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PubMed2005

GATA: a graphic alignment tool for comparative sequence analysis.

BACKGROUND: Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. RESULTS: To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA http://gata.sourceforge.net/). GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF) file. CONCLUSIONS: GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA sequences. It provides researchers with a fine-grained alignment and visualization tool aptly suited for non-coding, 0-200 kb, pairwise, sequence analysis. It functions independent of sequence feature ordering or orientation, and readily visualizes both large and small sequence inversions, duplications, and segment shuffling. Since the alignment is visual and does not contain gaps, gene annotation can be added to both sequences to create a thoroughly descriptive picture of DNA conservation that is well suited for comparative sequence analysis.

Algorithms↗

PubMed2026

Genome-wide characterization of BraABCB transporters reveals their potential roles in hormone responses in Brassica rapa var. parachinensis.

Thirty-six BraABCB genes were identified in Brassica rapa var. parachinensis; expression and interaction analyses suggest BraABCB27 and BraABCB28 as hormone-responsive candidates associated with BRI1-related proteins. ABCB transporters are ATP-dependent membrane proteins that mediate the transport of diverse substrates, including phytohormones, and play important roles in plant development and environmental adaptation. Previous studies in Arabidopsis have shown that several ABCB proteins participate in phytohormone transport, including auxin and brassinosteroid transport, whereas the functions of their homologs in Brassica rapa var. parachinensis remain poorly understood. In this study, 36 BraABCB genes were identified and classified into four phylogenetic groups. Conserved domain analysis showed that BraABCB proteins contain typical nucleotide-binding domains and transmembrane domains. Chromosomal distribution, collinearity, and Ka/Ks analyses suggested that the BraABCB family is evolutionarily conserved and mainly subject to purifying constraints. Promoter analysis and RT-qPCR assays of selected Group IV BraABCB genes revealed diverse expression patterns and responses to drought, high temperature, brassinolide, and indole-3-acetic acid treatments. Subcellular localization assays showed that selected Group IV BraABCB proteins exhibited predominant plasma membrane localization. Notably, BraABCB27 and BraABCB28, two close AtABCB1/AtABCB19-related homologs, showed detectable physical associations with BRI1-related proteins in BiFC and split-ubiquitin yeast two-hybrid assays. Together, these results provide a genome-wide characterization of the BraABCB gene family and identify BraABCB27 and BraABCB28 as candidate genes for future studies of their possible associations with BR-related membrane processes and hormone-regulated growth responses in B. rapa var. parachinensis.

Plant Growth Regulators↗

PubMed1999

Effect of furosemide on performance of Thoroughbreds racing in the United States and Canada.

OBJECTIVE: To determine the effect of furosemide on performance of Thoroughbreds racing on dirt surfaces at tracks in the United States and Canada. DESIGN: Cross-sectional study. ANIMALS: All Thoroughbreds (n = 22,589) that finished a race on dirt surfaces at tracks in the United States and Canada between June 28 and July 13, 1997 in jurisdictions that allowed the use of furosemide. PROCEDURE: Race records were analyzed by use of multivariable ANOVA procedures and logistic regression analyses to determine the effect of furosemide on estimated 6-furlong race time, estimated racing speed, race earnings, and finish position. Principal component analysis was used to create orthogonal scores from multiple collinear variables for inclusion in the models. RESULTS: Furosemide was administered to 16,761 (74.2%) horses. Horses that received furosemide raced faster, earned more money, and were more likely to win or finish in the top 3 positions than horses that did not. The magnitude of the effect of furosemide on estimated 6-furlong race time varied with sex, with the greatest effect in males. When comparing horses of the same sex, horses receiving furosemide had an estimated 6-furlong race time that ranged from 0.56 +/- 0.04 seconds (least-squares mean +/- SE) to 1.09 +/- 0.07 seconds less than that for horses not receiving furosemide, a difference equivalent to 3 to 5.5 lengths. CONCLUSIONS AND CLINICAL RELEVANCE: Because of the pervasive use of furosemide and its apparent association with superior performance in Thoroughbred racehorses, further consideration of the use of furosemide and investigation of its effects in horses is warranted.

