Biology subjects

Maloof, J. N.

Publications and source records attributed to Maloof, J. N..

8 recordsLinked to original sources

bioRxiv2025

LEAFY demonstrates ancestral reproductive functions in the gametophyte and not the sporophyte of the fern Ceratopteris richardii

Flowers are a key reproductive innovation of the angiosperms. They evolved as a modification of the ancestral plant life cycle whereby the haploid gamete-producing generation (gametophyte) became enclosed within the diploid, spore-producing generation (sporophyte). The transcription factor LEAFY (LFY) initiates angiosperm floral development, yet its lineage predates flowers and is found across all land plants. LFY function outside angiosperms is known from the moss Physcomitrium patens, where they control the first division of the sporophyte, and from the model fern Ceratopteris richardii, a vascular plant without seeds or flowers, where CrLFY1 and CrLFY2 maintain vegetative meristem activity. However, how LFYs reproductive role evolved remains unclear. Using over-expression, we uncover new roles for CrLFY1/2 in fern gametophyte reproduction, particularly in sperm cells and in the gametophytes multicellular notch meristem. No sporophytic reproductive function was detected, but over-expression supports a role in fern frond compounding and a conserved role in the zygotes first division. Our findings highlight an ancestral LFY function in fern haploid-stage reproduction, which may have been co-opted into the sporophyte during the origin of the flower. Summary StatementThe origin of LEAFYs floral function is unknown, with only vegetative roles known from seedless plants. We identify ancestral reproductive roles for the first time, unexpectedly in the fern gametophyte.

developmental biology↗

bioRxiv2024

Accelerated phenology fails to buffer fitness loss from delayed rain onset in a clade of wildflowers

The timing of early life cycle events has cascading effects on phenology and fitness. These effects may be critical for climate resilience of plant populations, especially in Mediterranean environments, where delayed rainfall onset causes delayed germination. To examine impacts of germination timing on ten species of the Streptanthus/Caulanthus clade, we induced germination across a range of dates in ambient seasonal conditions and recorded phenological and fitness traits. Later germination cohorts accelerated flowering, partially stabilizing flowering date, but the degree of this compensatory plasticity differed across species. Fitness declined with later germination; the magnitude of this decline depended on the balance between direct negative effects of later germination and compensatory positive effects of accelerated flowering. The resulting species differences in fitness responses suggest differential vulnerability to climate change. Species from wetter, cooler, less variable habitats accelerated flowering more and declined less in seed set with later germination, suggesting climate adaptation. However, other fitness responses to germination timing, like first year fitness, were evolutionarily labile across the clade and unrelated to climate. Although compensatory phenological plasticity may buffer the impacts of delayed germination, it cannot prevent long term declines in population fitness as fall rains come later with climate change.

evolutionary biology↗

bioRxiv2024

A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus genera in the Thelypodieae tribe (Brassicaceae) is an emerging model system for ecological and evolutionary studies. This Complex spans the full range of the California Floristic Province including desert, foothill, and mountain environments. The ability of these related species to radiate into dramatically different environments makes them a desirable study subject for exploring how plant species expand their ranges and adapt to new environments over time. Ecological and evolutionary studies for this complex have revealed fascinating variation in serpentine soil adaptation, defense compounds, germination, flowering, and life history strategies. Until now a lack of available genomic resources has hindered the ability to relate these phenotypic observations to their underlying genetic and molecular mechanisms. To help remedy this situation we present here a chromosome-level genome assembly of Streptanthus diversifolius, a member of the Streptanthoid Complex, developed using Illumina, Hi-C, and HiFi sequencing technologies. Construction of this assembly also provides further evidence to support the previously reported recent whole genome duplication unique to the Thelypodieae tribe. This whole genome duplication may have provided individuals in the Streptanthoid Complex the genetic arsenal to rapidly radiate throughout the California Floristic Province and to occupy commonly inhospitable environments including serpentine soils.

genomics↗

bioRxiv2023

Assembly and analysis of the genome of Notholithocarpus densiflorus

Tanoak (Notholithocarpus densiflorus) is an evergreen tree in the Fagaceae family found in California and southern Oregon. Historically, tanoak acorns were an important food source for Native American tribes and the bark was used extensively in the leather tanning process. Long considered a disjunct relictual element of the Asian stone oaks (Lithocarpus spp.), phylogenetic analysis has determined that the tanoak is an example of convergent evolution. Tanoaks are deeply divergent from oaks (Quercus) of the Pacific Northwest and comprise a new genus with a single species. These trees are highly susceptible to sudden oak death (SOD), a plant pathogen (Phytophthora ramorum) that has caused widespread mortality of tanoaks. Here, we set out to assemble the genome and perform comparative studies among a number of individuals that demonstrated varying levels of susceptibility to SOD. First, we sequenced and de novo assembled a draft reference genome of N. densiflorus using co-barcoded library processing methods and an MGI DNBSEQ-G400 sequencer. To increase the contiguity of the final assembly, we also sequenced Oxford Nanopore (ONT) long reads to 30X coverage. To our knowledge, the draft genome reported here is one of the more contiguous and complete genomes of a tree species published until now, with a contig N50 of [~]1.2 Mb and a scaffold N50 of [~]2.1 Mb. In addition, we sequenced 11 genetically distinct individuals and mapped these onto the draft reference genome enabling the discovery of almost 25 million single nucleotide polymorphisms and [~]4.4 million small insertions and deletions. Finally, using co-barcoded data we were able to generate complete haplotype coverage of all 11 genomes.

