Difference between revisions of "Jatropha curcas"

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==Description==
 
==Description==
−
[[File:REFqPCR2017005-1.jpg|right|327px|]]
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[[File:Jatropha curcas.png|right|200px|link=Jatropha curcas]]
−
* '''''Jatropha curcas''''' is a deciduous oil tree species and widely distributed in tropical and subtropical areas, especially in Central and South America, Africa, India and Southeast Asia. As one of the most important energy plants, J. curcas has been considered as a drought-resistant plant and can survive in marginal land. Possibly due to its tropical origin, J. curcas is a chilling sensitive plant and its sensitivity to chilling stress restricts its extensive cultivation and distribution, which further severely inhibits its cultivation and commercialization. <ref name="ref1"/> <ref name="ref2"/>.
+
* '''''Jatropha curcas''''' is a deciduous oil tree species and widely distributed in tropical and subtropical areas, especially in Central and South America, Africa, India and Southeast Asia. As one of the most important energy plants, J. curcas has been considered as a drought-resistant plant and can survive in marginal land. Possibly due to its tropical origin, J. curcas is a chilling sensitive plant and its sensitivity to chilling stress restricts its extensive cultivation and distribution, which further severely inhibits its cultivation and commercialization <ref name="ref1"/> <ref name="ref2"/>.
 
* <font color=blue>'''Common Name:'''</font> '''Physic nut'''
 
* <font color=blue>'''Common Name:'''</font> '''Physic nut'''
 
* [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=180498 <font color=blue>'''NCBI Taxonomy'''</font>]
 
* [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=180498 <font color=blue>'''NCBI Taxonomy'''</font>]
  
 
=='''''Staminate & Pistillate Flowers'''''==
 
=='''''Staminate & Pistillate Flowers'''''==
−
===Reference Genes===
+
===Internal Control Genes===
 
{|class="wikitable sortable" style="font-size:10pt; width:100%"
 
{|class="wikitable sortable" style="font-size:10pt; width:100%"
 
|-
 
|-
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|nowrap style="font-size:9pt"|
 
|nowrap style="font-size:9pt"|
 
* F:TTCTGGAATGGGAACTCTGTTGA
 
* F:TTCTGGAATGGGAACTCTGTTGA
−
* R:TTCTGGAATGGGAACTCTGTTGA
+
* R:TTGATGTACAGAAAGGGTGGCAT
 
|align="center"|  142  
 
|align="center"|  142  
 
|align="center"| 59 ~ 61
 
|align="center"| 59 ~ 61
Line 38: Line 38:
 
|nowrap style="font-size:9pt"|
 
|nowrap style="font-size:9pt"|
 
* F:GTCTGTTGAGATGCACCATGAAG
 
* F:GTCTGTTGAGATGCACCATGAAG
−
* R:GTCTGTTGAGATGCACCATGAAG
+
* R:TAGAGGCAACAAAACCACGTTTC
 
|align="center"|  108  
 
|align="center"|  108  
 
|align="center"| 59 ~ 61
 
|align="center"| 59 ~ 61
Line 50: Line 50:
 
|nowrap style="font-size:9pt"|
 
|nowrap style="font-size:9pt"|
 
* F:TCTGCTGATGCACCAATGTTTG
 
* F:TCTGCTGATGCACCAATGTTTG
−
* R:TCTGCTGATGCACCAATGTTTG
+
* R:ACCTTAGCAAGAGGAGCAAGAC
 
|align="center"|  116  
 
|align="center"|  116  
 
|align="center"| 59 ~ 61
 
|align="center"| 59 ~ 61
 
|align="center"| SYBR
 
|align="center"| SYBR
 
|}
 
|}
−
===Moleculer Types===
+
 
 +
===Molecular Types===
 
*mRNA
 
*mRNA
 
===Evaluation Methods===  
 
===Evaluation Methods===  
Line 70: Line 71:
  