Age Factors↗

PubMed1992

PETSIM: Monte Carlo simulation of all sensitivity and resolution parameters of cylindrical positron imaging systems.

Monte Carlo simulation techniques are applied to track the annihilation photons from positron decay, and store the photon histories. Reasonably realistic models of the isotope distribution in the brain and heart during typical PET studies, as well as the traditional phantoms used for measuring PET scanner performance can be built out of up to 10 hollow or solid cylinders. Separate programs model the source distribution and its attenuation characteristics, the collimators and the detectors. These modules are connected by compact gamma history files which are stored on disc or tape. Over 50 million gamma ray histories can be saved on a 1 Gbyte disc, representing the decay of several billion atoms. This allows for good precision even for single thin slices in scanners with wide axial acceptance. The simulation results include spectrum analysis, sensitivity to true coincident events, scattered coincident and single rays, and the effects on these parameters of detector dead time. The storage of intermediate results on tape reduces simulation time, since most common source geometries need be generated only once. The sensitivities in multi-slice systems are presented as matrices of coincident crystal planes. The matrix shows the true count sensitivity and the scatter fraction together for each valid combination of planes. This presentation is very useful for assessing the effects of various degrees of inter-plane collimation. The spatial resolution analysis includes the effects of positron range, non-collinearity of the gamma rays, multiple interaction within the detectors, and the effects of quantization into single crystals in multiple-crystal block detectors. Each of these effects can be turned on or off without repeating the simulation. Both in-plane and axial resolutions are calculated as a function of location of the positron-emitting nucleus and the angle of incidence of gamma rays on the crystals. Single crystals, blocks and crystals with depth of interaction encoding can be specified, as can the method of backprojection (planar, or 3D), so that the detector geometry can be optimized.

Computer Simulation↗

PubMed2005

Measurement of electric field by interferometric spectral trace observation.

We present a new methodology that obtains, in an analytical way, the complex electric field of ultrashort pulses. This methodology is based only on Fourier analysis of the frequency components of spectrally resolved interferometric collinear autocorrelations. We present an experimental demonstration of this technique and the results are compared with the conventional second-harmonic generation frequency-resolved optical gating technique.

Journal Article↗

PubMedDate not supplied

[Water structure formation by weak magnetic fields and xenon. Electron microscopic analysis].

Exposure of deionized water of high purity grade to weak magnetic fields (collinear fields: the constant component 42 +/- 0.1 microT; the alternating component: amplitude 60 +/- 2 nT, frequency 3.7 Hz) for 12 h affects the structure formation in a water-xenon system. This is evidenced by the formation of xenon clathrate crystals a few submicrons and microns in size whereas in initial water solution these crystals were absent. The changes in water properties persist for at least two days after the treatment with magnetic fields. The addition into water of calcium ions at a concentration close to physiological completely eliminates the effect of the formation of submicron and micron crystals of xenon gas hydrates.

Electromagnetic Fields↗

PubMedDate not supplied

Short-term effects of air pollution on mortality in the cities of Rouen and Le Havre, France, 1990-1995.

