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Emura N, Muranaka T, Iwasaki T, Honjo MN, Nagano AJ, Isagi Y, Kudoh H. Effects of fruit dimorphism on genetic structure and gene flow in the coastal shrub Scaevola taccada. Ann Bot 2022; 130:1029-1040. [PMID: 36534688 PMCID: PMC9851332 DOI: 10.1093/aob/mcac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Plant propagules often possess specialized morphologies that facilitate dispersal across specific landscapes. In the fruit dimorphism of a coastal shrub, Scaevola taccada, individual plants produce either cork-morph or pulp-morph fruits. The former is buoyant and common on sandy beaches, whereas the latter does not float, is bird-dispersed, and is common on elevated sites such as slopes on sea cliffs and behind rocky shores. We hypothesized that beach populations bridge the heterogeneous landscapes by serving as a source of both fruit types, while dispersal is biased for the pulp morph on elevated sites within the islands and for the cork morph between beaches of different islands. Based on this hypothesis, we predicted that populations in elevated sites would diverge genetically over time due to isolation by distance, whereas beach populations would maintain high genetic similarity via current gene flow. METHODS The genetic structure and gene flow in S. taccada were evaluated by investigating genome-wide single nucleotide polymorphisms in plants from 17 sampling sites on six islands (belonging to the Ryukyu, Daito and Ogasawara Islands) in Japan. KEY RESULTS Geographical isolation was detected among the three distant island groups. Analyses within the Ryukyu Islands suggested that sandy beach populations were characterized by genetic admixture, whereas populations in elevated sites were relatively isolated between the islands. Pairwise FST values between islands were lowest between sandy beaches, intermediate between sandy beaches and elevated sites, and highest between elevated sites. CONCLUSIONS Dispersal across the ocean by cork morphs is sufficiently frequent to prevent genetic divergence between beaches of different islands. Stronger genetic isolation of elevated sites between islands suggests that bird dispersal by pulp morphs is restricted mainly within islands. These contrasting patterns of gene flow realized by fruit dimorphism provide evidence that fruit characteristics can strongly mediate genetic structure.
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Affiliation(s)
- Naoko Emura
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu 520-2113, Japan
- Department of Environmental Sciences and Technology, Faculty of Agriculture, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Tomoaki Muranaka
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu 520-2113, Japan
- Department of Environmental Sciences and Technology, Faculty of Agriculture, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Takaya Iwasaki
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu 520-2113, Japan
- Natural Science Division, Faculty of Core Research, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu 520-2113, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Yuji Isagi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu 520-2113, Japan
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Simon NML, Sugisaka J, Honjo MN, Tunstad SA, Tunna G, Kudoh H, Dodd AN. Altered stomatal patterning accompanies a trichome dimorphism in a natural population of Arabidopsis. Plant Direct 2020; 4:e00262. [PMID: 32995701 PMCID: PMC7507053 DOI: 10.1002/pld3.262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 07/09/2020] [Accepted: 08/07/2020] [Indexed: 05/27/2023]
Abstract
Trichomes are large epidermal cells on the surface of leaves that are thought to deter herbivores, yet the presence of trichomes can also negatively impact plant growth and reproduction. Stomatal guard cells and trichomes have shared developmental origins, and experimental manipulation of trichome formation can lead to changes in stomatal density. The influence of trichome formation upon stomatal development in natural populations of plants is currently unknown. Here, we show that a natural population of Arabidopsis halleri that includes hairy (trichome-bearing) and glabrous (no trichomes) morphs has differences in stomatal density that are associated with this trichome dimorphism. We found that glabrous morphs had significantly greater stomatal density and stomatal index than hairy morphs. One interpretation is that this arises from a trade-off between the proportions of cells that have trichome and guard cell fates during leaf development. The differences in stomatal density between the two morphs might have impacts upon environmental adaptation, in addition to herbivory deterrence caused by trichome development.
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Affiliation(s)
| | - Jiro Sugisaka
- Center for Ecological Research Kyoto University Otsu Shiga Japan
| | - Mie N Honjo
- Center for Ecological Research Kyoto University Otsu Shiga Japan
| | | | - George Tunna
- School of Biological Sciences University of Bristol Bristol UK
| | - Hiroshi Kudoh
- Center for Ecological Research Kyoto University Otsu Shiga Japan
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3
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Tsujimoto M, Araki KS, Honjo MN, Yasugi M, Nagano AJ, Akama S, Hatakeyama M, Shimizu-Inatsugi R, Sese J, Shimizu KK, Kudoh H. Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq. AoB Plants 2020; 12:plz080. [PMID: 32002176 PMCID: PMC6983914 DOI: 10.1093/aobpla/plz080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/18/2019] [Indexed: 06/10/2023]
Abstract
To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N50 = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.