 
===Citation Statistics===
 
===Citation Statistics===
−
Cited by '''2''' (Based on Google Scholar [2017-06-01])
+
Cited by [https://scholar.google.com/scholar?cites=10173178948383450853&as_sdt=2005&sciodt=0,5&hl=en '''3'''] (Based on Google Scholar [2017-09-01])
 +
 
 +
=='''''Different tissues & Developmental stages & Abiotic stress'''''==
 +
===Internal Control Genes===
 +
{|class="wikitable sortable" style="font-size:10pt; width:100%"
 +
|-
 +
! Gene Symbol 
 +
! Gene Name
 +
! style="width=25%　font-size:9pt　"|Application Scope
 +
! Accession Number
 +
! Primers (5'-3')<br>[Forward/Reverse]
 +
! Size [bp]
 +
! Tm [℃]
 +
! Detection
 +
|-
 +
|align="center"|actin <ref name="ref3"/>
 +
|align="center"|Actin
 +
|
 +
* Different developmental stages
 +
* Various abiotic stress treatments
 +
* Vegetative stage
 +
* Cold stress
 +
|align="center"| [http://www.kazusa.or.jp/jatropha/cgi-bin/orfinfo.cgi?db=jatropha&id=Jcr4S06558.10 '''Jcr4S06558.10''']
 +
|nowrap style="font-size:9pt"|
 +
* F:5'-CTCCTCTCAACCCCAAAGCCAA-3'
 +
* R:5'-CACCAGAATCCAGCACGATACCA-3'
 +
|align="center"|147 
 +
|align="center"|65
 +
|align="center"|SYBR
 +
|-
 +
|align="center"|GAPDH <ref name="ref3"/>
 +
|align="center"|Glyceraldehyde-3-phosphate dehydrogenase
 +
|
 +
* Different developmental stages
 +
* Abiotic stress treatments
 +
* Reproductive stage
 +
* Cold stress
 +
|align="center"| [http://www.kazusa.or.jp/jatropha/cgi-bin/orfinfo.cgi?db=jatropha&id=Jcr4U29393.10 '''Jcr4U29393.10''']
 +
|nowrap style="font-size:9pt"|
 +
* F:5'-TGAAGGACTGGAGAGGTGGAAGAGC-3'
 +
* R:5'-ATCAACAGTTGGAACACGGAAAGCC-3'
 +
|align="center"|140 
 +
|align="center"|65
 +
|align="center"|SYBR
 +
|-
 +
|align="center"|EF1α <ref name="ref3"/>
 +
|align="center"|Eukaryotic translation elongation factor 1 alpha 1
 +
|
 +
* Different developmental stages
 +
* Reproductive stage
 +
|align="center"| [http://www.kazusa.or.jp/jatropha/cgi-bin/orfinfo.cgi?db=jatropha&id=Jcr4S00542.10 '''Jcr4S00542.10''']
 +
|nowrap style="font-size:9pt"|
 +
* F:5'-AAGATGATTCCCACCAAGCCCA-3'
 +
* R:5'-CACAGCAAAACGACCCAGAGGA-3'
 +
|align="center"|72 
 +
|align="center"|65
 +
|align="center"|SYBR
 +
|-
 +
|align="center"|TUB5 <ref name="ref3"/>
 +
|align="center"|Tubulin beta-5 chain
 +
|
 +
* Desiccation stress
 +
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW878948.1 '''GW878948.1''']
 +
|nowrap style="font-size:9pt"|
 +
* F:5'-TATGTTCCCAGGGCGGTTCTAATG-3'
 +
* R:5'-GGACTGCCCAAAGACAAAGTTATCG-3'
 +
|align="center"|111
 +
|align="center"|65
 +
|align="center"|SYBR
 +
|-
 +
|align="center"|TUB8 <ref name="ref3"/>
 +
|align="center"|Tubulin beta 8
 +
|
 +
* Vegetative stage
 +
* Desiccation stress
 +
|align="center"| [https://www.ncbi.nlm.nih.gov/nucest/GW877086.1 '''GW877086.1''']
 +
|nowrap style="font-size:9pt"|
 +
* F:5'-GCAGGGAATAACTGGGCTAAAGGT-3'
 +
* R:5'-CTCCACCCAACGAATGACAAACTT-3'
 +
|align="center"|136
 +
|align="center"|65
 +
|align="center"|SYBR
 +
|}
 +
 
 +
===Molecular Types===
 +
*mRNA
 +
 
 +
===Evaluation Methods===
 +
* [https://genorm.cmgg.be/ '''geNorm method''']  && [https://www.ncbi.nlm.nih.gov/pubmed/12184808 '''Related Reference''']
 +
* [http://www.biogazelle.com/qbaseplus '''qBase'''] && [https://www.ncbi.nlm.nih.gov/pubmed/?term=23977142 '''Related Reference''']
 +
 
 +
===Contact===
 +
*'''Name''': Zeng-Fu Xu
 +
*'''Email''': zfxu@xtbg.ac.cn
 +
*'''Institution''': Key Laboratory of Tropica l Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China
 +
 
 +
===Citation Statistics===
 +
Cited by [https://scholar.google.com.hk/scholar?cites=6468203890798931038&as_sdt=2005&sciodt=0,5&hl=en '''31'''] (Based on Google Scholar [2017-10-15])
  
 
=='''References'''==
 
=='''References'''==
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Peng X, Wang Q, Liu H, Shen S (2017) Phylogenetic and functional analysis of the basic transcription factor gene BTF3 from Jatropha curcas. Plant Growth Regulation 82, 247-257
 
Peng X, Wang Q, Liu H, Shen S (2017) Phylogenetic and functional analysis of the basic transcription factor gene BTF3 from Jatropha curcas. Plant Growth Regulation 82, 247-257
 
</ref>
 
</ref>
 +
<ref name="ref3">
 +
Zhang L, He LL, Fu QT, Xu ZF. Selection of reliable reference genes for gene expression studies in the biofuel plant Jatropha curcas using real-time quantitative PCR. Int J Mol Sci. 2013 Dec 13;14(12):24338-54. doi: 10.3390/ijms141224338</ref>
 
</references>
 
</references>
  
 +
=='''Categories'''==
 
[[Category:Plants]]
 
[[Category:Plants]]
−
[[Category:mRNA]]　
+
[[Category:mRNA]][[Category:SYBR]]
−
[[Category:SYBR]]
 
 
[[Category:EF1α]] [[Category:GAPDH]] [[Category:Tubulin]]
 
[[Category:EF1α]] [[Category:GAPDH]] [[Category:Tubulin]]
 
[[Category:Specific Tissue]]
 
[[Category:Specific Tissue]]
 +
[[Category:geNorm]]
 +
[[Category:NormFinder]]
 +
[[Category:BestKeeper]]
 +
[[Category:Delta Ct]]
 +
[[Category:RefFinder]]

Latest revision as of 04:04, 21 October 2017

Description

Jatropha curcas.png
  • Jatropha curcas is a deciduous oil tree species and widely distributed in tropical and subtropical areas, especially in Central and South America, Africa, India and Southeast Asia. As one of the most important energy plants, J. curcas has been considered as a drought-resistant plant and can survive in marginal land. Possibly due to its tropical origin, J. curcas is a chilling sensitive plant and its sensitivity to chilling stress restricts its extensive cultivation and distribution, which further severely inhibits its cultivation and commercialization [1] [2].
  • Common Name: Physic nut
  • NCBI Taxonomy