In this study, the authors examined the short-term effects of ambient air pollution on mortality across 2 French cities: Rouen and Le Havre. In Poisson regression models, which controlled for day-of-week effects, the authors used nonparametric smoothing to control for temporal trend, weather, and influenza epidemics. In Rouen, an interquartile range increase of 60.5-94.1 microg/m3 of ozone was associated with an increase of 4.1% (95% confidence interval = 0.6, 7.8) of total mortality. Daily variations in sulfur dioxide (interquartile range increase = 17.6-36.4 microg/m3) were also associated with an 8.2% increase (95% confidence interval = 0.4, 16.6) in respiratory mortality. An increase of 6.1% (95% confidence interval = 1.5, 10.9) of cardiovascular mortality was also observed with an interquartile range increase of nitrogen dioxide (i.e., 25.3-42.2 microg/m3). With respect to Le Havre, an interquartile range increase in daily levels of sulfur dioxide (11.3-35.6 microg/m3) was associated with an increase of approximately 3% (95% confidence interval = 0.8, 5) of cardiovascular mortality. For particulate matter less than or equal to 13 microm in diameter (interquartile increase = 21.5, 45.4 microg/m3), an increase of 6.2% (95% confidence interval = 0.1, 12.8) was observed. The estimates of pollutant effects and their standard deviations were slightly affected by the degree of smoothing temporal variations in this study. When low collinearity was present, the 2-pollutant models provided acceptable estimates of pollutant effects. They suggested that the ozone effect was independent of the Black Smoke effect, and that the effects of sulfur dioxide and nitrogen dioxide were unlikely to be confounded by ozone concentrations. However, high collinearity leads to large estimates of the pollutant coefficient variances and, therefore, leads to inaccurate estimates of pollutant effects. The analysis of the contributory effects of different pollutant mixtures requires further investigation in those instances in which high collinearity between pollutants is present.

Air Pollutants↗

PubMed1997

Theoretical estimates of cruciate ligament forces: effects of tibial surface geometry and ligament orientations.

A mathematical model of the knee in the sagittal plane was used to analyse the effect of tibial surface geometry and ligament orientations on the estimates of cruciate ligament forces. An elementary mechanical analysis was used to calculate the ligament forces L during a simulated antero-posterior (A-P) laxity test (passive test), and during isometric quadriceps contraction (IQE). Three sets of anatomical parameters (sites of bony attachments and lengths of the ligaments) were used from the literature. Flat, concave and convex shapes were considered for the tibial plateau articulating with a compatible convex femoral condyle. Also, the effects of position and posterior tilt of the tibial plateau were analysed for the concave and flat surfaces. The analysis showed that the ligament forces rose steeply as they approached collinearity with the contact force, C. For a flat tibia, the direction of C remained independent of flexion angle or position of the tibial plateau. For the concave tibia, the direction of C varied with flexion as well as with position of the centre of curvature, O, of the tibial plateau. C had an anterior component synergistic with the posterior cruciate ligament (PCL) when the point of contact, F, was anterior to O. On the other hand, C had a posterior component synergistic with the anterior cruciate ligament (ACL) when F was posterior to O. Also, posterior tilt of the flat or concave surfaces resulted in an increase in the anterior component of C. The effects of the convex tibial surface were opposite to those of the concave surface. During the A-P laxity test, the ligament forces arising from the concave tibia were very sensitive to the A-P position of O and to the posterior tilt of the plateau which allowed C and L to approach collinearity. Proximo-distal movement of O had a relatively insignificant effect on the ligament force. Similarly, compared to the concave surface, the posterior tilt of the flat tibia had a lesser effect on the ligament forces. Compared to the passive test, use of the muscle forces during IQE resulted in larger ligament forces, though the trends in force behaviour over the flexion range remained the same. The analysis emphasizes the importance of correct graft placement during ligament reconstruction, and the need to avoid steep inclination (more than 70 degrees to tibial plateau). Increasing the inclination from 70 to 80 degrees doubles the ligament force. Further, the analysis suggests that, in bicompartmental knee replacement, the efficacy of concave surfaces in replacing cruciate ligament function depends critically on the horizontal placement of the tibial component and its orientation about the mediolateral axis.

Anterior Cruciate Ligament↗

PubMed2001

Vascular patients' preferences for local treatment: an application of conjoint analysis.