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Affiliation(s)
| | - Kiwako S Araki
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Life Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Engineering, Utsunomiya University, Yoto, Utsunomiya, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Yokatani, Seta Ohe-cho, Otsu, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Functional Genomics Center Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan
- Humanome Lab., Inc. 2-4-10-2F, Tsukiji, Chuo-ku, Tokyo, Japan
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ku, Yokohama, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano Otsu, Japan
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Honjo MN, Kudoh H. Arabidopsis halleri: a perennial model system for studying population differentiation and local adaptation. AoB Plants 2019; 11:plz076. [PMID: 31832127 PMCID: PMC6899346 DOI: 10.1093/aobpla/plz076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/26/2019] [Indexed: 05/21/2023]
Abstract
Local adaptation is assumed to occur when populations differ in a phenotypic trait or a set of traits, and such variation has a genetic basis. Here, we introduce Arabidopsis halleri and its life history as a perennial model system to study population differentiation and local adaptation. Studies on altitudinal adaptation have been conducted in two regions: Mt. Ibuki in Japan and the European Alps. Several studies have demonstrated altitudinal adaptation in ultraviolet-B (UV-B) tolerance, leaf water repellency against spring frost and anti-herbivore defences. Studies on population differentiation in A. halleri have also focused on metal hyperaccumulation and tolerance to heavy metal contamination. In these study systems, genome scans to identify candidate genes under selection have been applied. Lastly, we briefly discuss how RNA-Seq can broaden phenotypic space and serve as a link to underlying mechanisms. In conclusion, A. halleri provides us with opportunities to study population differentiation and local adaptation, and relate these to the genetic systems underlying target functional traits.
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Affiliation(s)
- Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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Ito T, Nishio H, Tarutani Y, Emura N, Honjo MN, Toyoda A, Fujiyama A, Kakutani T, Kudoh H. Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment. Genes (Basel) 2019; 10:genes10070544. [PMID: 31319612 PMCID: PMC6679105 DOI: 10.3390/genes10070544] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/14/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.
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Affiliation(s)
- Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Yoshiaki Tarutani
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Naoko Emura
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
- Department of Environmental Sciences and Technology, Faculty of Agriculture, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asao Fujiyama
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tetsuji Kakutani
- Department of Chromosome Science, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.
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Kamitani M, Nagano AJ, Honjo MN, Kudoh H. A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq. Microb Ecol 2019; 78:113-121. [PMID: 30357428 DOI: 10.1007/s00248-018-1271-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
Studies on plant viruses are biased towards crop diseases and little is known about viruses in natural vegetation. We conducted extensive surveys of plant viruses in wild Brassicaceae plants occurring in three local plant communities in central Japan. We applied RNA-Seq with selective depletion of rRNA, which allowed us to detect infections of all genome-reported viruses simultaneously. Infections of Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV), Brassica yellows virus, Pelargonium zonate spot virus, and Arabidopsis halleri partitivirus 1 were detected from the two perennial species, Arabidopsis halleri subsp. gemmifera and Rorippa indica. De novo assembly further detected partial sequences of a putative novel virus in Arabis fragellosa. Virus species composition and infection rate differed depending on site and plant species. Viruses were most frequently detected from the perennial clonal plant, A. halleri, in which a high clonal transmission rate of viruses across multiple years was confirmed. Phylogenetic analysis of TuMV and CMV showed that virus strains from wild Brassicaceae were included as a major clade of these viruses with other reported strains from crop plants, suggesting that viruses were shared among wild plants and crops. Our studies indicated that distribution of viruses in natural plant populations are determined by the combinations of life histories of viruses and hosts. Revealing viral distribution in the natural plant communities improves our knowledge on the ecology of plant viruses.
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Affiliation(s)
- Mari Kamitani
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan.
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2914, Japan.
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga, 520-2914, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga, 520-2113, Japan.
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Nagano AJ, Kawagoe T, Sugisaka J, Honjo MN, Iwayama K, Kudoh H. Publisher Correction: Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation. Nat Plants 2019; 5:329. [PMID: 30737451 DOI: 10.1038/s41477-019-0381-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Fig. 3b of the version of this Article originally published, a number of arrows indicating repression of downstream processes were mistakenly formatted as arrows indicating activation of downstream processes. This has now been amended in all versions of the Article.
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Affiliation(s)
- Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | | | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Koji Iwayama
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Center for Data Science Education and Research, Shiga University, Hikone, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan.
