By organism › Green plants › Amborellaceae › Amborella

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

The findings are consistent with derived dioecy in Amborella.

Taxon: AmborellaAmborellae0
Outcome: dioecy is derivede0

Verbatim

e0
“These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated”
✓ located verbatim in the source · abstract, characters 976–1123

Title

ZW sex chromosome structure in Amborella trichopoda

Sarah B. Carey; Laramie Aközbek; John T. Lovell; et al. Nature Plants 2024. doi:10.1038/s41477-024-01858-x

Other claims from this paper (6)

Observationauthor interpretationoriginal resultmeasured

Claim · model-written summary

The findings are consistent with little degeneration of the Amborella sex chromosome pair.

Taxon: AmborellaAmborellae0
Outcome: sex chromosome pair has not significantly degeneratede0

Verbatim

e0
“These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated”
✓ located verbatim in the source · abstract, characters 976–1123

Title

ZW sex chromosome structure in Amborella trichopoda

Sarah B. Carey; Laramie Aközbek; John T. Lovell; et al. Nature Plants 2024. doi:10.1038/s41477-024-01858-x

Other claims from this paper (6)

Method / resource A haplotype-resolved Amborella genome assembly includes highly contiguous Z and W chromosomes.
Observation The sex-determination region spans about 3 megabases and two strata.
Observation The sex-determination region includes a roughly 300-kilobase inversion enriched in repeats.
Observation The inversion contains a homologue of Arabidopsis MTN1-2 genes.
Observation The rest of the SDR lacks typical repeat accumulation and gene loss.
Observation The findings are consistent with derived dioecy in Amborella.

Observationobservedoriginal resultmeasured

Claim · model-written summary

Amborella AtrGT47A-VII lacked MBGT activity in vivo.

Taxon: AmborellaAmborellae0
Gene: AtrGT47A-VIIe0
Outcome: MBGT activity in vivoe0
Direction: did not showe0

Verbatim

e0
“Candidate AtMBGT1 orthologues from rice (OsGT47A-VII) and Amborella (AtrGT47A-VII) did not show MBGT activity in vivo.”
✓ located verbatim in the source · abstract, characters 723–841

e1
“Candidate AtMBGT1 orthologues from rice (OsGT47A-VII) and Amborella (AtrGT47A-VII) did not show MBGT activity in vivo.”
✓ located verbatim in the source · abstract, characters 723–841

Title

Differing structures of galactoglucomannan in eudicots and non-eudicot angiosperms

Konan Ishida; Yusuke Ohba; Yoshihisa Yoshimi; et al. PLoS ONE 2023. doi:10.1371/journal.pone.0289581

Other claims from this paper (6)

Observationobservedoriginal resultmeasured

Claim · model-written summary

Secretome analysis of in vitro grown pollen tubes of Amborella, maize and tobacco identified cell wall, signaling and metabolism components and novel small secreted peptides.

Taxon: Amborella, maize and tobaccoNicotiana tabacum Zea maysAmborellae0
Organ / stage: pollen tubese0
Outcome: novel small secreted peptidese0

Verbatim

e0
“Analyses of secretomes of in vitro grown pollen tubes from Amborella, maize and tobacco identified many components of processes associated with the cell wall, signaling and metabolism as well as novel small secreted peptides”
✓ located verbatim in the source · abstract, characters 13–237

Title

Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides

María Flores-Tornero; Lele Wang; David Potěšil; et al. Plant Reproduction 2020. doi:10.1007/s00497-020-00399-5

Other claims from this paper (1)

Observation Expansins, pectin methylesterase inhibitors and RALFs were enriched in the maize pollen tube secretome.

Method / resourceobservedoriginal resultpositivemeasured

Claim · model-written summary

A method isolated Amborella egg apparatus cells for transcriptome profiling.

Taxon: AmborellaAmborellae0
Organ / stage: egg apparatus cellse0
Outcome: isolate Amborella egg apparatus cellse0
Value: genome-wide gene expression profilese0

Verbatim

e0
“a method to isolate Amborella egg apparatus cells and on genome-wide gene expression profiles in these cells”
✓ located verbatim in the source · abstract, characters 908–1016

Title

Transcriptomics of manually isolated Amborella trichopoda egg apparatus cells

María Flores-Tornero; Sebastian Proost; Marek Mutwil; et al. Plant Reproduction 2019. doi:10.1007/s00497-019-00361-0