An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifolia
Publication Date
January 08, 2015
Journal
PLOS Genetics
Authors
Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima R. Sinha, et al
Volume
11
Issue
1
Pages
e1004900
DOI
https://dx.plos.org/10.1371/journal.pgen.1004900
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004900
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25569326
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287348
Europe PMC
http://europepmc.org/abstract/MED/25569326
Web of Science
000349314600021
Scopus
84924358948
Mendeley
http://www.mendeley.com/research/intracellular-transcriptomic-atlas-giant-coenocyte-caulerpa-taxifolia
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1862143"], "description"=>"<p><b>A</b>) Principal Component Analysis (PCA) performed on transcript accumulation across sampled regions (the inverse of the PCA presented in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004900#pgen-1004900-g001\" target=\"_blank\"><b>Fig. 1D</b></a>). Four major densities in the transcript accumulation variance structure are indicated by arrow. <b>B</b>) PCA was performed to visualize results of clustering by transcripts using Self-Organizing Maps (SOMs), visualized as different colors corresponding to nodes. <b>C</b>) Transcript accumulation profiles of genes belonging to different nodes, arranged with increasing abundance in an apical-to-basal direction. Scaled transcript abundance is such that the average abundance level across pseudo-organs for each transcript is 0 and variance is equal to 1. Scaled transcript abundance is shown as a boxplot and individual genes as jittered points (randomly displaced along the x-axis) to visualize transcript abundance distributions. Text for each node indicating those regions with scaled transcript abundance >0 is indicated.</p>", "links"=>[], "tags"=>["transcript accumulation patterns", "morphology", "giant coenocyte Caulerpa taxifolia", "land plants", "Giant Coenocyte Caulerpa taxifolia Convergent morphologies", "intracellular transcriptomic atlas"], "article_id"=>1285901, "categories"=>["Biological Sciences"], "users"=>["Aashish Ranjan", "Brad T. Townsley", "Yasunori Ichihashi", "Neelima R. Sinha", "Daniel H. Chitwood"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004900.g002", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intracellular_accumulation_of_transcripts_in_a_giant_single_celled_organism_/1285901", "title"=>"Intracellular accumulation of transcripts in a giant, single-celled organism.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1862162"], "description"=>"<p><b>A</b>) Intersection of transcript accumulation profiles by their <i>Caulerpa</i> node membership (x-axis) and corresponding accumulation pattern in tomato (<i>Solanum lycopersicum</i>). Each point corresponds to a <i>Caulerpa</i> transcript and its corresponding best BLAST-hit tomato homolog. χ<b><sup>2</sup></b> p values indicate probability of <i>Caulerpa</i> transcript membership among tomato nodes differing from expected null distribution. Along the side of the graph is indicated averaged scaled transcript abundance across sampled regions in tomato. Intersections of transcript accumulation detailed in <b>C–E</b> are indicated with red boxes. <b>B</b>) Bar graphs showing expected (gray) and observed (yellow, Node 2; red, Node 4; blue, Node 6) distributions of <i>Caulerpa</i> BLAST hits in tomato against tomato nodes. Intersections of transcript accumulation detailed in <b>C–E</b> are indicated. <b>C–E</b>) Line graphs of select intersections of transcripts with similar accumulation profiles in <i>Caulerpa</i>, the homologs of which are enriched for specific transcript accumulation patterns in tomato. Details of gene identities are discussed in the text. Inflor.  =  inflorescence, Leaf  =  leaf, Root  =  root, Sdling  =  seedling, Stem  =  stem, Veg  =  vegetative apex.</p>", "links"=>[], "tags"=>["transcript accumulation patterns", "morphology", "giant coenocyte Caulerpa taxifolia", "land plants", "Giant Coenocyte Caulerpa taxifolia Convergent morphologies", "intracellular transcriptomic atlas"], "article_id"=>1285907, "categories"=>["Biological Sciences"], "users"=>["Aashish Ranjan", "Brad T. Townsley", "Yasunori Ichihashi", "Neelima R. Sinha", "Daniel H. Chitwood"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004900.g004", "stats"=>{"downloads"=>3, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recurrent_recruitment_of_transcript_accumulation_to_morphological_structures_in_a_land_plant_and_Caulerpa_/1285907", "title"=>"Recurrent recruitment of transcript accumulation to morphological structures in a land plant and <i>Caulerpa</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1862142"], "description"=>"<p><b>A</b>) Evolutionary relationships among green algae with unicellular, siphonous, siphonocladous, and uninucleate multicellular lifestyles. Diagrams indicate body plan, redrawn from Cocquyt et al. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004900#pgen.1004900-Cocquyt1\" target=\"_blank\">[40]</a>. <b>B</b>) The growing frond apex of <i>Caulerpa taxifolia</i>, producing young pinnules. <b>C</b>) Diagram of sampled regions. <b>D</b>) Principal Component Analysis (PCA) performed on organ RNA-Seq replicates based on transcript accumulation levels. 95% confidence ellipses are indicated for each sampled region. For convenience, a dotted line is provided separating apical from basal pseudo-organ types to relate data back to morphology. Colors indicate different sampled regions (as opposed to nodes in subsequent figures). Red, apex; orange, pinnules; yellow, rachis; green, frond base; blue, stolon; purple, holdfast.</p>", "links"=>[], "tags"=>["transcript accumulation patterns", "morphology", "giant coenocyte Caulerpa taxifolia", "land plants", "Giant Coenocyte Caulerpa taxifolia Convergent morphologies", "intracellular transcriptomic atlas"], "article_id"=>1285900, "categories"=>["Biological Sciences"], "users"=>["Aashish Ranjan", "Brad T. Townsley", "Yasunori Ichihashi", "Neelima R. Sinha", "Daniel H. Chitwood"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004900.g001", "stats"=>{"downloads"=>3, "page_views"=>120, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_evolutionary_and_developmental_context_of_siphonous_morphology_in_Caulerpa_taxifolia_/1285900", "title"=>"The evolutionary and developmental context of siphonous morphology in <i>Caulerpa taxifolia.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1862209", "https://ndownloader.figshare.com/files/1862210", "https://ndownloader.figshare.com/files/1862211", "https://ndownloader.figshare.com/files/1862212", "https://ndownloader.figshare.com/files/1862213", "https://ndownloader.figshare.com/files/1862214", "https://ndownloader.figshare.com/files/1862215", "https://ndownloader.figshare.com/files/1862216", "https://ndownloader.figshare.com/files/1862217", "https://ndownloader.figshare.com/files/1862218", "https://ndownloader.figshare.com/files/1862219", "https://ndownloader.figshare.com/files/1862220", "https://ndownloader.figshare.com/files/1862221", "https://ndownloader.figshare.com/files/1862222", "https://ndownloader.figshare.com/files/1862223", "https://ndownloader.figshare.com/files/1862224", "https://ndownloader.figshare.com/files/1862225", "https://ndownloader.figshare.com/files/1862226", "https://ndownloader.figshare.com/files/1862227", "https://ndownloader.figshare.com/files/1862228", "https://ndownloader.figshare.com/files/1862229", "https://ndownloader.figshare.com/files/1862230", "https://ndownloader.figshare.com/files/1862232", "https://ndownloader.figshare.com/files/1862233", "https://ndownloader.figshare.com/files/1862234", "https://ndownloader.figshare.com/files/1862235", "https://ndownloader.figshare.com/files/1862236", "https://ndownloader.figshare.com/files/1862237", "https://ndownloader.figshare.com/files/1862238", "https://ndownloader.figshare.com/files/1862239", "https://ndownloader.figshare.com/files/1862240"], "description"=>"<div><p>Convergent morphologies have arisen in plants multiple times. In non-vascular and vascular land plants, convergent morphology in the form of roots, stems, and leaves arose. The morphology of some green algae includes an anchoring holdfast, stipe, and leaf-like fronds. Such morphology occurs in the absence of multicellularity in the siphonous algae, which are single cells. Morphogenesis is separate from cellular division in the land plants, which although are multicellular, have been argued to exhibit properties similar to single celled organisms. Within the single, macroscopic cell of a siphonous alga, how are transcripts partitioned, and what can this tell us about the development of similar convergent structures in land plants? Here, we present a <i>de novo</i> assembled, intracellular transcriptomic atlas for the giant coenocyte <i>Caulerpa taxifolia</i>. Transcripts show a global, basal-apical pattern of distribution from the holdfast to the frond apex in which transcript identities roughly follow the flow of genetic information in the cell, transcription-to-translation. The analysis of the intersection of transcriptomic atlases of a land plant and <i>Caulerpa</i> suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances. Our results not only provide an intracellular atlas of transcript localization, but also demonstrate the contribution of transcript partitioning to morphology, independent from multicellularity, in plants.