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Nagano AJ, Kawagoe T, Sugisaka J, Honjo MN, Iwayama K, Kudoh H. Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation. Nat Plants 2019; 5:74-83. [PMID: 30617252 DOI: 10.1038/s41477-018-0338-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/26/2018] [Indexed: 05/18/2023]
Abstract
As most organisms have evolved in seasonal environments, their environmental responses should be adapted to seasonal transitions. Here we show that the combination of temperature and day length shapes the seasonal dynamics of the transcriptome and adaptation to seasonal environments in a natural habitat of a perennial plant Arabidopsis halleri subsp. gemmifera. Weekly transcriptomes for two years and bihourly diurnal transcriptomes on the four equinoxes/solstices, identified 2,879 and 7,185 seasonally- and diurnally-oscillating genes, respectively. Dominance of annual temperature changes for defining seasonal oscillations of gene expressions was indicated by controlled environment experiments manipulating the natural 1.5-month lag of temperature behind day length. We found that plants have higher fitness in 'natural' chambers than in 'unnatural' chambers simulating in-phase and anti-phase oscillations between temperature and day length. Seasonal temperature responses were disturbed in unnatural chambers. Our results demonstrate how plants use multiple types of environmental information to adapt to seasonal environments.
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Affiliation(s)
- Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Japan
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
| | | | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Koji Iwayama
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Center for Data Science Education and Research, Shiga University, Hikone, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Japan.
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Aryal B, Shinohara W, Honjo MN, Kudoh H. Genetic differentiation in cauline-leaf-specific wettability of a rosette-forming perennial Arabidopsis from two contrasting montane habitats. Ann Bot 2018; 121:1351-1360. [PMID: 29579149 PMCID: PMC6007675 DOI: 10.1093/aob/mcy033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 02/22/2018] [Indexed: 05/09/2023]
Abstract
Background and Aims An altitudinal gradient of leaf wettability is often observed between and within species. To understand its functional significance, positional variation of leaf surfaces within plants should be taken into account. In rosette-forming plants, rosette leaves are near the ground and their adaxial surfaces are exposed, whereas cauline leaves are lifted from the ground throughout the reproductive season, and their abaxial surfaces are more exposed. Here, we investigated leaf wettability of cauline and rosette leaves of Arabidopsis halleri subsp. gemmifera growing in contrasting montane habitats along an altitudinal gradient at Mt Ibuki, Japan. Methods We conducted field investigations and a growth chamber experiment to determine whether field-observed variation in leaf wettability was caused by genetic differentiation. We further performed gene expression analysis of a wax-related gene, i.e. AhgCER1, a homologue of A. thaliana ECERIFERUM1 (CER1) that may be involved in differentiation of leaf wettability. Key Results We found cauline-leaf specific genetic differentiation in leaf wettability between contrasting montane habitats. Cauline leaves of semi-alpine plants, especially on abaxial surfaces, were non-wettable. Cauline leaves of low-altitudinal understorey plants were wettable, and rosette leaves were also wettable in both habitats. AhgCER1 expression corresponded to observed leaf wettability patterns. Conclusions Low wettability of cauline leaves is hypothesized to keep exposed surfaces dry when they are wrapping flowering buds in early spring, and presumably protects flowering buds from frost damage. The genetic system that controls wax content, specifically for cauline leaves, should be involved in the observed genetic differentiation, and AhgCER1 control is a strong candidate for the underlying genetic mechanism.
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Affiliation(s)
- Biva Aryal
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Wataru Shinohara
- Faculty of Education, Kagawa University, Saiwaicho, Takamatsu, Kagawa, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
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Sakaguchi S, Kimura T, Kyan R, Maki M, Nishino T, Ishikawa N, Nagano AJ, Honjo MN, Yasugi M, Kudoh H, Li P, Choi HJ, Chernyagina OA, Ito M. Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes. Ann Bot 2018; 121:489-500. [PMID: 29300816 PMCID: PMC5838820 DOI: 10.1093/aob/mcx182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS The processes and mechanisms underlying lineage diversification are major topics in evolutionary biology. Eurasian goldenrod species of the Solidago virgaurea complex show remarkable morphological and ecological diversity in the Japanese Archipelago, with ecotypic taxa well adapted to specific environments (climate, edaphic conditions and disturbance regimes). The species complex is a suitable model to investigate the evolutionary processes of actively speciating plant groups, due to its ability to evolve in relation to environmental adaptation and its historical population dynamics. METHODS Two chloroplast markers, 18 nuclear microsatellite markers and ddRAD-sequencing were used to infer population genetic demography of S. virgaurea complex with its related species/genera. KEY RESULTS Our analysis showed that populations in Japan form an evolutionary unit, which was genetically diverged from adjacent continental populations. The phylogenetic structure within the archipelago strongly corresponds to the geography, but interestingly there is no concordance between genetic structure and ecotypic boundaries; neighbouring populations of distinct ecotypes share a genetic background. CONCLUSIONS We propose that the traits specific to the ecotypic entities are maintained by natural selection or are very recently generated and have little effect on the genomes, making genome-wide genetic markers unsuitable for detecting ecotypic differentiation. Furthermore, some sporadically distributed taxa (found as rheophytes and alpine plants) were repeatedly generated from a more widespread taxon in geographically distant areas by means of selection. Overall, this study showed that the goldenrod complex has a high ability to evolve, enabling rapid ecological diversification over a recent timeframe.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, Japan
