Additional file 1: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

Open link

Publication date

August 2018

DOI

10.6084/m9.figshare.6963791.v1

Abstract

Table S1. Primer sequences of candidate genes on polyembryonic locus for RT-PCR. (XLSX 10 kb

Extracted data

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Additional file 1: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

Open link

Publication date

August 2018

DOI

10.6084/m9.figshare.6963791.v1

Abstract

Table S1. Primer sequences of candidate genes on polyembryonic locus for RT-PCR. (XLSX 10 kb

Extracted data

G. Mott (3567821)
Shalabh Thakur (3524480)
Elwira Smakowska (3567818)
Pauline Wang (3567824)
Youssef Belkhadir (3567827)
Darrell Desveaux (69192)
David Guttman (3524483)

May 2016

Confirmation of T-DNA insertions for two independent xps1 T-DNA insertion lines. a T-DNA insertion p...

Additional file 9: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S8. List of DC-clusters differentially expressed (DE) in galls versus uninfected root at 7 and...

Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S6. List of DC-clusters differentially expressed (DE) in galls versus uninfected roots at 7 dp...

Additional file 2: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

August 2018

Table S2. Highly expressed genes in polyembryonic reproductive tissues selected by microarray analys...

Additional file 3: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

August 2018

Table S3. Weakly expressed genes in polyembryonic reproductive tissues selected by microarray analys...

Additional file 6: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Table S2. Information of newly inserted MITEs in different genomic regions of three Citrus species. ...

Additional file 5: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Table S1. Information of conserved and non-conserved MITEs insertion between different genomic regio...

Additional file 4: of Comparative analysis of miniature inverted–repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Figure S4. Manually confirmed DTM63 insertion sites. (A) Manually confirmed case of C. grandis. (B)....

Additional file 2: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Figure S2. The pipeline of LTR retrotransposons classification and annotation. (DOCX 475 kb

Additional file 5: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S4. Lists of DC-clusters exclusively expressed in galls or roots at 7 and 14 dpi and located w...

Additional file 4: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S3. Lists of DC-clusters differentially expressed in galls at 7 and 14 dpi and located within ...

Additional file 1: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

Diogo MagalhĂŁes (3522338)
Larissa Scholte (3466481)
Nicholas Silva (3522335)
Guilherme Oliveira (128322)
Cyril Zipfel (223013)
Marco Takita (3497726)
Alessandra De Souza (3522332)

August 2016

Amino acid sequences from Arabidopsis thaliana LRR-RLKs. Dataset containing 209 LRR-RLK sequences ob...

Additional file 1: of Development of leafhopper cell culture to trace the early infection process of a nucleorhabdovirus, rice yellow stunt virus, in insect vector cells

Haitao Wang (165102)
Juan Wang (115708)
Yunjie Xie (5126780)
Zhijun Fu (5126777)
Taiyun Wei (123590)
Xiao-Feng Zhang (597472)

April 2018

Sequences of the forward primer and reverse primer for RYSV N, P, M and Nephotettix cincticeps actin...

Additional file 3: Table S1. of New insights into the roles of cucumber TIR1 homologs and miR393 in regulating fruit/seed set development and leaf morphogenesis

Jian Xu (31545)
Ji Li (207201)
Li Cui (37567)
Ting Zhang (102583)
Zhe Wu (582498)
Pin-Yu Zhu (4279495)
Yong-Jiao Meng (4279504)
Kai-Jing Zhang (4279507)
Xia-Qing Yu (4279498)
Qun-Feng Lou (4279492)
Jin-Feng Chen (4279501)

July 2017

The oligonucleotide primer for qRT-PCR and semi-quantitative RT-PCR. (DOCX 14Â kb

Additional file 3: Table S1. of Expression and functional analysis of citrus carotene hydroxylases: unravelling the xanthophyll biosynthesis in citrus fruits

Gang Ma (52569)
Lancui Zhang (1548157)
Witchulada Yungyuen (3495725)
Issei Tsukamoto (3495728)
Natsumi Iijima (3495722)
Michiru Oikawa (3495719)
Kazuki Yamawaki (1548163)
Masaki Yahata (1548160)
Masaya Kato (462514)

June 2016

Primer sequences used for isolating full-length cDNAs of CitCYP97A, CitCYP97B, CitCYP97C. (DOCX 12 k...

G. Mott (3567821)
Shalabh Thakur (3524480)
Elwira Smakowska (3567818)
Pauline Wang (3567824)
Youssef Belkhadir (3567827)
Darrell Desveaux (69192)
David Guttman (3524483)

May 2016

Confirmation of T-DNA insertions for two independent xps1 T-DNA insertion lines. a T-DNA insertion p...

Additional file 9: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S8. List of DC-clusters differentially expressed (DE) in galls versus uninfected root at 7 and...

Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S6. List of DC-clusters differentially expressed (DE) in galls versus uninfected roots at 7 dp...

Additional file 2: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

August 2018

Table S2. Highly expressed genes in polyembryonic reproductive tissues selected by microarray analys...

