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      KCI등재 SCOPUS SCIE

      Discovery and profiling of microRNAs and their targets in Paulownia ‘Yuza 1’ plants via high-throughput sequencing and degradome analysis

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      https://www.riss.kr/link?id=A104430756

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      다국어 초록 (Multilingual Abstract)

      Polyploid breeding is an effective method that has been used widely for the development of new varieties of plants. MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate gene expression at the posttranscriptional level. To understand the functions of miRNAs in autotetraploid and diploid Paulownia ‘Yuza 1’ plants, two small RNA libraries and two degradome sequencing libraries of the autotetraploid and the corresponding diploid plants were constructed and analyzed. A total of 49 conserved miRNAs that were grouped into 15 families, and 25 novel miRNAs were obtained from two sRNA libraries. Among these miRNAs, 28 were differentially expressed at a significant level in the autotetraploid relative to the diploid. Moreover, the miRNA target genes were identified by degradome sequencing and some of the differently expressed miRNAs and their target genes were validated by quantitative RT-PCR analysis. This study has provided valuable information on P. ‘Yuza 1’ miRNAs and their targets, which will enrich the Paulownia miRNA information resources and will contribute to our understanding of miRNA-mediated regulation in autotetraploid Paulownia plantlets.
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      Polyploid breeding is an effective method that has been used widely for the development of new varieties of plants. MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate gene expression at the posttranscriptional level. To understand t...

      Polyploid breeding is an effective method that has been used widely for the development of new varieties of plants. MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate gene expression at the posttranscriptional level. To understand the functions of miRNAs in autotetraploid and diploid Paulownia ‘Yuza 1’ plants, two small RNA libraries and two degradome sequencing libraries of the autotetraploid and the corresponding diploid plants were constructed and analyzed. A total of 49 conserved miRNAs that were grouped into 15 families, and 25 novel miRNAs were obtained from two sRNA libraries. Among these miRNAs, 28 were differentially expressed at a significant level in the autotetraploid relative to the diploid. Moreover, the miRNA target genes were identified by degradome sequencing and some of the differently expressed miRNAs and their target genes were validated by quantitative RT-PCR analysis. This study has provided valuable information on P. ‘Yuza 1’ miRNAs and their targets, which will enrich the Paulownia miRNA information resources and will contribute to our understanding of miRNA-mediated regulation in autotetraploid Paulownia plantlets.

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      참고문헌 (Reference)

      1 Frary A, "fw2.2: a quantitative trait locus key to the evolution of tomato fruit size" 289 : 85-88, 2000

      2 Niu S, "Transcriptome/Degradome-wide discovery of microRNAs and transcript targets in two Paulownia australis Genotypes" 9 : e106736-, 2014

      3 Audic S, "The significance of digital gene expression profiles" 7 : 986-995, 1997

      4 Doebley J, "The evolution of apical dominance in maize" 386 : 485-488, 1997

      5 Zhai X, "Study on Wood Physical Properties of Tetraploid Paulownia fortunei" 46 : 651-654, 2012

      6 Lu S, "Stress-responsive microRNAs in Populus" 55 : 131-151, 2008

      7 Lim KY, "Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years" 175 : 756-763, 2007

      8 Wu L, "Rice MicroRNA effector complexes and targets" 21 : 3421-3435, 2009

      9 Chen C, "Real-time quantification of microRNAs by stem-loop RT-PCR" 33 : e179-, 2005

      10 Ramsey J, "Polyploidy and ecological adaptation in wild yarrow" 108 : 7096-7101, 2011

      1 Frary A, "fw2.2: a quantitative trait locus key to the evolution of tomato fruit size" 289 : 85-88, 2000

      2 Niu S, "Transcriptome/Degradome-wide discovery of microRNAs and transcript targets in two Paulownia australis Genotypes" 9 : e106736-, 2014

      3 Audic S, "The significance of digital gene expression profiles" 7 : 986-995, 1997

      4 Doebley J, "The evolution of apical dominance in maize" 386 : 485-488, 1997

      5 Zhai X, "Study on Wood Physical Properties of Tetraploid Paulownia fortunei" 46 : 651-654, 2012

      6 Lu S, "Stress-responsive microRNAs in Populus" 55 : 131-151, 2008

      7 Lim KY, "Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years" 175 : 756-763, 2007

      8 Wu L, "Rice MicroRNA effector complexes and targets" 21 : 3421-3435, 2009

      9 Chen C, "Real-time quantification of microRNAs by stem-loop RT-PCR" 33 : e179-, 2005

      10 Ramsey J, "Polyploidy and ecological adaptation in wild yarrow" 108 : 7096-7101, 2011

      11 Zhang X, "Observation on microstructure of leaves and stress tolerance analysis of different Tetraploid Paulownia" 46 : 646-650, 2012