- For correspondence. E-mail
| | - Takuma Kimura
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Ryuta Kyan
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Masayuki Maki
- Botanical Gardens, Tohoku University, Kawauchi, Sendai, Japan
| | - Takako Nishino
- Graduate School of Science, Osaka Prefecture University, Osaka, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- JST CREST, Honcho, Kawaguchi, Saitama, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama, Myodaiji, Okazaki, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hyeok Jae Choi
- Department of Biology & Chemistry, Changwon National University, Changwon, Gyeongnam, Korea
| | - Olga A Chernyagina
- Kamchatka Branch of Pacific Geographical Institute, Petropavlovsk-Kamchatskyi, Russia
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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Kudoh H, Honjo MN, Nishio H, Sugisaka J. The Long-Term "In Natura" Study Sites of Arabidopsis halleri for Plant Transcription and Epigenetic Modification Analyses in Natural Environments. Methods Mol Biol 2018; 1830:41-57. [PMID: 30043363 DOI: 10.1007/978-1-4939-8657-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The majority of organismal phenomena show functional significance in the context of natural environments. However, we know little about how dynamic gene expression is controlled under natural complex conditions. One of the most attractive challenges in current biology is to understand organismal functions in natural environments. We established and have developed long-term "in natura" study sites of Arabidopsis halleri to evaluate precise control of gene expression in natural environments. At the sites, we monitored meteorological factors, recorded plant growth and phenology, and collected RNA and chromatin samples to investigate dynamics of transcription and epigenetic modifications. Here, we introduce the in natura study sites, especially with the emphasis on methodologies for setting up study sites in natural plant populations and collecting samples used in transcriptomics and epigenetics in natural environments. Although the methods introduced here need to be modified depending on situations of one's study systems, our case can be a model for planning new in natura studies.
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Affiliation(s)
- Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan.
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Haruki Nishio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Jiro Sugisaka
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
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12
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Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ, Honjo MN, Shimizu-Inatsugi R, Kudoh H, Shimizu KK, Isagi Y. The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha
(Myrtaceae). Mol Ecol 2017; 26:1515-1532. [DOI: 10.1111/mec.14016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/13/2016] [Accepted: 12/28/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Ayako Izuno
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Kanehiro Kitayama
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yusuke Onoda
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Yuki Tsujii
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Functional Genomics Center Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Atsushi J. Nagano
- Faculty of Agriculture; Ryukoku University; 1-5 Yokatani, Seta Ohe-cho Otsu Shiga 520-2194 Japan
- PRESTO, Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Mie N. Honjo
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Hiroshi Kudoh
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
- Center for Ecological Research; Kyoto University; 2-509-3 Hirano Otsu Shiga 520-2113 Japan
- Kihara Institute for Biological Research; Yokohama City University; 641-12 Maioka, Totsuka-ward Yokohama Kanagawa 244-0813 Japan
| | - Yuji Isagi
- Graduate School of Agriculture; Kyoto University; Kitashirakawa Oiwake-cho, Sakyo-ku Kyoto 606-8502 Japan
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13
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Penjor T, Mimura T, Kotoda N, Matsumoto R, Nagano AJ, Honjo MN, Kudoh H, Yamamoto M, Nagano Y. RAD-Seq analysis of typical and minor Citrus accessions, including Bhutanese varieties. Breed Sci 2016; 66:797-807. [PMID: 28163596 PMCID: PMC5282754 DOI: 10.1270/jsbbs.16059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/11/2016] [Indexed: 05/30/2023]
Abstract
We analyzed the reduced-representation genome sequences of Citrus species by double-digest restriction site-associated DNA sequencing (ddRAD-Seq) using 44 accessions, including typical and minor accessions, such as Bhutanese varieties. The results of this analysis using typical accessions were consistent with previous reports that citron, papeda, pummelo, and mandarin are ancestral species, and that most Citrus species are derivatives or hybrids of these four species. Citrus varieties often reproduce asexually and heterozygosity is highly conserved within each variety. Because this approach could readily detect conservation of heterozygosity, it was able to discriminate citrus varieties such as satsuma mandarin from closely related species. Thus, this method provides an inexpensive way to protect citrus varieties from unintended introduction and to prevent the provision of incorrect nursery stocks to customers. One Citrus variety in Bhutan was morphologically similar to Mexican lime and was designated as Himalayan lime. The current analysis confirmed the previous proposition that Mexican lime is a hybrid between papeda and citron, and also suggested that Himalayan lime is a probable hybrid between mandarin and citron. In addition to Himalayan lime, current analysis suggested that several accessions were formed by previously undescribed combinations.