Staminate & Pistillate Flowers

Internal Control Genes

Gene Symbol Gene Name Application Scope Accession Number Primers (5'-3')
[Forward/Reverse] 		Size [bp] Tm [℃] Detection
TUB[1] Tubulin beta-5 chain
  • Staminate flower
 XM_012218098.1
  • F:TTCTGGAATGGGAACTCTGTTGA
  • R:TTGATGTACAGAAAGGGTGGCAT
 142 59 ~ 61 SYBR
EF[1] Elongation factor 1-alpha
  • Staminate flower
  • Pistillate flowers
 XM_012226913.1
  • F:GTCTGTTGAGATGCACCATGAAG
  • R:TAGAGGCAACAAAACCACGTTTC
 108 59 ~ 61 SYBR
GAPDH1[1] Glyceraldehyde 3-phosphate dehydrogenase
  • Pistillate flowers
 XM_012231954.1
  • F:TCTGCTGATGCACCAATGTTTG
  • R:ACCTTAGCAAGAGGAGCAAGAC
 116 59 ~ 61 SYBR

Molecular Types

  • mRNA

Evaluation Methods

Contact

  • Name: Fang Chen
  • Email: fangchenscu@163.com
  • Institution: Department of Botany, Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, Sichuan University, Chengdu, China

Citation Statistics

Cited by 3 (Based on Google Scholar [2017-09-01])

Different tissues & Developmental stages & Abiotic stress

Internal Control Genes

Gene Symbol Gene Name Application Scope Accession Number Primers (5'-3')
[Forward/Reverse] 		Size [bp] Tm [℃] Detection
actin [3] Actin
  • Different developmental stages
  • Various abiotic stress treatments
  • Vegetative stage
  • Cold stress
 Jcr4S06558.10
  • F:5'-CTCCTCTCAACCCCAAAGCCAA-3'
  • R:5'-CACCAGAATCCAGCACGATACCA-3'
 147 65 SYBR
GAPDH [3] Glyceraldehyde-3-phosphate dehydrogenase
  • Different developmental stages
  • Abiotic stress treatments
  • Reproductive stage
  • Cold stress
 Jcr4U29393.10
  • F:5'-TGAAGGACTGGAGAGGTGGAAGAGC-3'
  • R:5'-ATCAACAGTTGGAACACGGAAAGCC-3'
 140 65 SYBR
EF1α [3] Eukaryotic translation elongation factor 1 alpha 1
  • Different developmental stages
  • Reproductive stage
 Jcr4S00542.10
  • F:5'-AAGATGATTCCCACCAAGCCCA-3'
  • R:5'-CACAGCAAAACGACCCAGAGGA-3'
 72 65 SYBR
TUB5 [3] Tubulin beta-5 chain
  • Desiccation stress
 GW878948.1
  • F:5'-TATGTTCCCAGGGCGGTTCTAATG-3'
  • R:5'-GGACTGCCCAAAGACAAAGTTATCG-3'
 111 65 SYBR
TUB8 [3] Tubulin beta 8
  • Vegetative stage
  • Desiccation stress
 GW877086.1
  • F:5'-GCAGGGAATAACTGGGCTAAAGGT-3'
  • R:5'-CTCCACCCAACGAATGACAAACTT-3'
 136 65 SYBR

Molecular Types

  • mRNA

Evaluation Methods

Contact

  • Name: Zeng-Fu Xu
  • Email: zfxu@xtbg.ac.cn
  • Institution: Key Laboratory of Tropica l Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, Yunnan, China

Citation Statistics

Cited by 31 (Based on Google Scholar [2017-10-15])

References

  1. ↑ 1.0 1.1 1.2 1.3 Karuppaiya P, Yan XX, Liao W, et al. (2017) Identification and validation of superior reference gene for gene expression normalization via RT-qPCR in staminate and pistillate flowers of Jatropha curcas - A biodiesel plant. PLoS One 12, e0172460
  2. ↑ Peng X, Wang Q, Liu H, Shen S (2017) Phylogenetic and functional analysis of the basic transcription factor gene BTF3 from Jatropha curcas. Plant Growth Regulation 82, 247-257
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Zhang L, He LL, Fu QT, Xu ZF. Selection of reliable reference genes for gene expression studies in the biofuel plant Jatropha curcas using real-time quantitative PCR. Int J Mol Sci. 2013 Dec 13;14(12):24338-54. doi: 10.3390/ijms141224338

Categories

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