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      Taxonomic revision of Chloromonas nivalis (Volvocales, Chlorophyceae) strains, with the new description of two snow-inhabiting Chloromonas species

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          Abstract

          Chloromonas nivalis (Volvocales, Chlorophyceae) is considered a cosmopolitan species of a snow-inhabiting microalga because cysts morphologically identifiable as zygotes of the species are distributed worldwide. However, recent molecular data demonstrated that field-collected cysts identified as the zygotes consist of multiple species. Recently, we demonstrated that species identification of snow-inhabiting Chloromonas species is possible based on light and electron microscopy of asexual life cycles in strains and molecular phylogenetic analyses. Vegetative cells without eyespots and of inverted-teardrop shape have been reported once in North American material of C. nivalis; however, strains with such vegetative cells in snow-inhabiting species of Chloromonas have not been examined taxonomically in detail. Here, we used light and transmission electron microscopy together with molecular analyses of multiple DNA sequences to examine several C. nivalis strains. The morphological data demonstrated that one North American strain could be identified as C. nivalis, whereas three other strains should be re-classified as C. hoshawii sp. nov. and C. remiasii sp. nov. based on vegetative cell morphology, the number of zoospores within the parental cell wall during asexual reproduction, and whether cell aggregates (resulting from repeated divisions of daughter cells retained within a parental cell wall) were observed in the culture. This taxonomic treatment was supported by multigene phylogeny and comparative molecular analyses that included a rapidly evolving DNA region. Our molecular phylogenetic analyses also demonstrated that the North American strain of C. nivalis was phylogenetically separated from the Austrian and Japanese specimens previously identified as C. nivalis based on zygote morphology.

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          Fast-Find: A novel computational approach to analyzing combinatorial motifs

          Background Many vital biological processes, including transcription and splicing, require a combination of short, degenerate sequence patterns, or motifs, adjacent to defined sequence features. Although these motifs occur frequently by chance, they only have biological meaning within a specific context. Identifying transcripts that contain meaningful combinations of patterns is thus an important problem, which existing tools address poorly. Results Here we present a new approach, Fast-FIND (Fast-Fully Indexed Nucleotide Database), that uses a relational database to support rapid indexed searches for arbitrary combinations of patterns defined either by sequence or composition. Fast-FIND is easy to implement, takes less than a second to search the entire Drosophila genome sequence for arbitrary patterns adjacent to sites of alternative polyadenylation, and is sufficiently fast to allow sensitivity analysis on the patterns. We have applied this approach to identify transcripts that contain combinations of sequence motifs for RNA-binding proteins that may regulate alternative polyadenylation. Conclusion Fast-FIND provides an efficient way to identify transcripts that are potentially regulated via alternative polyadenylation. We have used it to generate hypotheses about interactions between specific polyadenylation factors, which we will test experimentally.
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            ITS2 is a double-edged tool for eukaryote evolutionary comparisons.

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              Is there a molecular key to the level of "biological species" in eukaryotes? A DNA guide.

              DNA sequences, powerful for phylogeny, have not yet proven as rewarding for taxonomic categorization purposes. However, further analyses of one locus, the second Internal Transcribed Spacer of the nuclear ribosomal gene cistron, has suggested a high degree of predictability across eukaryotes. Comparison of the secondary structure of ITS2 transcripts reveals its most conserved region, on the 5'-side of helix III. Comparison of this 5' 30 bp highly conserved region with the extent of sexual compatibility in a clade of organisms produces two useful predictions: identity of this region predicts meaningful intercrossing ability, and, difference of even one CBC pairing in this region predicts total failure of crossing. Previous to the appearance of the first CBC in the highly conserved portion, all gametic compatibility has been lost, thanks to the parallel evolutionary changes in genes controlling mating. These two landmark events help to delimit the level of interbreeding taxa.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                23 March 2018
                2018
                : 13
                : 3
                : e0193603
                Affiliations
                [1 ] Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
                [2 ] Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
                Donald Danforth Plant Science Center, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8989-5933
                Article
                PONE-D-17-42481
                10.1371/journal.pone.0193603
                5865719
                29570718
                8b1c2a1d-cedf-4bea-b32c-cc982261ad2b
                © 2018 Matsuzaki et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 3 December 2017
                : 14 February 2018
                Page count
                Figures: 5, Tables: 1, Pages: 17
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 15H06148
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001691, Japan Society for the Promotion of Science;
                Award ID: 16J09828
                Award Recipient :
                RM was supported by Grants-in-Aid for Research Activity Start-up (No. 15H06148) and JSPS Research Fellow (No. 16J09828) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI ( https://www.jsps.go.jp/english/e-grants/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Germ Cells
                OVA
                Zygotes
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Chloroplasts
                Biology and Life Sciences
                Cell Biology
                Plant Cell Biology
                Chloroplasts
                Biology and Life Sciences
                Plant Science
                Plant Cell Biology
                Chloroplasts
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Plant Cells
                Chloroplasts
                Biology and Life Sciences
                Cell Biology
                Plant Cell Biology
                Plant Cells
                Chloroplasts
                Biology and Life Sciences
                Plant Science
                Plant Cell Biology
                Plant Cells
                Chloroplasts
                Biology and Life Sciences
                Taxonomy
                Computer and Information Sciences
                Data Management
                Taxonomy
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Cell Walls
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Research and Analysis Methods
                Microscopy
                Light Microscopy
                Custom metadata
                New sequence data, alignments used for our phylogenetic analyses, and the holotype specimens are available under the DDBJ/ENA/GenBank accession numbers (LC360463–LC360497, and LC361432), TreeBASE ID (S22105), and the herbarium specimen numbers for the holotypes (TNS-AL-58946 and TNS-AL-58947), respectively. All other relevant data are within the manuscript and its Supporting Information files.

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