds of ancient genome duplications. 2021 Mar 8;22(5):2733. doi: 10.3390/ijms22052733. Epub 2019 Sep 4. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. For instance, the EPA uses Lemna minor to test water quality. GC and gene content are positively, repeat and gene densities negatively correlated, whereas GAGA-repeats are present both in gene- and repeat-rich regions. ( a ) A schematic diagram of nitrogen assimilation in, National Library of Medicine Figure 7. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. genome assembly Defining structural differences in progress . Nat. The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. Clipboard, Search History, and several other advanced features are temporarily unavailable. -. Systematics and biology of the. We examine genomewide genetic diversity in Spirodela polyrhiza, a duckweed that reproduces primarily asexually. 2017 Dec;126(6):729-739. doi: 10.1007/s00412-017-0636-7. National Library of Medicine Long-read sequencing, such as SMRT (Single Molecule Real-Time) technology emerged in 2009 [ 17] has been widely applied in sequencing the chloroplast genomes with the improved contiguity and accuracy. The chloroplast genome sequencing has become routine and less expensive with the delivery of high-throughput sequencing technologies, allowing us to deeply investigate genomics and transcriptomics of duckweed organelles. The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome Comparison of genome compositional heterogeneity. 8600 Rockville Pike Spirodela polyrhiza; duckweeds; fluorescence insitu hybridization (FISH); genome integration; molecular cytogenetic map. Epub 2014 Jul 4. A clone of S. polyrhiza 7498 from North Carolina, United States, had been subjected to physical mapping and whole-genome shotgun sequencing using the 454 platform (7). Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Linear dependency between genome size, Figure 4. 8600 Rockville Pike Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of. Core monocots are shown in brown, known WGDs are shown as blue circles. Comparison of genome compositional heterogeneity in several plants. Would you like email updates of new search results? of GC content defined in fragments of fixed length sampled along the genome. For each genomic segment, the copy number of paralogous regions is shown as bar chart in the innermost circle, duplication history is illustrated by red ribbons. Prevention and treatment information (HHS). & Stomp A. M. Growing duckweed to recover nutrients from wastewaters and for production of fuel ethanol and animal feed. Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Linear dependency between genome size and LTR retrotransposon content for small-sized (, ( a ) The percentage of tandem repeats in, Figure 6. FOIA BMC Plant Biol. Systematics and biology of the Lemnoideae . We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. The dendrogram is a simplified version redrawn from ref. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). ASM198140v1 Organism: Spirodela polyrhiza (great duckweed) Submitter: Donald Danforth Plant Science Center Date: 2017/01/17 Assembly level: Chromosome Genome representation: full RefSeq category: representative genome doi: 10.1093/gbe/evaa220. DNA barcoding of the Lemnaceae, a family of aquatic monocots. Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). Epub 2017 Jul 29. 2018 Nov;96(3):670-684. doi: 10.1111/tpj.14049. NCI CPTC Antibody Characterization Program. Epub 2019 Sep 4. eCollection 2020. Plant Biol (Stuttg). 1. 2021 Jan 8;11:617830. doi: 10.3389/fpls.2020.617830. Please enable it to take advantage of the complete set of features! The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Jones DH, Atkinson BS, Ware A, Sturrock CJ, Bishopp A, Wells DM. Results: Here, the complete chloroplast genome of Spirodela polyrhiza 7498 (SpV2) is assembled by PacBio sequencing. Epub 2014 Jul 4. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. 2021 Feb 3;13(2):evaa220. 2021 Feb 3;13(2):evaa220. Hoang PNT, Michael TP, Gilbert S, Chu P, Motley ST, Appenroth KJ, Schubert I, Lam E. Plant J. Annu. BACKGROUND: Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. 2015 Jan;17 Suppl 1:24-32. doi: 10.1111/plb.12171. 2019 Sep 17;116(38):18893-18899. doi: 10.1073/pnas.1910401116. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. 2015 IPK Gatersleben. Would you like email updates of new search results? A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications. Epub 2016 Jun 15. Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. 2021 Jan 13;11(1):93. doi: 10.3390/biom11010093. Curr Opin Plant Biol. Flowering and Seed Production across the Lemnaceae. -. Hoang PTN, Fiebig A, Novk P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I. Sci Rep. 2020 Nov 5;10(1):19230. doi: 10.1038/s41598-020-75728-9. The outer circle shows the 32 pseudomolecules of, ( a ) Metaphase spread indicating a chromosome number of, Figure 4. Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P, Zhang H, Xia J, Zhou J, Peng H, El Baidouri M, Ten Hallers B, Hastie AR, Liang T, Acosta K, Gilbert S, McEntee C, Jackson SA, Mockler TC, Zhang W, Lam E. Plant J. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. Commun. The level of composition heterogeneity of genomic sequence is measured by s.d. Kato A, Vega JM, Han F, Lamb JC, Birchler JA. This site needs JavaScript to work properly. New Phytologist 2015 New Phytologist Trust. . The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species. 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. Figure 8. Unable to load your collection due to an error, Unable to load your delegates due to an error. OrthoMCL analysis of gene families. Research Progress of a Potential Bioreactor: Duckweed. 