Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

Publication date

March 2016

DOI

10.6084/m9.figshare.c.3635057_d5.v1

Abstract

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0. 05, TMM-normalized FPKM > 0.3) unigenes from Armillaria mellea compared to juvenile tuber of G. elata. (PDF 125 kb

Extracted data

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Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

Open link

Publication date

March 2016

DOI

10.6084/m9.figshare.c.3635057_d5.v1

Abstract

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0. 05, TMM-normalized FPKM > 0.3) unigenes from Armillaria mellea compared to juvenile tuber of G. elata. (PDF 125 kb

Extracted data

N. Sierro (6032063)
J. Battey (6032069)
L. Bovet (6032075)
V. Liedschulte (6032081)
S. Ouadi (6032084)
J. Thomas (6032087)
H. Broye (6032090)
H. Laparra (6032093)
A. Vuarnoz (6032096)
G. Lang (6032099)
S. Goepfert (6032102)
M. Peitsch (6032105)
N. Ivanov (6032108)

November 2018

Figure S4. Phylogenic tree of the putrescine methyltransferaseÂ (a), cytochrome P450 nicotine N-deme...

Additional file 5: of Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors

Louise Thatcher (3525779)
Angela Williams (292362)
Gagan Garg (180909)
Sally-Anne Buck (3525776)
Karam Singh (3525773)

November 2016

Gene Ontology (GO) assignments associated with in planta upregulated DEGs. (XLSX 13 kb

Additional file 3: Table S1. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Sixty-nine unigenes were significantly up-regulated (log2-FC ≥1, q-value < 0.05, TMM-normalized FPKM...

Additional file 10: Table S7. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0.05, TMM-normalized FP...

Additional file 2: Figure S2. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Unigenes identified solely or both for Armillaria mellea and juvenile tuber of Gastrodia elata in th...

Additional file 9: Table S6. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

405 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > ...

Additional file 1: Table S1. of Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

Anita Dirks-Mulder (3859090)
Roland Butôt (3593165)
Peter van Schaik (3859102)
Jan Wijnands (3859084)
Roel van den Berg (3859087)
Louie Krol (3859096)
Sadhana Doebar (3859105)
Kelly van Kooperen (3859108)
Hugo de Boer (745485)
Elena Kramer (3859099)
Erik Smets (206615)
Rutger Vos (3504797)
Alexander Vrijdaghs (3859093)
Barbara Gravendeel (579289)

March 2017

List of sequences used in the alignments and phylogenetic analyses. Table S2. Transcript primer sequ...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 5: of Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium

Sana Khan (3626855)
Swati Upadhyay (3626858)
Feroz Khan (462714)
Sudeep Tandon (653852)
Rakesh Shukla (709813)
Sumit Ghosh (464456)
Vikrant Gupta (398109)
Suchitra Banerjee (3626852)
Laiq ur Rahman (1383300)

January 2017

List of tissue specific unigenes assigned to KEGG pathway with their KEGG IDs and Annotation for PYT...

Additional file 1 of Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734

Arburon Sulja (14071920)
Joël F. Pothier (12491626)
Jochen Blom (104512)
Chiaraluce Moretti (9075053)
Roberto Buonaurio (14071923)
Fabio Rezzonico (213623)
Theo H. M. Smits (11233824)

November 2022

Additional file 1: Text S1. Metabolic versatility in Pantoea agglomerans DAPP-PG 734. Table S1. Anti...

Additional file 1: Figure S1. of Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Anchal Garg (3525479)
Lalit Agrawal (1892533)
Rajesh Misra (3525482)
Shubha Sharma (3525476)
Sumit Ghosh (464456)

September 2015

Flow chart displaying strategies employed for de novo transcriptome analysis. Figure S2. Flow chart ...

Additional file 4: of Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus

Diana Sánchez-Rangel (5808863)
Eric-Edmundo Hernández-Domínguez (5808866)
Claudia-Anahí Pérez-Torres (5808869)
Randy Ortiz-Castro (5808872)
Emanuel Villafán (3585212)
Benjamín Rodríguez-Haas (4984823)
Alexandro Alonso-Sánchez (3585224)
Abel López-Buenfil (5808875)
Nayeli Carrillo-Ortiz (5808878)
Lervin Hernández-Ramos (5808881)
Enrique Ibarra-Laclette (123694)

October 2018

Figure S1. Metabolic network (and their corresponding pathways) represented in the nr-unigene set fr...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Additional file 5: of The impact of genome evolution on the allotetraploid Nicotiana rustica â an intriguing story of enhanced alkaloid production

N. Sierro (6032063)
J. Battey (6032069)
L. Bovet (6032075)
V. Liedschulte (6032081)
S. Ouadi (6032084)
J. Thomas (6032087)
H. Broye (6032090)
H. Laparra (6032093)
A. Vuarnoz (6032096)
G. Lang (6032099)
S. Goepfert (6032102)
M. Peitsch (6032105)
N. Ivanov (6032108)

November 2018

Figure S4. Phylogenic tree of the putrescine methyltransferaseÂ (a), cytochrome P450 nicotine N-deme...