genomics↗

bioRxiv2023

Germination responses to experimental rainfall timing identify potential vulnerability to climate change across a clade of California wildflowers

The timing of germination, driven by seasonal cues, is critical for the life cycle of plants. Variation among species in germination responses can reflect evolutionary processes and adaptation to local climate and can affect vulnerability to changing conditions. Indeed, climate change is altering the timing of precipitation and associated temperatures, which may interact with germination cueing to affect the timing, quantity, and speed of germination. Germination responses to change can then have consequences for individual fitness, population dynamics, and species distributions. Here, we assessed responses to the timing of germination-triggering rains and corresponding temperatures for 11 species spanning the Streptanthus (s.l.) clade (Brassicaceae). To do so, we experimentally manipulated the onset date of rainfall events, measured effects on germination fraction and rate, and evaluated whether responses were constrained by evolutionary relationships across the phylogeny. We then explored the possible consequences of these responses to contemporary shifts in precipitation timing. Later onset rains and cooler temperatures significantly reduced germination rates for all species. Germination fractions decreased with later rains and cooler temperatures for all but three Caulanthus species. Species germination responses to the timing of rainfall and seasonal temperatures were phylogenetically constrained, with Caulanthus species appearing less sensitive. Further, six species are likely already experiencing significant decreases in germination fractions or rates (or both) with observed climate change, which has shifted the timing of rainfall towards the cooler, winter months in California. Overall, our findings highlight the importance of the germination responses to seasonal timing, how they have evolved across the clade, and their implications under climate change.

plant biology↗

bioRxiv2020

Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth

Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) has emerged as a stress signal transduced into a diverse ensemble of response outputs. Here we demonstrate enhanced phytochrome B protein abundance in red-light grown MEcPP-accumulating mutant (ceh1) plant relative to wild-type seedlings. We further establish MEcPP-mediated coordination of phytochrome B with auxin and ethylene signaling pathways, and uncover differential hypocotyl growth of red-light grown seedlings in response to these phytohormones. Genetic and pharmacological interference with ethylene and auxin pathways outline the hierarchy of responses, placing auxin epistatic to the ethylene signaling pathway. Collectively, our finding establishes the key role of a plastidial retrograde metabolite in orchestrating the transduction of a repertoire of signaling cascades, and positions plastids at the zenith of relaying information coordinating external signals and internal regulatory circuitry to secure organismal integrity. Two sentence summaryThe plastidial retrograde metabolite, MEcPP, orchestrates coordination of light and hormonal signaling cascade through induction of phytochrome B abundance and modulation of auxin and ethylene levels for optimal adaptive responses to light environment.

plant biology↗

bioRxiv2019

Leaf shape is a predictor of fruit quality and cultivar performance in tomato

O_LICommercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits.\nC_LIO_LIHere the role of leaf morphology was investigated for its impact on fruit quality. Heirloom cultivars were grown in field conditions and BRIX by Yield (BY) and other traits measured over a fourteen-week period. The complex relationships among these morphological and physiological traits were evaluated using PLS-Path Modeling, and a consensus model developed.\nC_LIO_LIPhotosynthesis contributed strongly to vegetative biomass and sugar content of fruits but had a negative impact on yield. Conversely leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield. Cultivars such as Stupice and Glacier, with very round leaves, had the highest performance in both fruit sugar and yield. Our model accurately predicted BY for two commercial cultivars using leaf shape data as input.\nC_LIO_LIThis study revealed the importance of leaf shape to fruit quality in tomato, with rounder leaves having significantly improved fruit quality. This correlation was maintained across a range of diverse genetic backgrounds and shows the importance of leaf morphology in tomato crop improvement.\nC_LI

plant biology↗

bioRxiv2019

Integrating transcriptomic network reconstruction and QTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development

Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use a hierarchical Bayesian Function-Valued Trait (FVT) approach to estimate Brassica rapa growth curves throughout ontogeny, across two treatments and in two growing seasons. We find that the shape of growth curves is relatively plastic across environments compared to final height, and that there are trade-offs between growth rate and duration. We determined that combining FVT Quantitative Trait Loci (QTL) and genes/eigengene expression identified via transcriptomic co-expression network reconstructions best characterized phenotypic variation. Further, targeted eQTL analyses identified regulatory hotspots that colocalized with FVT QTL and co-expression network identified genes and mechanistically link FVT QTL with structural trait variation throughout development in agroecologically relevant field settings.

genomics↗