10, 205 (2010). Transcriptome . The S. polyrhiza genome would be the first monocot that is not a grass, thus providing an important link in the evolutionary relationships between higher plants. A comprehensive genomic study of S. polyrhiza was published in February 2014. We propose to use duckweed as a model for the partitioning of carbon in this simplest of higher plants. Privacy, Help We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. Bethesda, MD 20894, Copyright Cheng J. J. Unable to load your collection due to an error, Unable to load your delegates due to an error. Biomolecules. Here we select Spirodela polyrhiza for whole-genome sequencing. 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. Spirodela characteristic pathways. Yang GL, Feng D, Liu YT, Lv SM, Zheng MM, Tan AJ. Characteristics of the Spirodela genome. Many species are currently developed for industrial uses. CLEAN Soil Air Water 37, 1726 (2009). Molecular mechanism underlying the effect of maleic hydrazide treatment on starch accumulation in S. polyrrhiza 7498 fronds. Here, we studied the genome and proteome of Spirodela polyrhiza, or Greater Duckweed, which has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). The dendrogram is a simplified version redrawn from ref.. Here we select Spirodela polyrhiza for whole-genome sequencing. Hoang PTN, Schubert V, Meister A, Fuchs J, Schubert I. Sci Rep. 2019 Mar 1;9(1):3234. doi: 10.1038/s41598-019-39332-w. Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. FOIA The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. 2017 Feb;89(3):617-635. doi: 10.1111/tpj.13400. Percentage of repetitive DNA is plotted against the genome size of different plant genomes, At for Arabidopsis, Sp for Spirodela, Bd for Brachypodium, Os for rice and Sb for sorghum. 2005 Apr;8(2):148-54. doi: 10.1016/j.pbi.2005.01.014. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Here, we studied the genome and proteome of Spirodela polyrhiza, or Greater Duckweed, which has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Figure 1. Standard deviation (s.d.) 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. Figure 9. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. Epub 2021 Jan 14. See this image and copyright information in PMC. Figure 1. -, Stomp A. M. The duckweeds: a valuable plant for biomanufacturing. Planta. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution Hieu Xuan Cao1, Giang Thi Ha Vu1, Wenqin Wang2, Klaus J. Appenroth3, Joachim Messing2 and Ingo Schubert1,4 1Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466 Stadt Seeland, Germany; 2Waksman Institute of Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in 2021 Apr 19;14(1):99. doi: 10.1186/s13068-021-01932-y. Biotechnol. The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Prevention and treatment information (HHS). Bogner J. Figure 6. Accessibility The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. 2016 Oct;244(4):893-9. doi: 10.1007/s00425-016-2555-x. Please enable it to take advantage of the complete set of features! 2019 Sep 17;116(38):18893-18899. doi: 10.1073/pnas.1910401116. Spirodela polyrhiza 9509 v3 Organism: Spirodela polyrhiza (great duckweed) Submitter: J CRAIG VENTER INSTITUTE Date: 2018/08/31 Assembly level: Scaffold Genome representation: full GenBank assembly accession: GCA_900492545.1 (latest) RefSeq assembly accession: n/a IDs: 2184171[UID] 8142738 [GenBank] Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant. Phylogeny of monocotyledonous orders. The free-floating Aroids (Araceae)-living and fossil. A new Spirodela polyrhiza genome and proteome reveal a conserved chromosomal structure with high abundances of proteins favoring energy production. Spirodela_polyrhiza_v01 Organism: Spirodela polyrhiza (great duckweed) Submitter: Waksman Institute Date: 2013/12/06 Assembly level: Contig Genome representation: full GenBank assembly accession: GCA_000504445.1 (latest) RefSeq assembly 2021 Mar;130(1):15-25. doi: 10.1007/s00412-020-00749-2. An D, Zhou Y, Li C, Xiao Q, Wang T, Zhang Y, Wu Y, Li Y, Chao DY, Messing J, Wang W. Proc Natl Acad Sci U S A. 5:3311 doi: 10.1038/ncomms4311 (2014). Chromosoma. Limitation of current probe design for oligo-cross-FISH, exemplified by chromosome evolution studies in duckweeds. Spirodela polyrhiza (L.) Schleid. Careers. Here we select Spirodela polyrhiza for whole-genome sequencing. Wang W. et al. taxonomy/phylogenetic: USDA-ARS GRIN Taxonomy: search W3TROPICOS: taxonomy/phylogenetic: Vascular Tropicos: WebScipio: Spirodela polyrhiza: organism-specific: WebScipio - eukaryotic gene identification: diArk: Spirodela polyrhiza: organism-specific: diArk - a resource for eukaryotic genome research The outer circle shows the 32 pseudomolecules of the Spirodela genome assembly, tick scaling is 500kb and blue and red bars depict position of telomeric and centromeric clusters. The Spirodela genome has continued to be improved by integrating the evidences from cytogenomic, optical mapping and Nanopore sequences [ 16 ]. Darwin-Wallace Demons: survival of the fastest in populations of duckweeds and the evolutionary history of an enigmatic group of angiosperms. This site needs JavaScript to work properly. Preparation, Scanning and Analysis of Duckweed Using X-Ray Computed Microtomography. Accessibility Rev. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Front Plant Sci. Int J Mol Sci. Spirodela polyrhiza is a fastgrowing aquatic monocot with highly reduced morphology, genome size and number of proteincoding genes. Spirodela polyrhiza Doug Bryant Bioinformatics Core Facility & Todd Mockler Group, Donald Danforth Plant Science Center . Here we select Spirodela polyrhiza for whole-genome sequencing. The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface.