Additional file 14: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

Publication date

May 2018

DOI

10.6084/m9.figshare.6319364.v1

Abstract

Figure S8. Heat map representation and hierarchical clustering of putative genes involved in glycolysis/gluconeogenesis pathway and pentose phosphate pathway. A: glycolysis/gluconeogenesis pathway (ko00010). B: pentose phosphate pathway (ko00030). (TIF 2539 kb

Extracted data

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Additional file 14: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

Open link

Publication date

May 2018

DOI

10.6084/m9.figshare.6319364.v1

Abstract

Extracted data

Aruna Kilaru (438417)
Xia Cao (18213)
Parker Dabbs (3585512)
Ha-Jung Sung (3585503)
Md. Rahman (3413858)
Nicholas Thrower (3585506)
Greg Zynda (3585509)
Ram Podicheti (2142478)
Enrique Ibarra-Laclette (123694)
Luis Herrera-Estrella (123696)
Keithanne Mockaitis (57727)
John Ohlrogge (118853)

August 2015

Comparison of transcript levels for genes associated with early glycolysis in cytosol (C) and plasti...

Additional file 12: of Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells

Jaime Santo-Domingo (6385733)
Antonio Galindo (37856)
Ornella Cominetti (1392541)
Umberto De Marchi (2508685)
Pedro Cutillas (5704640)
Loïc Dayon (2440888)
Andreas Wiederkehr (3950591)

February 2019

Table S8. List of genes assigned to different trajectory clusters and used for gene ontology analysi...

Additional file 5: Figure S4. of ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage

Francisco Romero-Campero (3566084)
Ignacio Perez-Hurtado (3566087)
Eva Lucas-Reina (3566090)
Jose Romero (3566093)
Federico Valverde (3566096)

March 2016

Metabolic Pathways Contained in Cluster 1 (Orange) and 4 (Purple) from FigureÂ 4. Analysis of the Ch...

Additional file 7: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Pathways identified in the Sacha Inchi transcriptome. Three hundred and fifty-three KEGG pathways id...

Additional file 1: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Table S1. Overview of the sequencing data of the Sacha Inchi transcriptomes. (XLS 25 kb

Additional file 5: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S4. Histogram presentation of clusters of orthologous group classification of assembled unige...

Additional file 9: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Detailed FPKM and Annotation information of organ-specific unigenes. (XLS 646 kb

Additional file 8: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S6. The statistics of unigenes in eight organs. a) The percentage of unigenes expressed in ea...

Additional file 15: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Overview of the SSRs detected in the assembled unigenes of Sacha Inchi. (XLS 4872 kb

Additional file 11: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S7. Histogram presentation of the KEGG pathway annotation of female flower (FF)-specific gene...

Additional file 6: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S5. Distribution of gene ontology (GO) categories of unigenes for Sacha Inchi. GO functional ...

Additional file 2: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S1. Overview of Sacha Inchi transcriptome assembly and the characteristics of the homology se...

Additional file 10: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

The list of GO terms that were significantly enriched in male flowers, female flowers, roots, seeds ...

Additional file 3: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S2. The Pearson correlation coefficient (r) was used to estimate the difference between the r...

Additional file 17: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in α-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S9. Pearson correlation analysis of the gene expression ratios obtained from RNA-Seq and qPCR...

Additional file 6: Figure S4. of Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp

Aruna Kilaru (438417)
Xia Cao (18213)
Parker Dabbs (3585512)
Ha-Jung Sung (3585503)
Md. Rahman (3413858)
Nicholas Thrower (3585506)
Greg Zynda (3585509)
Ram Podicheti (2142478)
Enrique Ibarra-Laclette (123694)
Luis Herrera-Estrella (123696)
Keithanne Mockaitis (57727)
John Ohlrogge (118853)

August 2015

Comparison of transcript levels for genes associated with early glycolysis in cytosol (C) and plasti...

