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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species

Abstract Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana , Brachypodium distachyon , and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. Furthermore, this provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

Arabidopsis↗
DOE OSTI2022

Complete Genome Sequences of Two Phylogenetically Distinct Nitrospina Strains Isolated from the Atlantic and Pacific Oceans

The complete genome sequences of two chemoautotrophic nitrite-oxidizing bacteria of the genus Nitrospina are reported. Nitrospina gracilis strain Nb-211 was isolated from the Atlantic Ocean, and Nitrospina sp. strain Nb-3 was isolated from the Pacific Ocean. We report two highly similar ~3.07-Mbp genome sequences that differ by the presence of ferric iron chelator (siderophore) biosynthesis genes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

HUNTRESS: a fast heuristic for reconstructing phylogenetic trees of tumor evolution (HUNTRESS) v0.1

We introduce HUNTRESS (Histogrammed UNion Tree REconStruction heuriStic), a computational method for tumor phylogeny reconstruction from noisy genotype matrices derived from single-cell sequencing data, whose running time is linear with the number of cells and quadratic with the number of mutations. Provided that the input genotype matrix includes no false positives, each cellular subpopulation is at least a user defined fraction of the total number of cells, and the number of cells are much bigger than the number of mutations considered, HUNTRESS computes the ground truth tumor phylogeny with high probability. On simulated data HUNTRESS is faster than available alternatives with comparable or better accuracy. Additionally, the phylogenies reconstructed by HUNTRESS on two single-cell sequencing data sets agree with the best known evolutionary scenarios for the associated tumors.

Buluc, Aydin↗
DOE OSTI2024

Molecular phylogenetic reassessment of eastern Atlantic Callinectes (Brachyura, Portunidae)

Abstract Several species from the genusCallinectesare economically important, yet the number of species and their geographic distributions remain unclear. Recently, one of the American species,Callinectes larvatus, was synonymized with one of the African species,C. marginatus, makingC. marginatusthe only species of the genus regarded to be amphi-Atlantic in distribution. However, there was no formal taxonomic study to support this taxonomic change, which was in contradiction to earlier studies that had provided morphological characters to support the taxonomic separation of the eastern Atlantic species from those of western Atlantic distribution.Callinectes maracaiboensishas also been questionably resurrected. Here we present a molecular based analysis for all species ofCallinectes, using the two common mitochondrial genes 16S and 12S. Our molecular data support the presence of three eastern Atlantic, three eastern Pacific, and nine western Atlantic species. Historically, it appears that the separation of Africa and South America with the opening of the Atlantic basin gave rise to sister species distributed on opposite sides of the Atlantic Ocean. In a second isolation event, the emergence of the Panamanian isthmus resulted in pairs of geminate species distributed in eastern Pacific and western Atlantic waters.

Marine & Freshwater Biology↗
DOE OSTI2024

New species and records of the symbiotic shrimp genus Leptalpheus Williams, 1965, with notes on Fenneralpheus Felder & Manning, 1986, and preliminary molecular analysis of phylogenetic relationships (Crustacea: Decapoda: Alpheidae)

The shrimp genera Leptalpheus Williams, 1965 and Fenneralpheus Felder & Manning, 1986 are composed entirely of symbiotic species that co-inhabit burrows of infaunal macrocrustaceans. We report extensive collections of these genera from western Atlantic, eastern Pacific and Indo-West Pacific regions. Integrative taxonomy methods, including morphological comparisons and analysis of three mitochondrial genetic markers, are used to test species hypotheses and evolutionary relationships among members of these genera. Our molecular analysis failed to recover Leptalpheus or Fenneralpheus as monophyletic groups. Our results strongly supported the monophyly of three clades composed of species of Leptalpheus, loosely corresponding to previously proposed species groups. Three new species closely related to Leptalpheus forceps Williams, 1965, L. marginalis Anker, 2011, and L. mexicanus Ríos & Carvacho, 1983 are described. Leptalpheus ankeri n. sp., from the Caribbean Sea, Atlantic coast of Florida, and Gulf of Mexico, is a polymorphic species that exhibits two major cheliped morphotypes. Leptalpheus sibo n. sp., from the Pacific coast of Nicaragua, is morphologically very similar to L. ankeri n. sp., likely its transisthmian sister species, and shares its cheliped polymorphism. A reassessment of L. forceps concluded that records of this species from the Caribbean Sea and Brazil are not conspecific with L. forceps sensu stricto from the Atlantic coast of the USA and the Gulf of Mexico, and they are herein described as Leptalpheus degravei n. sp. Based on both molecular and morphological evidence, we found Leptalpheus bicristatus Anker, 2011 to be a junior synonym of L. mexicanus and Leptalpheus canterakintzi Anker & Lazarus, 2015 to be a junior synonym of Leptalpheus azuero Anker, 2011. First reports of Leptalpheus axianassae Dworschak & Coelho, 1999 in Texas and Mexico, Leptalpheus denticulatus Anker & Marin, 2009 in the Mariana Islands, Leptalpheus felderi Anker, Vera Caripe & Lira, 2006 and Leptalpheus lirai Vera Caripe, Pereda & Anker, 2021 in the USA, and Leptalpheus pereirai Anker & Vera Caripe, 2016 in Cuba are included.