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Affiliation(s)
- Tshering Penjor
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
- Renewable Natural Resources Research Centre Wengkhar,
Mongar,
Bhutan
| | - Takashi Mimura
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Nobuhiro Kotoda
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Ryoji Matsumoto
- Faculty of Agriculture, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
- JST PRESTO,
4-1-8, Honcho, Kawaguchi, Saitama 332-0012,
Japan
- Faculty of Agriculture, Ryukoku University,
1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194,
Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University,
509-3 2-chome, Hirano, Otsu, Shiga 520-2113,
Japan
| | - Masashi Yamamoto
- Faculty of Agriculture, Kagoshima University,
1-21-35 Korimoto, Kagoshima 890-0065,
Japan
| | - Yukio Nagano
- Analytical Research Center for Experimental Sciences, Saga University,
1 Honjo-machi, Saga 840-8502,
Japan
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14
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Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, Seki M, Kamiya A, Shiraki T, Carninci P, Asamizu E, Nishide H, Tanaka S, Park KI, Morita Y, Yokoyama K, Uchiyama I, Tanaka Y, Tabata S, Shinozaki K, Hayashizaki Y, Kohara Y, Suzuki Y, Sugano S, Fujiyama A, Iida S, Sakakibara Y. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun 2016; 7:13295. [PMID: 27824041 PMCID: PMC5105172 DOI: 10.1038/ncomms13295] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 09/21/2016] [Indexed: 12/18/2022] Open
Abstract
Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I. nil with a scaffold N50 of 2.88 Mb (contig N50 of 1.87 Mb), covering 98% of the 750 Mb genome. Scaffolds covering 91.42% of the assembly are anchored to 15 pseudo-chromosomes. The draft genome has enabled the identification and cataloguing of the Tpn1 family transposons, known as the major mutagen of I. nil, and analysing the dwarf gene, CONTRACTED, located on the genetic map published in 1956. Comparative genomics has suggested that a whole genome duplication in Convolvulaceae, distinct from the recent Solanaceae event, has occurred after the divergence of the two sister families.
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Affiliation(s)
- Atsushi Hoshino
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Eiji Nitasaka
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hideki Noguchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Tadasu Shin-I
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yohei Minakuchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Koda
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.,Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Asako Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Sachiko Tanaka
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kyeung-Il Park
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Horticulture &Life Science, Yeungnam University, Gyeongbuk 712-749, Korea
| | - Yasumasa Morita
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kohei Yokoyama
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yoshikazu Tanaka
- Suntory Global Innovation Center Ltd, Seika, Kyoto 619-0284, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Yuji Kohara
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 108-8639, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Shigeru Iida
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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15
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Kamitani M, Nagano AJ, Honjo MN, Kudoh H. RNA-Seq reveals virus-virus and virus-plant interactions in nature. FEMS Microbiol Ecol 2016; 92:fiw176. [PMID: 27549115 PMCID: PMC5854034 DOI: 10.1093/femsec/fiw176] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/10/2016] [Accepted: 08/16/2016] [Indexed: 11/17/2022] Open
Abstract
As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus-virus and virus-host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1 Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant-virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications.
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Affiliation(s)
- Mari Kamitani
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2914, Japan JST PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
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16
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Higashi T, Aoki K, Nagano AJ, Honjo MN, Fukuda H. Circadian Oscillation of the Lettuce Transcriptome under Constant Light and Light-Dark Conditions. Front Plant Sci 2016; 7:1114. [PMID: 27512400 PMCID: PMC4961695 DOI: 10.3389/fpls.2016.01114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/13/2016] [Indexed: 05/23/2023]
Abstract
Although, the circadian clock is a universal biological system in plants and it orchestrates important role of plant production such as photosynthesis, floral induction and growth, there are few such studies on cultivated species. Lettuce is one major cultivated species for both open culture and plant factories and there is little information concerning its circadian clock system. In addition, most of the relevant genes have not been identified. In this study, we detected circadian oscillation in the lettuce transcriptome using time-course RNA sequencing (RNA-Seq) data. Constant light (LL) and light-dark (LD) conditions were used to detect circadian oscillation because the circadian clock has some basic properties: one is self-sustaining oscillation under constant light and another is entrainment to environmental cycles such as light and temperature. In the results, 215 contigs were detected as common oscillating contigs under both LL and LD conditions. The 215 common oscillating contigs included clock gene-like contigs CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)-like, TOC1 (TIMING OF CAB EXPRESSION 1)-like and LHY (LATE ELONGATED HYPOCOTYL)-like, and their expression patterns were similar to those of Arabidopsis. Functional enrichment analysis by GO (gene ontology) Slim and GO Fat showed that the GO terms of response to light stimulus, response to stress, photosynthesis and circadian rhythms were enriched in the 215 common oscillating contigs and these terms were actually regulated by circadian clocks in plants. The 215 common oscillating contigs can be used to evaluate whether the gene expression pattern related to photosynthesis and optical response performs normally in lettuce.
