By organism › Green plants › Amborellaceae

Observationobservedoriginal resultmeasured

Claim · model-written summary

Gene retention in Amborella and Aristolochia reveals a single gene duplication peak predating seed plant diversification.

Taxon: Amborella and AristolochiaAristolochiaAmborellae1
Outcome: a single gene duplication peake1
Qualifier: predating the seed plant diversificatione1

Verbatim

e1
“gene retention patterns in Amborella and Aristolochia —early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD”
✓ located verbatim in the source · abstract, characters 505–741

Title

Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

Tao Shi; Yves Van de Peer Science Advances 2026. doi:10.1126/sciadv.aea9797

Other claims from this paper (4)

Observationobservedoriginal resultno effectmeasured

Claim · model-written summary

Gene retention in Amborella and Aristolochia shows no signal of an ancestral angiosperm WGD.

Taxon: Amborella and AristolochiaAristolochiaAmborellae1
Outcome: signal of ancestral angiosperm WGDe1

Verbatim

e1
“gene retention patterns in Amborella and Aristolochia —early-diverging plants lacking post–angiosperm origin WGDs—reveal a single gene duplication peak predating the seed plant diversification, with no signal of ancestral angiosperm WGD”
✓ located verbatim in the source · abstract, characters 505–741

Title

Revisiting ancient whole-genome duplications in the seed and flowering plants through the lens of dosage-sensitive genes

Tao Shi; Yves Van de Peer Science Advances 2026. doi:10.1126/sciadv.aea9797

Other claims from this paper (4)

Method / resourceobservedoriginal resultbasis n/a

Claim · model-written summary

GOLEM enables users to locate any motif of interest with respect to TSS or ATG within plant genomes across the plant Tree of Life.

Taxon: Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and ArabidopsisMarchantiaArabidopsisSolanumOryzaZeaAmborellaCharaCeratopterisPhyscomitriumAzollae2
Outcome: locate any motif of interest with respect to TSS or ATGe1
Comparator: TSS or ATGe1

Verbatim

e1
“which enables users to precisely locate any motif of interest with respect to TSS or ATG within the relevant plant genomes across the plant Tree of Life”
✓ located verbatim in the source · abstract, characters 828–980

e2
“Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis”
✓ located verbatim in the source · abstract, characters 982–1084

Title

GOLEM : A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

Lukáš Nevosád; Božena Klodová; Jiří Rudolf; et al. The Plant Journal 2025. doi:10.1111/tpj.70037

Other claims from this paper (1)

Method / resource Motif visualization is performed relative to transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution.

Method / resourceobservedoriginal resultbasis n/a

Claim · model-written summary

Motif visualization is performed relative to transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution.

Taxon: Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and ArabidopsisMarchantiaArabidopsisSolanumOryzaZeaAmborellaCharaCeratopterisPhyscomitriumAzollae2
Organ / stage: leaves and male reproductive tissuese3
Outcome: visualization of the motifse3
Comparator: genome-wide distributione3

Verbatim

e3
“The visualization of the motifs is performed with respect to the transcript levels of particular genes in leaves and male reproductive tissues and can be compared with genome-wide distribution regardless of the transcription level”
✓ located verbatim in the source · abstract, characters 1087–1317

e2
“Chara, Marchantia, Physcomitrium, Azolla, Ceratopteris, Amborella, Oryza, Zea, Solanum and Arabidopsis”
✓ located verbatim in the source · abstract, characters 982–1084

Title

GOLEM : A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte

Lukáš Nevosád; Božena Klodová; Jiří Rudolf; et al. The Plant Journal 2025. doi:10.1111/tpj.70037

Other claims from this paper (1)

Method / resource GOLEM enables users to locate any motif of interest with respect to TSS or ATG within plant genomes across the plant Tree of Life.

Observationauthor interpretationoriginal resultmeasured

Claim · model-written summary

H1 and L1 caleosin orthogroups already appear in Amborella trichopoda, supporting early divergence before angiosperm radiation.

Taxon: Amborella trichopodaAmborella trichopodae3
Outcome: H1 and L1e3
Qualifier: early divergence before angiosperm radiatione3

Verbatim

e3
“H1 and L1 have already appeared in the basal angiosperm Amborella trichopoda, supporting their early divergence before angiosperm radiation”
✓ located verbatim in the source · abstract, characters 809–948

Title

Characterization of Caleosin Genes in Carica papaya and Insights into Lineage-Specific Family Evolution in Brassicales

Zhi Zou; Xiaowen Fu; Xiaoping Yi; et al. Plants 2025. doi:10.3390/plants14213296

Other claims from this paper (10)

Method / resourceobservedoriginal resultmeasured

Claim · model-written summary

The survey identified 42 MADS-Box genes in A. trichopoda.

Taxon: A. trichopodaAmborella trichopodae0
Gene: MADS-Box gene familye0
Outcome: members of the MADS-Box gene familye0
Value: 42 memberse0

Verbatim

t0
“Amborella trichopoda”
✓ located verbatim in the source · title, characters 48–68

e0
“We identified 42 members of the MADS-Box gene family in A. trichopoda with a Hidden Markov Model (HMM)-based genome-wide survey”
✓ located verbatim in the source · abstract, characters 863–990

Title

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors

Sanam Parajuli; Bibek Adhikari; Madhav P. Nepal Scientific Reports 2025. doi:10.1038/s41598-025-88880-x

Other claims from this paper (7)

Observationobservedoriginal resultmeasured

Claim · model-written summary

Twenty-seven MADS-Box genes were classified as Type II or MIKC.