      12 Sunkar R, "Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis" 16 : 2001-2019, 2004

      13 Li X-Q, "Natural attributes and agricultural implications of somatic genome variation" 20 : 29-46, 2016

      14 Zhao M, "Involvement of miR169 in the nitrogen-starvation responses in Arabidopsis" 190 : 906-915, 2011

      15 Mackowiak SD, "Identification of novel and known miRNAs in deep-sequencing data with miRDeep2" 2011

      16 Ren Y, "Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress" 12 : 327-339, 2012

      17 Jin W, "Identification and verification of microRNA in wheat (Triticum aestivum)" 121 : 351-355, 2008

      18 Sarvepalli K, "Hyper-activation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation" 67 : 595-607, 2011

      19 Palin AC, "Human Neonatal Naive CD4^+ T Cells Have Enhanced Activation-Dependent Signaling Regulated by the MicroRNA miR-181a" 190 : 2682-2691, 2013

      20 Niu S, "High-throughput sequencing and degradome analysis reveal microRNA differential expression profiles and their targets in Paulownia fortunei" 119 : 457-468, 2014

      21 German MA, "Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends" 26 : 941-946, 2008

      22 Wang J, "Genomewide nonadditive gene regulation in Arabidopsis allotetraploids" 172 : 507-517, 2006

      23 Zhou ZS, "Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal" 35 : 86-99, 2012

      24 Li B, "Genome-wide characterization of new and drought stress responsive micro- RNAs in Populus euphratica" 62 : 3765-3779, 2011

      25 Dubcovsky J, "Genome plasticity a key factor in the success of polyploid wheat under domestication" 316 : 1862-1866, 2007

      26 Mallory AC, "Functions of microRNAs and related small RNAs in plants" 38 : S31-S36, 2006

      27 Addo-Quaye C, "Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome" 18 : 758-762, 2008

      28 Fan G, "Dynamic expression of novel and conserved microRNAs and their targets in diploid and tetraploid of Paulownia tomentosa" 102 : 68-77, 2014

      29 Ipekci Z, "Direct somatic embryogenesis and synthetic seed production from Paulownia elongata" 22 : 16-24, 2003

      30 Peng T, "Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa)" 62 : 4943-4954, 2011

      31 Ding D, "Differential expression of miRNAs in response to salt stress in maize roots" 103 : 29-38, 2009

      32 Meyers B, "Criteria for annotation of plant microRNAs" 20 : 3186-3190, 2008

      33 Palatnik JF, "Control of leaf morphogenesis by microRNAs" 425 : 257-263, 2003

      34 Sunkar R, "Cloning and characterization of microRNAs from rice" 17 : 1397-1411, 2005

      35 Zhang Q, "Characterization of resistance gene analogs with a nucleotide binding site isolated from a triploid white poplar" 10 : 310-322, 2008

      36 Lin C, "Catalog of Erycina pusilla miRNA and categorization of reproductive phase-related miRNAs and their target gene families" 82 : 193-204, 2013

      37 Mao W, "A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber" 7 : e33040-, 2012

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      학술지 이력
      연월일 이력구분 이력상세 등재구분
      2023 평가예정 해외DB학술지평가 신청대상 (해외등재 학술지 평가)
      2020-01-01 평가 등재학술지 유지 (해외등재 학술지 평가) KCI등재
      2015-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2012-05-07 학술지명변경 한글명 : 한국유전학회지 -> Genes & Genomics KCI등재
      2011-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2009-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2008-04-14 학술지명변경 외국어명 : Korean Journal of Genetics -> Genes and Genomics KCI등재
      2007-01-01 평가 등재학술지 유지 (등재유지) KCI등재
      2004-01-01 평가 등재학술지 선정 (등재후보2차) KCI등재
      2003-01-01 평가 등재후보 1차 PASS (등재후보1차) KCI등재후보
      2002-01-01 평가 등재후보학술지 유지 (등재후보1차) KCI등재후보
      1999-07-01 평가 등재후보학술지 선정 (신규평가) KCI등재후보
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      기준연도 WOS-KCI 통합IF(2년) KCIF(2년) KCIF(3년)
      2016 0.51 0.12 0.38
      KCIF(4년) KCIF(5년) 중심성지수(3년) 즉시성지수
      0.32 0.27 0.258 0.02
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