skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass
Abstract A number of crop wild relatives can tolerate extreme stress to a degree outside the range observed in their domesticated relatives. However, it is unclear whether or how the molecular mechanisms employed by these species can be translated to domesticated crops. Paspalum (Paspalum vaginatum) is a self-incompatible and multiply stress-tolerant wild relative of maize and sorghum. Here, we describe the sequencing and pseudomolecule level assembly of a vegetatively propagated accession ofP. vaginatum. Phylogenetic analysis based on 6,151 single-copy syntenic orthologues conserved in 6 related grass species places paspalum as an outgroup of the maize-sorghum clade. In parallel metabolic experiments, paspalum, but neither maize nor sorghum, exhibits a significant increase in trehalose when grown under nutrient-deficit conditions. Inducing trehalose accumulation in maize, imitating the metabolic phenotype of paspalum, results in autophagy dependent increases in biomass accumulation.  more » « less
Award ID(s):
1826781
PAR ID:
10385247
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; « less
Publisher / Repository:
Nature Publishing Group
Date Published:
Journal Name:
Nature Communications
Volume:
13
Issue:
1
ISSN:
2041-1723
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; (, PLOS ONE)
    Ginsberg, Stephen D. (Ed.)
    Lysosomes play important roles in catabolism, nutrient sensing, metabolic signaling, and homeostasis. NPC1 deficiency disrupts lysosomal function by inducing cholesterol accumulation that leads to early neurodegeneration in Niemann-Pick type C (NPC) disease. Mitochondria pathology and deficits in NPC1 deficient cells are associated with impaired lysosomal proteolysis and metabolic signaling. It is thought that activation of the transcription factor TFEB, an inducer of lysosome biogenesis, restores lysosomal-autophagy activity in lysosomal storage disorders. Here, we investigated the effect of trehalose, a TFEB activator, in the mitochondria pathology of NPC1 mutant fibroblastsin vitroand in mouse developmental Purkinje cellsex vivo. We found that in NPC1 mutant fibroblasts, serum starvation or/and trehalose treatment, both activators of TFEB, reversed mitochondria fragmentation to a more tubular mitochondrion. Trehalose treatment also decreased the accumulation of Filipin+cholesterol in NPC1 mutant fibroblasts. However, trehalose treatment in cerebellar organotypic slices (COSCs) from wild-type andNpc1nmf164mice caused mitochondria fragmentation and lack of dendritic growth and degeneration in developmental Purkinje cells. Our data suggest, that although trehalose successfully restores mitochondria length and decreases cholesterol accumulation in NPC1 mutant fibroblasts, in COSCs, Purkinje cells mitochondria and dendritic growth are negatively affected possibly through the overactivation of the TFEB-lysosomal-autophagy pathway. 
    more » « less
  2. ; ; ; ; ; (, Physiologia Plantarum)
    ABSTRACT Sorghum (Sorghum bicolor) plays a critical role in global agriculture, serving as a staple food source and contributing significantly to various industries. However, sorghum cultivation faces significant challenges, particularly from pests like the sugarcane aphid (SCA), which can cause substantial damage to crops. In this study, we investigated the role of the caffeoyl coenzyme‐AO‐methyltransferase (CCoAOMT) gene in sorghum defense against SCA. Feeding by SCA induced the expression of theSbCCoAOMTgene, which is involved in the monolignol biosynthesis pathway. Aphid no‐choice and choice bioassays revealed thatSbCCoAOMToverexpression in sorghum resulted in reduced SCA reproduction and decreased aphid settling, respectively, compared to wild‐type (RTx430) plants. Furthermore, electrical penetration graph (EPG) studies revealed thatSbCCoAOMToverexpression restricts aphid feeding from the sieve elements. SCA feeding also induced the accumulation of lignin in sorghum wild‐type andSbCCoAOMToverexpression plants. Moreover, artificial diet aphid feeding bioassays with hydroxycinnamic acids, ferulic and sinapic acids, showed direct adverse effects on SCA reproduction. Our findings highlight the potential of genetic modification to enhance sorghum resistance to SCA and emphasize the importance of lignin‐related genes in plant defense mechanisms. This study offers valuable insights into developing aphid‐resistant sorghum varieties and suggests avenues for further research on enhancing plant defenses against biotic stresses. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, Genome Biology)
    Abstract BackgroundCapturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. ResultsHere we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. ConclusionsThis study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research. 
    more » « less
  4. ; ; ; (, PLANTS, PEOPLE, PLANET)
    Societal Impact StatementThe current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and extinction threats of the Anthropocene. Using the biodiversity database, Botanical Information and Ecology Network (BIEN), and the Andropogoneae grass tribe as a case study, we demonstrate that large‐scale, preliminary conservation assessments can play a fundamental role in accelerating plant conservation pipelines and setting priorities for more in‐depth investigations. SummaryThe International Union for the Conservation of Nature (IUCN) Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we used The Red List's criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with ~1100 species, including maize, sorghum, and sugarcane and their wild relatives.We used georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time‐saving tools for conservation research. We validated our results with those from the IUCN‐recommended assessment tool, GeoCAT.We discovered a remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire dataset.Increasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation. 
    more » « less
  5. ; ; (, Plant Direct)
    Abstract The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4photosynthesis. Here, we used long‐read sequencing technology to characterize the transcriptomes of three C3panicoid grass species:Dichanthelium oligosanthes,Chasmanthium laxum, andHymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co‐opted into C4were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript‐based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long‐read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses—wild species and species utilizing C3photosynthesis—will aid in future studies of domestication and C4evolution by decreasing the evolutionary distance between C4and C3species within this clade, enabling more accurate comparisons associated with evolution of the C4pathway. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email