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Affiliation(s)
- Takanobu Higashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Koh Aoki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsu, Japan
- Core Research for Evolutional Science and Technology – Japan Science and Technology AgencyKawaguchi, Japan
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture UniversitySakai, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
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17
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Tanigaki Y, Higashi T, Takayama K, Nagano AJ, Honjo MN, Fukuda H. Correction: Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory. PLoS One 2016; 11:e0150788. [PMID: 26962862 PMCID: PMC4786304 DOI: 10.1371/journal.pone.0150788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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18
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Hagiwara-Komoda Y, Choi SH, Sato M, Atsumi G, Abe J, Fukuda J, Honjo MN, Nagano AJ, Komoda K, Nakahara KS, Uyeda I, Naito S. Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses. Sci Rep 2016; 6:21411. [PMID: 26898356 PMCID: PMC4761962 DOI: 10.1038/srep21411] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/22/2016] [Indexed: 01/09/2023] Open
Abstract
RNA viruses use various strategies to condense their genetic information into small genomes. Potyviruses not only use the polyprotein strategy, but also embed an open reading frame, pipo, in the P3 cistron in the -1 reading frame. PIPO is expressed as a fusion protein with the N-terminal half of P3 (P3N-PIPO) via transcriptional slippage of viral RNA-dependent RNA polymerase (RdRp). We herein show that clover yellow vein virus (ClYVV) produces a previously unidentified factor, P3N-ALT, in the +1 reading frame via transcriptional slippage at a conserved G(1-2)A(6-7) motif, as is the case for P3N-PIPO. The translation of P3N-ALT terminates soon, and it is considered to be a C-terminal truncated form of P3. In planta experiments indicate that P3N-ALT functions in cell-to-cell movement along with P3N-PIPO. Hence, all three reading frames are used to produce functional proteins. Deep sequencing of ClYVV RNA from infected plants endorses the slippage by viral RdRp. Our findings unveil a virus strategy that optimizes the coding capacity.
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Affiliation(s)
| | - Sun Hee Choi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masanao Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Go Atsumi
- Iwate Biotechnology Research Center, Kitakami 024-0003, Japan
- National Institute of Advanced Industrial Science and Technology, Sapporo 062-8517, Japan
| | - Junya Abe
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Junya Fukuda
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
| | - Atsushi J. Nagano
- Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan
- Japan Science and Technology Agency, PRESTO, Kawaguchi 332-0012, Japan
- Faculty of Agriculture, Ryukoku University, Otsu 520-2194, Japan
| | - Keisuke Komoda
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenji S. Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Ichiro Uyeda
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Satoshi Naito
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
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19
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Higashi T, Tanigaki Y, Takayama K, Nagano AJ, Honjo MN, Fukuda H. Detection of Diurnal Variation of Tomato Transcriptome through the Molecular Timetable Method in a Sunlight-Type Plant Factory. Front Plant Sci 2016; 7:87. [PMID: 26904059 PMCID: PMC4744910 DOI: 10.3389/fpls.2016.00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/17/2016] [Indexed: 05/19/2023]
Abstract
The timing of measurement during plant growth is important because many genes are expressed periodically and orchestrate physiological events. Their periodicity is generated by environmental fluctuations as external factors and the circadian clock as the internal factor. The circadian clock orchestrates physiological events such as photosynthesis or flowering and it enables enhanced growth and herbivory resistance. These characteristics have possible applications for agriculture. In this study, we demonstrated the diurnal variation of the transcriptome in tomato (Solanum lycopersicum) leaves through molecular timetable method in a sunlight-type plant factory. Molecular timetable methods have been developed to detect periodic genes and estimate individual internal body time from these expression profiles in mammals. We sampled tomato leaves every 2 h for 2 days and acquired time-course transcriptome data by RNA-Seq. Many genes were expressed periodically and these expressions were stable across the 1st and 2nd days of measurement. We selected 143 time-indicating genes whose expression indicated periodically, and estimated internal time in the plant from these expression profiles. The estimated internal time was generally the same as the external environment time; however, there was a difference of more than 1 h between the two for some sampling points. Furthermore, the stress-responsive genes also showed weakly periodic expression, implying that they were usually expressed periodically, regulated by light-dark cycles as an external factor or the circadian clock as the internal factor, and could be particularly expressed when the plant experiences some specific stress under agricultural situations. This study suggests that circadian clock mediate the optimization for fluctuating environments in the field and it has possibilities to enhance resistibility to stress and floral induction by controlling circadian clock through light supplement and temperature control.