Additional file 3: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Takehiko Shimada (746854)
Tomoko Endo (5626490)
Hiroshi Fujii (289510)
Michiharu Nakano (5626493)
Aiko Sugiyama (5626496)
Genya Daido (5626499)
Satoshi Ohta (3098031)
Terutaka Yoshioka (3098025)
Mitsuo Omura (5626502)

August 2018

Table S3. Weakly expressed genes in polyembryonic reproductive tissues selected by microarray analys...

Additional file 6: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Table S2. Information of newly inserted MITEs in different genomic regions of three Citrus species. ...

Additional file 5: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Table S1. Information of conserved and non-conserved MITEs insertion between different genomic regio...

Additional file 4: of Comparative analysis of miniature inverted–repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Figure S4. Manually confirmed DTM63 insertion sites. (A) Manually confirmed case of C. grandis. (B)....

Additional file 2: of Comparative analysis of miniature invertedârepeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species

Yan Liu (25061)
Muhammad Tahir ul Qamar (810497)
Jia-Wu Feng (6590777)
Yuduan Ding (6590780)
Shuo Wang (143908)
Guizhi Wu (3489674)
Lingjun Ke (6590783)
Qiang Xu (71522)
Ling-Ling Chen (47327)

April 2019

Figure S2. The pipeline of LTR retrotransposons classification and annotation. (DOCX 475 kb

Additional file 5: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S4. Lists of DC-clusters exclusively expressed in galls or roots at 7 and 14 dpi and located w...

Additional file 4: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S3. Lists of DC-clusters differentially expressed in galls at 7 and 14 dpi and located within ...

Additional file 1: of LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects

Diogo MagalhĂŁes (3522338)
Larissa Scholte (3466481)
Nicholas Silva (3522335)
Guilherme Oliveira (128322)
Cyril Zipfel (223013)
Marco Takita (3497726)
Alessandra De Souza (3522332)

August 2016

Amino acid sequences from Arabidopsis thaliana LRR-RLKs. Dataset containing 209 LRR-RLK sequences ob...

Additional file 1: of Development of leafhopper cell culture to trace the early infection process of a nucleorhabdovirus, rice yellow stunt virus, in insect vector cells

Haitao Wang (165102)
Juan Wang (115708)
Yunjie Xie (5126780)
Zhijun Fu (5126777)
Taiyun Wei (123590)
Xiao-Feng Zhang (597472)

April 2018

Sequences of the forward primer and reverse primer for RYSV N, P, M and Nephotettix cincticeps actin...

Additional file 3: Table S1. of New insights into the roles of cucumber TIR1 homologs and miR393 in regulating fruit/seed set development and leaf morphogenesis

Jian Xu (31545)
Ji Li (207201)
Li Cui (37567)
Ting Zhang (102583)
Zhe Wu (582498)
Pin-Yu Zhu (4279495)
Yong-Jiao Meng (4279504)
Kai-Jing Zhang (4279507)
Xia-Qing Yu (4279498)
Qun-Feng Lou (4279492)
Jin-Feng Chen (4279501)

July 2017

The oligonucleotide primer for qRT-PCR and semi-quantitative RT-PCR. (DOCX 14Â kb

Additional file 3: Table S1. of Expression and functional analysis of citrus carotene hydroxylases: unravelling the xanthophyll biosynthesis in citrus fruits

Gang Ma (52569)
Lancui Zhang (1548157)
Witchulada Yungyuen (3495725)
Issei Tsukamoto (3495728)
Natsumi Iijima (3495722)
Michiru Oikawa (3495719)
Kazuki Yamawaki (1548163)
Masaki Yahata (1548160)
Masaya Kato (462514)

June 2016

Primer sequences used for isolating full-length cDNAs of CitCYP97A, CitCYP97B, CitCYP97C. (DOCX 12 k...

G. Mott (3567821)
Shalabh Thakur (3524480)
Elwira Smakowska (3567818)
Pauline Wang (3567824)
Youssef Belkhadir (3567827)
Darrell Desveaux (69192)
David Guttman (3524483)

May 2016

Confirmation of T-DNA insertions for two independent xps1 T-DNA insertion lines. a T-DNA insertion p...

Additional file 9: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S8. List of DC-clusters differentially expressed (DE) in galls versus uninfected root at 7 and...

Additional file 7: of Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita

ClĂŠmence Medina (6100826)
Martine da Rocha (6100817)
Marc Magliano (223262)
AlizĂŠe Raptopoulo (6100829)
Nathalie Marteu (6100823)
Kevin Lebrigand (138002)
Pierre Abad (115959)
Bruno Favery (190085)
StĂŠphanie Jaubert-Possamai (6100832)

December 2018

Table S6. List of DC-clusters differentially expressed (DE) in galls versus uninfected roots at 7 dp...

Additional file 1: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Abstract

Extracted data

Additional file 1: of MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Abstract

Extracted data

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