Biology subjects

Graham, S. W.

Publications and source records attributed to Graham, S. W..

5 recordsLinked to original sources

bioRxiv2026

Liverwort MpSDR4 regulates abscisic acid sensitivity and gemma cup growth

Complex traits often evolve by co-opting pre-existing genetic components. Orthologs of the transcriptional co-factor SEED DORMANCY 4 (SDR4) are found across seed-bearing and seed-free land plants. In flowering plants, loss-of-function mutants of sdr4 orthologs in rice and Arabidopsis exhibit opposite phenotypes in seed germination, a trait regulated by the phytohormone abscisic acid (ABA). We uncovered a major gene duplication event that closely preceded the origin of seed plants, by using a structure-informed molecular phylogenetic analysis. This duplication gave rise to the paralogous SDR4 and DIG/DIL clades, which are broadly retained across the seed plants. Investigating the role of SDR4 homologs in the common liverwort Marchantia polymorpha, a seed-free model organism with only a single SDR4-like homolog (MpSDR4), may provide insights into how SDR4 evolved to regulate dormancy and germination in other land plants. Loss-of-function mutants of Mpsdr4 and transcriptome profiling showed that MpSDR4 modulates ABA sensitivity, consistent with the idea that SDR4 subsequently evolved to regulate hormone responses related to seed germination, with additional functional divergence between monocots and eudicots. Furthermore, Mpsdr4 mutants exhibit elevated growth of gemma cups, contrasting the roles of SDR4 orthologs in asexual reproduction in liverwort with the regulation of seed traits in flowering plants.

plant biology↗

bioRxiv2025

Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs

PremiseThe inclusion of heterotrophic plants in broadly focused systematic studies is challenging, reflecting substantial morphological modification, gene loss, and accelerated nucleotide substitution following photosynthesis loss. In particular, inclusion of very long branch (VLB) taxa with highly elevated rates may lead to phylogenomic misinference. MethodsWe explore how rapidly evolving plastomes behave in model-based phylogenetic inferences of the yam order Dioscoreales, which experienced convergent photosynthesis losses. The taxon sampling includes all photosynthetic genera, and mycoheterotrophic lineages with a broad range of substitution rates. ResultsWhen only moderately rapidly evolving heterotrophs are included, relationships within Dioscoreales are congruent with recent mitochondrial analysis, and generally strongly supported. Photosynthetic Stenomeris (represented by only three genes) is moderately supported as sister to Dioscoreaceae. Notably, Burmanniaceae and Thismiaceae, two mycoheterotrophic families including highly reduced plastomes, are strongly supported as distantly related within Dioscoreales. Constrained analysis rejects combining Thismiaceae with Burmanniaceae, conflicting with current angiosperm classification. Including VLB mycoheterotrophs in phylogenetic inference can lead to localized to broad reduction in branch support--substantially so for Afrothismiaceae, a family placing in disparate locations in Dioscoreales (and beyond) in variant analyses, with no ability to differentiate among its alternative placements. ConclusionsInclusion of highly rate-elevated taxa in analyses of Dioscoreales phylogeny can depress branch support. Inferred relationships in the order are otherwise congruent with studies based on mitochondrial data; the family-level classification needs updating. The extraordinarily rapidly evolving family Afrothismiaceae places inconsistently in diverse plastid analyses, pointing to probable analytical limits for plastid-based phylogenomic analyses of VLB heterotrophs.

evolutionary biology↗

bioRxiv2025

Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes

PremisePlastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. MethodsWe compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. ResultsPlastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. ConclusionsWe accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.

plant biology↗

bioRxiv2023

Afrothismiaceae (Dioscoreales), a new fully mycoheterotrophic family endemic to tropical Africa

Afrothismia is a genus of non-photosynthetic mycoheterotrophs from the forests of continental tropical Africa. Multiple phylogenetic inferences using molecular data recover the genus as sister to a clade comprising mycoheterotrophic Thismiaceae and the photosynthetic family Taccaceae, contrary to earlier placements of Afrothismia and Thismiaceae within Burmanniaceae. Morphological support for separating Afrothismia from the rest of Thismiaceae has depended on the zygomorphic flowers of Afrothismia (although some South American species of Thismia are also zygomorphic) and their clusters of root tubers, each with a terminal rootlet. The number of described species of Afrothismia has recently increased substantially, from four to 16, which has provided additional morphological characters that support its distinction from Thismiaceae. Most notably, the ovary in Afrothismia has a single stalked placenta, and circumscissile fruits from which seeds are exserted by placental elevation (in Thismiaceae, in contrast, there are three placentas, a deliquescing fruit lid, and the seeds are not exserted). Afrothismia stamens are inserted in the lower perianth tube where they are attached to the stigma, and individual flowers are subtended by a single large dorsal bract (in Thismiaceae, stamens are inserted at the mouth of the tube, free of and distant from the stigma, and each flower is subtended by a loose whorl of (2-)3(-4) bracts). Here we formally characterise Afrothismiaceae and review what is known of its development, seed germination, interactions with mycorrhizal Glomeromycota, biogeography, phylogeny and pollination biology. All but one (Afrothismia insignis; Vulnerable) of the 13 species assessed on the IUCN Red List of Threatened Species are either Endangered or Critically Endangered; one species (A. pachyantha Schltr.) is considered to be extinct.

plant biology↗

bioRxiv2017

The complex origins of strigolactone signalling in land plants

Strigolactones (SLs) are a class of plant hormones that control many aspects of plant growth. The SL signalling mechanism is homologous to that of karrikins (KARs), smoke-derived compounds that stimulate seed germination. In angiosperms, the SL receptor is an /{beta} hydrolase known as DWARF14 (D14); its close homologue, KARRIKIN INSENSITIVE2 (KAI2), functions as a KAR receptor, and likely recognizes an uncharacterized, endogenous signal. Previous phylogenetic analyses have suggested that the KAI2 lineage is ancestral in land plants, and that canonical D14-type SL receptors only arose in seed plants; this is paradoxical, however, as non-vascular plants synthesize and respond to SLs. Here, we have used a combination of phylogenetic and structural approaches to re-assess the evolution of the D14/KAI2 family in land plants. We analyzed 339 members of the D14/KAI2 family from land plants and charophyte algae. Our phylogenetic analyses show that the divergence between the eu-KAI2 lineage and the DDK (D14/DLK2/KAI2) lineage that includes D14 occurred very early in land plant evolution. We identify characteristic structural features of D14 and KAI2 proteins, and use homology modelling to show that the earliest members of the DDK lineage structurally resemble KAI2, and not D14 proteins. Furthermore, we show that probable SL receptors in non-seed plants do not have D14-like structure. Our results suggest that SL perception has relatively relaxed structural requirements, and that the evolution from KAI2-like to D14-like protein structure in the DDK lineage may have been driven by interactions with protein partners, rather than being required for SL perception itself.

plant biology↗