Zoology↗
DOE OSTI2025

Data for Phylogenetic diversity of light-dependent phosphorylation of Thr78 in Rubisco activase

Rubisco activase is an ATP-dependent chaperone that facilitates dissociation of inhibitory sugar phosphates from the catalytic sites of Rubisco during photosynthesis. In Arabidopsis, Rubisco activase is negatively regulated by dark-dependent phosphorylation of Thr78. The prevalence of Thr78 in Rubisco activase was investigated across sequences from 91 plant species, finding that 29 (∼32%) species shared a threonine in the same position. Analysis of seven C3 species with an antibody raised against a Thr78 phospho-peptide demonstrated that this position is phosphorylated in multiple genera. However, light-dependent dephosphorylation of Thr78 was observed only in Arabidopsis. Further, phosphorylation of Thr78 could not be detected in any of the four C4 grass species examined. The results suggest that despite conservation of Thr78 in Rubisco activase from a wide range of species, a regulatory role for phosphorylation at this site is more limited. This provides a case study for how variation in post-translational regulation can amplify functional divergence across the phylogeny of plants beyond what is explained by sequence variation in a metabolically important protein.

photosynthesis↗
DOE OSTI2020

Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics

Sinapis alba is a wild member of the Brassicaceae family reported to possess genetic resistance against major biotic and abiotic stresses of oilseed brassicas. However, the resistance nature of S. alba was not exploited generously due to the unavailability of usable genome sequences in public databases. Therefore, the present study was conducted to assemble the first draft genome from raw whole genome shotgun sequences with annotation and develop simple sequence repeat markers for molecular genetics and marker-assisted breeding. Results The raw genome sequences had 96x coverage on the Illumina platform with 170 Gbp data. The developed assembly by SOAPdenovo2 has ~459 Mbp genome size covered in 403,423 contigs with an average size of 1138.04 bp. The assembly was BLASTX with Arabidopsis thaliana which showed 32.9% positive hits between both plants. The top hit species distribution analysis showed the highest similarity with A. thaliana. A total of 809,597 GO level annotations were recorded after BLASTX results, and 34,012 sequences were annotated with different enzyme codes grouped under seven classes. The gene prediction tool AUGUSTUS identified 113,107 probable genes with an average size of 684 bp. The biochemical pathway annotation assigned 16,119 potential genes to 152 KEGG maps and 1751 enzyme codes. The development of potential SSRs from the de-novo assembly yielded 70731 unique primer pairs. Out of 159 randomly selected SSR markers for validation, 149 successfully amplified in S. alba. However, 10 SSR markers did not amplify during the validation experiment. Conclusion The annotated genome assembly with a large number of SSRs was developed in the present study. To the best of our knowledge, this is the first report of S. alba genome assembly development, annotation, and SSRs mining to date. The data presented here will be a very important resource for future crop improvement programs, especially for resistant breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome

Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama ( Bouteloua gracilis ), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota , Thermoproteota (formerly Thaumarchaeota ), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.

Goemann, Hannah M.↗
NASA NTRS1978

The augmentation algorithm and molecular phylogenetic trees

Moore's (1977) augmentation procedure is discussed, and it is concluded that the procedure is valid for obtaining estimates of the total number of fixed nucleotide substitutions both theoretically and in practice, for both simulated and real data, and in agreement, for experimentally dense data sets, with stochastic estimates of the divergence, provided the restrictions on codon mutability resulting from natural selection are explicitly allowed for. Tateno and Nei's (1978) critique that the augmentation procedure has a systematic bias toward overestimation of the total number of nucleotide replacements is disputed, and a data analysis suggests that ancestral sequences inferred by the method of parsimony contain a large number of incorrectly assigned nucleotides.

Holmquist, R.↗