OBJECTIVES: To investigate whether and to what extent vascular patients are willing to trade expected health outcomes for improvements in non-health benefits, such as the availability of local services, in the provision of peripheral vascular surgery. METHODS: Conjoint analysis was used to elicit patient preferences via a mailed questionnaire. Respondents were asked to consider pairwise descriptions of vascular services described in terms of a number of key attributes and asked to indicate which scenario description they preferred. Multivariate regression analysis was used to estimate the relative importance of the attributes to respondents. RESULTS: Of the 339 patients invited to participate, 161 (47%) returned a completed questionnaire, although 36 (11%) were found to be internally inconsistent and could not be used, leaving 125 (36%) for analysis. An unexpected problem arose with respect to the design of the conjoint analysis questionnaire. Specifically, three of the attributes in the regression model were found to be collinear. The source of this problem, how it was overcome and how it can be avoided in future studies is discussed. The results of the regression analysis indicated that the patients who responded had a preference for local treatment to the extent that they were willing to incur increased risks of perioperative mortality and amputation to receive treatment at their local hospital. These results are discussed in connection with those from a different study which elicited patient preferences for local treatment using a standard gamble technique. CONCLUSIONS: Policy-makers, when considering the potential benefits of regionalising health care, should seek to elicit the preferences of those patients who will be affected by the reorganisation.

Community Health Services↗

PubMed2003

Probabilistic analysis indicates discordant gene trees in chloroplast evolution.

Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome. Plastids and their genomes are transmitted as a single block without recombination, hence homogeneity among gene trees within this genome is expected. Nevertheless, previous work has revealed clear heterogeneity among plastid genes (e.g., Delwiche and Palmer 1996). Other studies, using whole plastid genomes of various algae and land plants, found little additional heterogeneity (Martin et al. 1998; Adachi et al. 2000). We augment the earlier studies by using a data set of 14 taxa: 6 land plants, 2 green algae, a diatom, 2 red algae and a cryptophyte, the cyanelle of the glaucocystophyte Cyanophora, and the blue-green alga Synechocystis as an outgroup. Contrary to the earlier analyses, we cannot find even a single, dominant consensus tree. Therefore, we formulate a probabilistic model that divides the genes into two sets: those that follow the consensus tree and those that have independent gene trees. No particular tree is supported by more than three-fourths of the genes. But the set of genes that follows a certain tree is fairly independent of data processing and the method of analysis. With one possible exception, we find no evidence for collinear or functionally related genes to follow similar trees. The phylogenetic pattern also seems independent of bias in amino acid composition. Among possible explanations for the observed phenomenon, the hypothesis that different genes have different covarion structures is difficult to assess. But gene duplication may be possible through the inverted or direct repeat regions, while horizontal gene transfer seems less likely. In contrast to green algae and land plants, inverted repeat regions in red algae and in Cyanophora show abundant differences among the copies. Thus, genes may get duplicated when they are recruited into the inverted repeat region and one of the two copies may be lost after leaving the inverted repeat region.

Chloroplasts↗

PubMedDate not supplied

Levels of data: the whys and hows of selection and analysis.

There are many challenges in selecting the level of a variable for data collection and analysis. Meeting these challenges is labor intensive and requires considerable skill; however, if a performance improvement project is to produce sound results, shortcuts cannot be taken. Studies that purport to show the impact of important variables on care influence the allocation of resources. The choice of a working unit level of analysis may be highly useful in meeting project goals and statistical requirements, but familiarity with multilevel techniques remains essential. If all or some of the variables must be aggregated, information about individual response rate, the extent and treatment of missing data, and tests of the collinearity of the aggregate data need to be made before proceeding with the analysis.

Benchmarking↗

PubMed2007

Multi-model statistical process monitoring and diagnosis of a sequencing batch reactor.