Louise Thatcher (3525779)
Angela Williams (292362)
Gagan Garg (180909)
Sally-Anne Buck (3525776)
Karam Singh (3525773)

November 2016

Gene Ontology (GO) assignments associated with in planta upregulated DEGs. (XLSX 13 kb

Additional file 3: Table S1. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Sixty-nine unigenes were significantly up-regulated (log2-FC ≥1, q-value < 0.05, TMM-normalized FPKM...

Additional file 10: Table S7. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Mapping of KEGG biological pathways for up-regulated (log2-FC ≥ 1, q-value < 0.05, TMM-normalized FP...

Additional file 2: Figure S2. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

Unigenes identified solely or both for Armillaria mellea and juvenile tuber of Gastrodia elata in th...

Additional file 9: Table S6. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Chi-Chu Tsai (668824)
Keh-Ming Wu (174958)
Tzen-Yuh Chiang (138945)
Chun-Yen Huang (3548543)
Chang-Hung Chou (504877)
Shu-Ju Li (3548540)
Yu-Chung Chiang (114878)

March 2016

405 unigenes were significantly down-regulated (log2-FC ≤ -1, q-value < 0.05, TMM-normalized FPKM > ...

Additional file 1: Table S1. of Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system

Anita Dirks-Mulder (3859090)
Roland Butôt (3593165)
Peter van Schaik (3859102)
Jan Wijnands (3859084)
Roel van den Berg (3859087)
Louie Krol (3859096)
Sadhana Doebar (3859105)
Kelly van Kooperen (3859108)
Hugo de Boer (745485)
Elena Kramer (3859099)
Erik Smets (206615)
Rutger Vos (3504797)
Alexander Vrijdaghs (3859093)
Barbara Gravendeel (579289)

March 2017

List of sequences used in the alignments and phylogenetic analyses. Table S2. Transcript primer sequ...

Additional file 1: of De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Lokesh Narnoliya (3638002)
Girija Kaushal (3638005)
Sudhir Singh (619883)
Rajender Sangwan (174658)

January 2017

Figure S1. A phylogenetic tree generated on the basis of a plastid marker trnL-F in 57 Pelargonium s...

Additional file 5: of Comparative transcriptome analysis reveals candidate genes for the biosynthesis of natural insecticide in Tanacetum cinerariifolium

Sana Khan (3626855)
Swati Upadhyay (3626858)
Feroz Khan (462714)
Sudeep Tandon (653852)
Rakesh Shukla (709813)
Sumit Ghosh (464456)
Vikrant Gupta (398109)
Suchitra Banerjee (3626852)
Laiq ur Rahman (1383300)

January 2017

List of tissue specific unigenes assigned to KEGG pathway with their KEGG IDs and Annotation for PYT...

Additional file 1 of Comparative genomics to examine the endophytic potential of Pantoea agglomerans DAPP-PG 734

Arburon Sulja (14071920)
Joël F. Pothier (12491626)
Jochen Blom (104512)
Chiaraluce Moretti (9075053)
Roberto Buonaurio (14071923)
Fabio Rezzonico (213623)
Theo H. M. Smits (11233824)

November 2022

Additional file 1: Text S1. Metabolic versatility in Pantoea agglomerans DAPP-PG 734. Table S1. Anti...

Additional file 1: Figure S1. of Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes

Anchal Garg (3525479)
Lalit Agrawal (1892533)
Rajesh Misra (3525482)
Shubha Sharma (3525476)
Sumit Ghosh (464456)

September 2015

Flow chart displaying strategies employed for de novo transcriptome analysis. Figure S2. Flow chart ...

Additional file 4: of Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus

Diana Sánchez-Rangel (5808863)
Eric-Edmundo Hernández-Domínguez (5808866)
Claudia-Anahí Pérez-Torres (5808869)
Randy Ortiz-Castro (5808872)
Emanuel Villafán (3585212)
Benjamín Rodríguez-Haas (4984823)
Alexandro Alonso-Sánchez (3585224)
Abel López-Buenfil (5808875)
Nayeli Carrillo-Ortiz (5808878)
Lervin Hernández-Ramos (5808881)
Enrique Ibarra-Laclette (123694)

October 2018

Figure S1. Metabolic network (and their corresponding pathways) represented in the nr-unigene set fr...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Additional file 5: of The impact of genome evolution on the allotetraploid Nicotiana rustica â an intriguing story of enhanced alkaloid production

N. Sierro (6032063)
J. Battey (6032069)
L. Bovet (6032075)
V. Liedschulte (6032081)
S. Ouadi (6032084)
J. Thomas (6032087)
H. Broye (6032090)
H. Laparra (6032093)
A. Vuarnoz (6032096)
G. Lang (6032099)
S. Goepfert (6032102)
M. Peitsch (6032105)
N. Ivanov (6032108)

November 2018

Figure S4. Phylogenic tree of the putrescine methyltransferaseÂ (a), cytochrome P450 nicotine N-deme...

Louise Thatcher (3525779)
Angela Williams (292362)
Gagan Garg (180909)
Sally-Anne Buck (3525776)
Karam Singh (3525773)

November 2016

Gene Ontology (GO) assignments associated with in planta upregulated DEGs. (XLSX 13 kb

Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Abstract

Extracted data

Additional file 5: Table S3. of Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes

Abstract

Extracted data

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