Additional file 5: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

Publication date

February 2018

DOI

10.6084/m9.figshare.5902939.v1

Abstract

Manual curation of the genomic regions surrounding MIC1 genes in Brachypodium and rice. (A) MIC1 NLR-IDs and surrounding genes. (B) Additional microsynteny analyses between rice and B. distachyon. (PPTX 150 kb

Extracted data

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Data Protection

Additional file 5: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

Open link

Publication date

February 2018

DOI

10.6084/m9.figshare.5902939.v1

Abstract

Extracted data

Lei Tian (369281)
Shaohua Shi (553560)
Fahad Nasir (5126789)
Chunling Chang (4593529)
Weiqiang Li (1646440)
Lam-Son Tran (5126786)
Chunjie Tian (607531)

April 2018

Figure S4. MapMan analysis of the genes and pathways responsive to the pathogenic invasion using the...

Additional file 9: Figure S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Ratio distribution of Nipponbare or Minghui63 highly expressed genes to every 100 mapped genes. (PDF...

Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49...

Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight gras...

Additional file 14: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

All NLR-IDs found in nine grasses (e-value at relaxed cut-offâ<â0.05), including the genes that ...

Additional file 13: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Bar plot of number of NLRs in each clade and percent of NLRs from each clade that overlap with predi...

Additional file 15: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

The alignment of NB, ARC1, and ARC2 used to train the HMM for NLR proteins used for phylogenetic ana...

Additional file 1: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Quality assessment of the gene datasets used for phylogenetic analysis: N50 and size of the correspo...

Additional file 2: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Clade memberships of all NLRs present in the tree in Fig.Â 1 and corresponding integrated domains pr...

Additional file 12: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

The AP2b/MYB-NLR domain shuffling includes duplication of AP2 gene and inter-chromosomal transfer of...

Additional file 11: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Potential donor - NLR acceptor gene sets, as observed from phylogenetic trees of the donor ID genes....

Additional file 3: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Maximum likelihood phylogeny based on the NB-ARC domain of all NLRs and NLR-IDs for each of the nine...

Data for: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4742760)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (3861778)
Ksenia Krasileva (3435623)

January 2018

This Figshare project contains data for paper entitled "Dominant integration locus drives continuous...

Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb

Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in th...

Lei Tian (369281)
Shaohua Shi (553560)
Fahad Nasir (5126789)
Chunling Chang (4593529)
Weiqiang Li (1646440)
Lam-Son Tran (5126786)
Chunjie Tian (607531)

April 2018

Figure S4. MapMan analysis of the genes and pathways responsive to the pathogenic invasion using the...

Additional file 9: Figure S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Ratio distribution of Nipponbare or Minghui63 highly expressed genes to every 100 mapped genes. (PDF...

Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49...

Additional file 4: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Locations, gene identifiers, and tandem classifications for all discovered tandem NLRs in eight gras...

Additional file 14: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

All NLR-IDs found in nine grasses (e-value at relaxed cut-offâ<â0.05), including the genes that ...

Additional file 13: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Bar plot of number of NLRs in each clade and percent of NLRs from each clade that overlap with predi...

Additional file 15: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

The alignment of NB, ARC1, and ARC2 used to train the HMM for NLR proteins used for phylogenetic ana...

Additional file 1: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Quality assessment of the gene datasets used for phylogenetic analysis: N50 and size of the correspo...

Additional file 2: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Clade memberships of all NLRs present in the tree in Fig.Â 1 and corresponding integrated domains pr...

Additional file 12: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

The AP2b/MYB-NLR domain shuffling includes duplication of AP2 gene and inter-chromosomal transfer of...

Additional file 11: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Potential donor - NLR acceptor gene sets, as observed from phylogenetic trees of the donor ID genes....

Additional file 3: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4864429)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (4822788)
Ksenia Krasileva (3435623)

February 2018

Maximum likelihood phylogeny based on the NB-ARC domain of all NLRs and NLR-IDs for each of the nine...

Data for: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Paul Bailey (4742760)
Christian Schudoma (4746453)
William Jackson (253435)
Erin Baggs (4746450)
Gulay Dagdas (3435620)
Wilfried Haerty (3539540)
Matthew Moscou (3861778)
Ksenia Krasileva (3435623)

January 2018

This Figshare project contains data for paper entitled "Dominant integration locus drives continuous...

Additional file 15: Table S7. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of global jiDE genes of the NM combination. (XLSX 57Â kb) (XLSX 52Â kb

Additional file 5: Table S3. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Highly expressed genes and the two types of jiDE genes of the two japonica-indica combinations in th...

Lei Tian (369281)
Shaohua Shi (553560)
Fahad Nasir (5126789)
Chunling Chang (4593529)
Weiqiang Li (1646440)
Lam-Son Tran (5126786)
Chunjie Tian (607531)

April 2018

Figure S4. MapMan analysis of the genes and pathways responsive to the pathogenic invasion using the...

Additional file 9: Figure S5. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

Ratio distribution of Nipponbare or Minghui63 highly expressed genes to every 100 mapped genes. (PDF...

Additional file 17: Table S9. of Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

Youko Horiuchi (3578636)
Yoshiaki Harushima (3578639)
Hironori Fujisawa (20354)
Takako Mochizuki (3370862)
Masahiro Fujita (355423)
Hajime Ohyanagi (14083)
Nori Kurata (233527)

December 2015

GO enrichment analysis of tissue specific changed-tissues jiDE genes of the NM combination. (XLSX 49...

Additional file 5: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Abstract

Extracted data

Additional file 5: of Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions

Abstract

Extracted data

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