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Affiliation(s)
- Takanobu Higashi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture UniversitySakai, Japan
| | - Yusuke Tanigaki
- Graduate School of Engineering, Osaka Prefecture UniversitySakai, Japan
| | | | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku UniversityOtsu, Japan
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto UniversityOtsu, Japan
| | - Hirokazu Fukuda
- Graduate School of Engineering, Osaka Prefecture UniversitySakai, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencyKawaguchi, Japan
- *Correspondence: Hirokazu Fukuda
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20
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Tanigaki Y, Higashi T, Takayama K, Nagano AJ, Honjo MN, Fukuda H. Transcriptome Analysis of Plant Hormone-Related Tomato (Solanum lycopersicum) Genes in a Sunlight-Type Plant Factory. PLoS One 2015; 10:e0143412. [PMID: 26624004 PMCID: PMC4666670 DOI: 10.1371/journal.pone.0143412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 11/04/2015] [Indexed: 11/18/2022] Open
Abstract
In plant factories, measurements of plant conditions are necessary at an early stage of growth to predict harvest times of high value-added crops. Moreover, harvest qualities depend largely on environmental stresses that elicit plant hormone responses. However, the complexities of plant hormone networks have not been characterized under nonstress conditions. In the present study, we determined temporal expression profiles of all genes and then focused on plant hormone pathways using RNA-Seq analyses of gene expression in tomato leaves every 2 h for 48 h. In these experiments, temporally expressed genes were found in the hormone synthesis pathways for salicylic acid, abscisic acid, ethylene, and jasmonic acid. The timing of CAB expression 1 (TOC1) and abscisic acid insensitive 1 (ABA1) and open stomata 1 (OST1) control gating stomata. In this study, compare with tomato and Arabidopsis thaliana, expression patterns of TOC1 have similarity. In contrast, expression patterns of tomato ABI1 and OST1 had expression peak at different time. These findings suggest that the regulation of gating stomata does not depend predominantly on TOC1 and significantly reflects the extracellular environment. The present data provide new insights into relationships between temporally expressed plant hormone-related genes and clock genes under normal sunlight conditions.
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Affiliation(s)
- Yusuke Tanigaki
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takanobu Higashi
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Kotaro Takayama
- Faculty of Agriculture, National University Corporation Ehime University, Matsuyama, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, Otsu-shi, Shiga, Japan
- JST PRESTO, Honcho, Kawaguchi, Saitama, Japan
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Mie N. Honjo
- Center for Ecological Research, Kyoto University, Hirano, Otsu, Shiga, Japan
| | - Hirokazu Fukuda
- Department of Mechanical Engineering, Graduate School of Engineering, Osaka Prefecture University, Sakai, Osaka, Japan
- * E-mail:
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21
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Ushio M, Yamasaki E, Takasu H, Nagano AJ, Fujinaga S, Honjo MN, Ikemoto M, Sakai S, Kudoh H. Microbial communities on flower surfaces act as signatures of pollinator visitation. Sci Rep 2015; 5:8695. [PMID: 25733079 PMCID: PMC4346974 DOI: 10.1038/srep08695] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/02/2015] [Indexed: 11/30/2022] Open
Abstract
Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flower's surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 105 microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant–pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a “fingerprint” of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines.
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Affiliation(s)
- Masayuki Ushio
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Eri Yamasaki
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hiroyuki Takasu
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Atsushi J Nagano
- 1] Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan [2] PRESTO, Japan Science and Technology Agency, Japan
| | - Shohei Fujinaga
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Mito Ikemoto
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Shoko Sakai
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga 520-2113, Japan
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Abstract
Sequencing of RNA by next generation sequencers, RNA-Seq, is revolutionizing virus detection. In addition to the unbiased detection of various viruses from wild plants in natural environments, RNA-Seq also allows for the parallel collection of host plant transcriptome data. Host transcriptome data are highly valuable for studying the responses of hosts to viral infections, as well as viral host manipulation. When detecting viruses using RNA-Seq, it is critical to choose appropriate methods for the removal of rRNA from total RNA. Although viruses with polyadenylated genomes can be detected by RNA-Seq following mRNA purification using oligo-dT beads, viruses with non-polyadenylated genomes are not effectively detected. However, such viruses can be detected by RNA-Seq using the rRNA selective depression method. The high-throughput and cost-effective method of RNA-Seq library preparation which is described here allows us to detect a broad range of viruses in wild plants.