Additional file 12: of Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells

Jaime Santo-Domingo (6385733)
Antonio Galindo (37856)
Ornella Cominetti (1392541)
Umberto De Marchi (2508685)
Pedro Cutillas (5704640)
Loïc Dayon (2440888)
Andreas Wiederkehr (3950591)

February 2019

Table S8. List of genes assigned to different trajectory clusters and used for gene ontology analysi...

Francisco Romero-Campero (3566084)
Ignacio Perez-Hurtado (3566087)
Eva Lucas-Reina (3566090)
Jose Romero (3566093)
Federico Valverde (3566096)

March 2016

Metabolic Pathways Contained in Cluster 1 (Orange) and 4 (Purple) from FigureÂ 4. Analysis of the Ch...

Additional file 7: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Pathways identified in the Sacha Inchi transcriptome. Three hundred and fifty-three KEGG pathways id...

Additional file 1: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Table S1. Overview of the sequencing data of the Sacha Inchi transcriptomes. (XLS 25 kb

Additional file 5: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S4. Histogram presentation of clusters of orthologous group classification of assembled unige...

Additional file 9: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Detailed FPKM and Annotation information of organ-specific unigenes. (XLS 646 kb

Additional file 8: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S6. The statistics of unigenes in eight organs. a) The percentage of unigenes expressed in ea...

Additional file 15: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Overview of the SSRs detected in the assembled unigenes of Sacha Inchi. (XLS 4872 kb

Additional file 11: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S7. Histogram presentation of the KEGG pathway annotation of female flower (FF)-specific gene...

Additional file 6: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S5. Distribution of gene ontology (GO) categories of unigenes for Sacha Inchi. GO functional ...

Additional file 2: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S1. Overview of Sacha Inchi transcriptome assembly and the characteristics of the homology se...

Additional file 10: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

The list of GO terms that were significantly enriched in male flowers, female flowers, roots, seeds ...

Additional file 3: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S2. The Pearson correlation coefficient (r) was used to estimate the difference between the r...

Additional file 17: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in α-linolenic acid metabolism

Xiao-Di Hu (5258429)
Bang-Zhen Pan (5258435)
Qiantang Fu (5258423)
Longjian Niu (5258426)
Mao-Sheng Chen (5258438)
Zeng-Fu Xu (5258432)

May 2018

Figure S9. Pearson correlation analysis of the gene expression ratios obtained from RNA-Seq and qPCR...

Additional file 6: Figure S4. of Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp

Aruna Kilaru (438417)
Xia Cao (18213)
Parker Dabbs (3585512)
Ha-Jung Sung (3585503)
Md. Rahman (3413858)
Nicholas Thrower (3585506)
Greg Zynda (3585509)
Ram Podicheti (2142478)
Enrique Ibarra-Laclette (123694)
Luis Herrera-Estrella (123696)
Keithanne Mockaitis (57727)
John Ohlrogge (118853)

August 2015

Comparison of transcript levels for genes associated with early glycolysis in cytosol (C) and plasti...

Additional file 12: of Glucose-dependent phosphorylation signaling pathways and crosstalk to mitochondrial respiration in insulin secreting cells

Jaime Santo-Domingo (6385733)
Antonio Galindo (37856)
Ornella Cominetti (1392541)
Umberto De Marchi (2508685)
Pedro Cutillas (5704640)
Loïc Dayon (2440888)
Andreas Wiederkehr (3950591)

February 2019

Table S8. List of genes assigned to different trajectory clusters and used for gene ontology analysi...

Francisco Romero-Campero (3566084)
Ignacio Perez-Hurtado (3566087)
Eva Lucas-Reina (3566090)
Jose Romero (3566093)
Federico Valverde (3566096)

March 2016

Metabolic Pathways Contained in Cluster 1 (Orange) and 4 (Purple) from FigureÂ 4. Analysis of the Ch...

Additional file 14: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Abstract

Extracted data

Additional file 14: of De novo transcriptome assembly of the eight major organs of Sacha Inchi (Plukenetia volubilis) and the identification of genes involved in Îą-linolenic acid metabolism

Abstract

Extracted data

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