Taxon: Amborella trichopodaAmborella trichopodat0
Outcome: classified into Type II or MIKC groupe0
Value: 27e0

Verbatim

t0
“Amborella trichopoda”
✓ located verbatim in the source · title, characters 48–68

e0
“Among them, 27 were classified into Type II or MIKC group”
✓ located verbatim in the source · abstract, characters 992–1049

Title

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors

Sanam Parajuli; Bibek Adhikari; Madhav P. Nepal Scientific Reports 2025. doi:10.1038/s41598-025-88880-x

Other claims from this paper (7)

Method / resource The survey identified 42 MADS-Box genes in A. trichopoda.
Observation A direct APETALA1 ortholog was absent in A. trichopoda.
Observation MIKC-type genes were differentially expressed between male and female flowers.
Observation APETALA3 showed differential expression between the two sexes.
Observation PISTILLATA showed differential expression between the two sexes.
Observation E-function orthologs were upregulated in female flowers.
Mechanism Authors propose a modified Fading Borders Model with modified A-function and sex-specific B- and E-function expression.

Observationobservedoriginal resultmeasured

Claim · model-written summary

A direct APETALA1 ortholog was absent in A. trichopoda.

Taxon: A. trichopodaAmborella trichopodae0
Gene: APETALA1 (AP1)e0
Outcome: a direct ortholog APETALA1 (AP1)e0

Verbatim

e0
“a direct ortholog APETALA1 (AP1), an A-class floral MADS-Box gene was absent in A. trichopoda”
✓ located verbatim in the source · abstract, characters 1103–1196

Title

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors

Sanam Parajuli; Bibek Adhikari; Madhav P. Nepal Scientific Reports 2025. doi:10.1038/s41598-025-88880-x

Other claims from this paper (7)

Method / resource The survey identified 42 MADS-Box genes in A. trichopoda.
Observation Twenty-seven MADS-Box genes were classified as Type II or MIKC.
Observation MIKC-type genes were differentially expressed between male and female flowers.
Observation APETALA3 showed differential expression between the two sexes.
Observation PISTILLATA showed differential expression between the two sexes.
Observation E-function orthologs were upregulated in female flowers.
Mechanism Authors propose a modified Fading Borders Model with modified A-function and sex-specific B- and E-function expression.

Observationobservedoriginal resultmeasured

Claim · model-written summary

MIKC-type genes were differentially expressed between male and female flowers.

Taxon: Amborella trichopodaAmborella trichopodat0
Organ / stage: male and female flowerse0
Gene: MIKC-type genese0
Outcome: differentially expressed between male and female flowerse0

Verbatim

t0
“Amborella trichopoda”
✓ located verbatim in the source · title, characters 48–68

e0
“MIKC-type genes were differentially expressed between male and female flowers”
✓ located verbatim in the source · abstract, characters 1238–1315

Title

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors

Sanam Parajuli; Bibek Adhikari; Madhav P. Nepal Scientific Reports 2025. doi:10.1038/s41598-025-88880-x

Other claims from this paper (7)

Method / resource The survey identified 42 MADS-Box genes in A. trichopoda.
Observation Twenty-seven MADS-Box genes were classified as Type II or MIKC.
Observation A direct APETALA1 ortholog was absent in A. trichopoda.
Observation APETALA3 showed differential expression between the two sexes.
Observation PISTILLATA showed differential expression between the two sexes.
Observation E-function orthologs were upregulated in female flowers.
Mechanism Authors propose a modified Fading Borders Model with modified A-function and sex-specific B- and E-function expression.

Observationobservedoriginal resultmeasured

Claim · model-written summary

APETALA3 showed differential expression between the two sexes.

Taxon: Amborella trichopodaAmborella trichopodat0
Gene: APETALA3 (AP3)e0
Outcome: differential expression between the two sexese0

Verbatim

t0
“Amborella trichopoda”
✓ located verbatim in the source · title, characters 48–68

e0
“B-function orthologs: APETALA3 (AP3) and PISTILLATA (PI) in the species having differential expression between the two sexes”
✓ located verbatim in the source · abstract, characters 1321–1445

Title

Insights into genetics of floral development in Amborella trichopoda Baill. through genome-wide survey and expression analysis of MADS-Box transcription factors

Sanam Parajuli; Bibek Adhikari; Madhav P. Nepal Scientific Reports 2025. doi:10.1038/s41598-025-88880-x

Other claims from this paper (7)

Method / resource The survey identified 42 MADS-Box genes in A. trichopoda.
Observation Twenty-seven MADS-Box genes were classified as Type II or MIKC.
Observation A direct APETALA1 ortholog was absent in A. trichopoda.
Observation MIKC-type genes were differentially expressed between male and female flowers.
Observation PISTILLATA showed differential expression between the two sexes.
Observation E-function orthologs were upregulated in female flowers.
Mechanism Authors propose a modified Fading Borders Model with modified A-function and sex-specific B- and E-function expression.

Amborellaceae 182 claims

182 claims