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Affiliation(s)
- Atsushi J Nagano
- Center for Ecological Research, Kyoto University, 2-509-3, Hirano, Otsu, Shiga, 520-2113, Japan,
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Uchii K, Minamoto T, Honjo MN, Kawabata Z. Seasonal reactivation enablesCyprinid herpesvirus 3to persist in a wild host population. FEMS Microbiol Ecol 2013; 87:536-42. [DOI: 10.1111/1574-6941.12242] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/29/2013] [Accepted: 10/22/2013] [Indexed: 12/01/2022] Open
Affiliation(s)
- Kimiko Uchii
- Department of General Systems Studies; The University of Tokyo; Meguro Tokyo Japan
- Research Institute for Humanity and Nature; Kita Kyoto Japan
| | - Toshifumi Minamoto
- Research Institute for Humanity and Nature; Kita Kyoto Japan
- Graduate School of Human Development and Environment; Kobe University; Nada Kobe Japan
| | - Mie N. Honjo
- Research Institute for Humanity and Nature; Kita Kyoto Japan
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Minamoto T, Honjo MN, Yamanaka H, Uchii K, Kawabata Z. Nationwide Cyprinid herpesvirus 3 contamination in natural rivers of Japan. Res Vet Sci 2012; 93:508-14. [DOI: 10.1016/j.rvsc.2011.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 06/07/2011] [Accepted: 06/08/2011] [Indexed: 11/30/2022]
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Uchii K, Telschow A, Minamoto T, Yamanaka H, Honjo MN, Matsui K, Kawabata Z. Transmission dynamics of an emerging infectious disease in wildlife through host reproductive cycles. ISME J 2010; 5:244-51. [PMID: 20740025 DOI: 10.1038/ismej.2010.123] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Emerging infectious diseases are major threats to wildlife populations. To enhance our understanding of the dynamics of these diseases, we investigated how host reproductive behavior and seasonal temperature variation drive transmission of infections among wild hosts, using the model system of cyprinid herpesvirus 3 (CyHV-3) disease in common carp. Our main findings were as follows: (1) a seroprevalence survey showed that CyHV-3 infection occurred mostly in adult hosts, (2) a quantitative assay for CyHV-3 in a host population demonstrated that CyHV-3 was most abundant in the spring when host reproduction occurred and water temperature increased simultaneously and (3) an analysis of the dynamics of CyHV-3 in water revealed that CyHV-3 concentration increased markedly in breeding habitats during host group mating. These results indicate that breeding habitats can become hot spots for transmission of infectious diseases if hosts aggregate for mating and the activation of pathogens occurs during the host breeding season.
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Affiliation(s)
- Kimiko Uchii
- Research Institute for Humanity and Nature, Kyoto, Japan.
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26
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Minamoto T, Honjo MN, Yamanaka H, Tanaka N, Itayama T, Kawabata Z. Detection of cyprinid herpesvirus-3 DNA in lake plankton. Res Vet Sci 2010; 90:530-2. [PMID: 20692005 DOI: 10.1016/j.rvsc.2010.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 06/15/2010] [Accepted: 07/03/2010] [Indexed: 10/19/2022]
Abstract
The disease caused by cyprinid herpesvirus-3 (CyHV-3) severely impacts the natural freshwater ecosystem and damages carp and koi farming, however, the pathway of CyHV-3 transmission remains unclear. It is possible that the virus adheres to plankton, which then facilitate viral movement and transmission, and therefore, it is hypothesised that plankton are involved in the disease dynamics. In this study, plankton were collected at eight sites in the Iba-naiko lagoon; we detected and quantified CyHV-3 DNA from plankton samples. The results of the correlation analysis showed a significant positive correlation between CyHV-3 copies and the number of Rotifera, suggesting that CyHV-3 binds to and/or is concentrated by Rotifera. Our results suggest that plankton affect viral ecology in the natural environment.
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Affiliation(s)
- Toshifumi Minamoto
- Research Institute for Humanity and Nature (RIHN), 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan.
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Minamoto T, Honjo MN, Uchii K, Yamanaka H, Suzuki AA, Kohmatsu Y, Iida T, Kawabata Z. Detection of cyprinid herpesvirus 3 DNA in river water during and after an outbreak. Vet Microbiol 2008; 135:261-6. [PMID: 19013729 DOI: 10.1016/j.vetmic.2008.09.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 09/26/2008] [Accepted: 09/29/2008] [Indexed: 10/21/2022]
Abstract
The disease caused by cyprinid herpesvirus 3 (CyHV-3) brings catastrophic damages to cultivated carp and koi and to natural carp populations; however, the dynamics of the virus in environmental waters are unclear. In July 2007, CyHV-3 DNA was detected in a dead common carp collected from the Yura River in Kyoto Prefecture, Japan, and this was followed by mass mortality. We collected water samples at eight sites along the Yura River for 3 months immediately after confirmation of the disease outbreak and attempted to detect and quantify CyHV-3 DNA in the water samples using molecular biological methods. The virus concentration was carried out by the cation-coated filter method, while the purification of DNA from the samples was achieved using phenol-chloroform extraction and a commercial DNA extraction kit. CyHV-3 was detected by PCR using six sets of conditions, three sets of primers (SphI-5, AP, and B22Rh exon 1), and two volumes of template DNA, and was quantified using real-time PCR. Our results indicate broader distribution of CyHV-3, even though dead fish were found only in a limited area; moreover, the virus was present at high levels in the river not only during the mass mortality caused by the disease but also for at least 3 months after the end of mass mortality. Our results suggest the possibility of infection by CyHV-3 via environmental water. The sequences of CyHV-3 collected from the Yura River matched perfectly with that of the CyHV-3 Japanese strain, suggesting that they share the same origin.
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Affiliation(s)
- Toshifumi Minamoto
- Research Institute for Humanity and Nature (RIHN), 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan.
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