Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica
Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequence...
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| Published in | PloS one Vol. 13; no. 3; p. e0193665 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
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Public Library of Science
12.03.2018
Public Library of Science (PLoS) |
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| Abstract | Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C. japonica. |
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| AbstractList | Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C . japonica . Deep sequencing of small RNAs (sRNAs) in developing male strobili of second-generation offspring originating from a nuclear genic male sterile tree of Cryptomeria japonica were performed to characterize sRNA populations in the male strobili at early pollen developmental stages. Comparing to sequences of microRNA (miRNA) families of plant species and sRNAs expressed in the reproductive organs of representative vascular plants, 37 conserved miRNA families were detected, of which eight were ubiquitously expressed in the reproductive organs of land plant species. In contrast, miR1083 was common in male reproductive organs of gymnosperm species but absent in angiosperm species. In addition to conserved miRNAs, 199 novel miRNAs candidates were predicted. The expression patterns of the obtained sRNAs were further investigated to detect the differentially expressed (DE) sRNAs between genic male sterile and fertile individuals. A total of 969 DE sRNAs were obtained and only three known miRNA families were included among them. These results suggest that both conserved and species-specific sRNAs contribute to the development of male strobili in C . japonica . |
| Audience | Academic |
| Author | Uchiyama, Kentaro Ujino-Ihara, Tokuko Ueno, Saneyoshi Futamura, Norihiro |
| AuthorAffiliation | University of Naples Federico II, ITALY Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan |
| AuthorAffiliation_xml | – name: University of Naples Federico II, ITALY – name: Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan |
| Author_xml | – sequence: 1 givenname: Tokuko orcidid: 0000-0002-9243-1638 surname: Ujino-Ihara fullname: Ujino-Ihara, Tokuko organization: Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan – sequence: 2 givenname: Saneyoshi surname: Ueno fullname: Ueno, Saneyoshi organization: Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan – sequence: 3 givenname: Kentaro surname: Uchiyama fullname: Uchiyama, Kentaro organization: Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan – sequence: 4 givenname: Norihiro surname: Futamura fullname: Futamura, Norihiro organization: Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Ibaraki, Japan |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29529051$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1186_s12864_019_6385_7 crossref_primary_10_1016_j_indcrop_2020_112724 crossref_primary_10_1016_j_plantsci_2024_111995 crossref_primary_10_1007_s00425_021_03568_6 crossref_primary_10_3389_fmicb_2018_02779 crossref_primary_10_3390_ijms22147246 crossref_primary_10_1016_j_pbi_2019_11_006 crossref_primary_10_1007_s00438_020_01689_3 crossref_primary_10_1007_s12298_021_01026_x |
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| Copyright | COPYRIGHT 2018 Public Library of Science 2018 Ujino-Ihara et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2018 Ujino-Ihara et al 2018 Ujino-Ihara et al |
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| SubjectTerms | Arabidopsis Biology and life sciences Biotechnology Cloning Cryptomeria japonica Cupressaceae Developmental stages Forest products Forestry Gene expression Genetic aspects Genomes Genomics Medicine and Health Sciences MicroRNAs miRNA Offspring Organs Oryza Plant reproduction Plants Pollen Properties Reproductive organs Research and analysis methods Ribonucleic acid RNA Species |
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| Title | Comprehensive analysis of small RNAs expressed in developing male strobili of Cryptomeria japonica |
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