</p></div>", "links"=>[], "tags"=>["transcript accumulation patterns", "morphology", "giant coenocyte Caulerpa taxifolia", "land plants", "Giant Coenocyte Caulerpa taxifolia Convergent morphologies", "intracellular transcriptomic atlas"], "article_id"=>1285953, "categories"=>["Biological Sciences"], "users"=>["Aashish Ranjan", "Brad T. Townsley", "Yasunori Ichihashi", "Neelima R. Sinha", "Daniel H. Chitwood"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004900.s001", "https://dx.doi.org/10.1371/journal.pgen.1004900.s002", "https://dx.doi.org/10.1371/journal.pgen.1004900.s003", "https://dx.doi.org/10.1371/journal.pgen.1004900.s004", "https://dx.doi.org/10.1371/journal.pgen.1004900.s005", "https://dx.doi.org/10.1371/journal.pgen.1004900.s006", "https://dx.doi.org/10.1371/journal.pgen.1004900.s007", "https://dx.doi.org/10.1371/journal.pgen.1004900.s008", "https://dx.doi.org/10.1371/journal.pgen.1004900.s009", "https://dx.doi.org/10.1371/journal.pgen.1004900.s010", "https://dx.doi.org/10.1371/journal.pgen.1004900.s011", "https://dx.doi.org/10.1371/journal.pgen.1004900.s012", "https://dx.doi.org/10.1371/journal.pgen.1004900.s013", "https://dx.doi.org/10.1371/journal.pgen.1004900.s014", "https://dx.doi.org/10.1371/journal.pgen.1004900.s015", "https://dx.doi.org/10.1371/journal.pgen.1004900.s016", "https://dx.doi.org/10.1371/journal.pgen.1004900.s017", "https://dx.doi.org/10.1371/journal.pgen.1004900.s018", "https://dx.doi.org/10.1371/journal.pgen.1004900.s019", "https://dx.doi.org/10.1371/journal.pgen.1004900.s020", "https://dx.doi.org/10.1371/journal.pgen.1004900.s021", "https://dx.doi.org/10.1371/journal.pgen.1004900.s022", "https://dx.doi.org/10.1371/journal.pgen.1004900.s023", "https://dx.doi.org/10.1371/journal.pgen.1004900.s024", "https://dx.doi.org/10.1371/journal.pgen.1004900.s025", "https://dx.doi.org/10.1371/journal.pgen.1004900.s026", "https://dx.doi.org/10.1371/journal.pgen.1004900.s027", "https://dx.doi.org/10.1371/journal.pgen.1004900.s028", "https://dx.doi.org/10.1371/journal.pgen.1004900.s029", "https://dx.doi.org/10.1371/journal.pgen.1004900.s030", "https://dx.doi.org/10.1371/journal.pgen.1004900.s031"], "stats"=>{"downloads"=>117, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_Intracellular_Transcriptomic_Atlas_of_the_Giant_Coenocyte_Caulerpa_taxifolia_/1285953", "title"=>"An Intracellular Transcriptomic Atlas of the Giant Coenocyte <i>Caulerpa taxifolia</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-01-08 02:47:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1862158"], "description"=>"<p>Panels within this figure correspond to each other, indicating a relationship between morphology, transcript accumulation, and cellular compartments. <b>A</b>) A diagram of <i>Caulerpa</i> morphology. Pseudo-organs roughly correspond to the apical-basal pattern of transcript accumulation shown in neighboring panel <b>B</b>) and the location of transcripts related to cellular compartments as shown in <b>C</b>). <b>B</b>) Heat map for genes belonging to select GO categories showing (left to right) node the parent GO term belongs to, transcript accumulation across pseudo-organs, and the general GO term category. Color indicates scaled transcript abundance, in which average transcript abundance is equal to 0 and variance equal to 1 for each transcript's abundance level across pseudo-organs. Green indicates low and magenta high scaled transcript abundance. <b>C</b>) Diagram of cellular compartments and the flow of genetic information from transcription to translation.</p>", "links"=>[], "tags"=>["transcript accumulation patterns", "morphology", "giant coenocyte Caulerpa taxifolia", "land plants", "Giant Coenocyte Caulerpa taxifolia Convergent morphologies", "intracellular transcriptomic atlas"], "article_id"=>1285903, "categories"=>["Biological Sciences"], "users"=>["Aashish Ranjan", "Brad T. Townsley", "Yasunori Ichihashi", "Neelima R. Sinha", "Daniel H. Chitwood"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004900.g003", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationship_between_cell_compartmentalization_and_morphology_/1285903", "title"=>"The relationship between cell compartmentalization and morphology.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-01-08 02:47:40"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}

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