Biological processes exhibit different behavior depending on the influent loads, temperature, microorganism activity, and so on. It has been shown that a combination of several models can provide a suitable approach to model such processes. In the present study, we developed a multiple statistical model approach for the monitoring of biological batch processes. The proposed method consists of four main components: (1) multiway principal component analysis (MPCA) to reduce the dimensionality of data and to remove collinearity; (2) multiple models with a posterior probability for modeling different operating regions; (3) local batch monitoring by the T(2)- and Q-statistics of the specific local model; and (4) a new discrimination measure (DM) to identify when the system has shifted to a new operating condition. Under this approach, local monitoring by multiple models divides the entire historical data set into separate regions, which are then modeled separately. Then, these local regions can be supervised separately, leading to more effective batch monitoring. The proposed method is applied to a pilot-scale 80-L sequencing batch reactor (SBR) for biological wastewater treatment. This SBR is characterized by nonstationary, batchwise, and multiple operation modes. The results obtained for the pilot-scale SBR indicate that the proposed method has the ability to model multiple operating conditions, to identify various operating regions, and also to determine whether the biosystem has shifted to a new operating condition. Our findings show that the local monitoring approach can give more reliable and higher resolution monitoring results than the global model.

Biodegradation, Environmental↗

PubMed1996

Cloning and comparative mapping of a gene from the commonly deleted region of DiGeorge and Velocardiofacial syndromes conserved in C. elegans.

We have identified and cloned a gene, ES2, encoding a putative 476 amino acid protein with a predicted Mr of 52,568. The gene is localized within the DiGeorge/Velocardiofacial syndrome locus on 22q11.2 and is deleted in all the patients in which a deletion within 22q11 could be demonstrated, with the exception of one patient. ES2 is expressed in all the tissues studied. Sequence comparison showed identity with five ESTs and at the amino acid level the sequence was highly similar to, and collinear with, a hypothetical C. elegans protein of unknown function. Mutation analysis was performed in 16 patients without deletion, but no mutation has been found. The cDNA sequence is conserved in mouse and is localized on MMU16B1-B3, known to contain a syntenic group in common with HSA 22q11.2.

Abnormalities, Multiple↗

PubMed1992

Neuroectodermal autonomy of Hox-2.9 expression revealed by rhombomere transpositions.

Involvement of the Hox genes in regional specifications of the vertebrate body axis is suggested by sequence similarity with the homeotic selector genes of Drosophila, the conservation of a collinear relationship between genomic organization and site of expression, and mutational analysis. Subdivision of vertebrate embryo hindbrain neuroepithelium into lineage compartments (rhombomeres) underlies segmental patterning of neuronal differentiation. The rhombomere boundaries delimit domains of expression of Hox genes, presumed to be determinants of rhombomere phenotype, suggesting that Hox genes confer positional value; the formation of rhombomere 4 (r4) is followed by strong expression of Hox-2.9 within its confines. If the Hox genes are determinants, their expression should be autonomous from the developmental stage at which regional commitment becomes fixed and irreversible. We have transplanted the future r4 region (from state-9-chick embryos) into the more anterior position of r2 and probed for Hox-2.9 transcripts. We report here that Hox-2.9 was expressed in the ectopic r4 as strongly as in the normal r4, whereas reciprocal grafts of future r2 to r4 position did not express Hox-2.9. The phenotype of ectopic rhombomeres developed according to their original position, as demonstrated by retrograde tracing of efferent cranial nerve nuclei. As early as stage-9-(six somites), both Hox-2.9 expression and segment identity are autonomous in the chick embryo hindbrain, independent both of position in the neuroepithelium and of signals from the underlying mesoderm.

Animals↗

PubMed1995

Identification and properties of the largest subunit of the DNA-dependent RNA polymerase of fish lymphocystis disease virus: dramatic difference in the domain organization in the family Iridoviridae.

Cytoplasmic DNA viruses encode a DNA-dependent RNA polymerase (DdRP) that is essential for transcription of viral genes. The amino acid sequences of the known largest subunits of DdRPs from different species contain highly conserved regions. Oligonucleotide primers, deduced from two conserved domains (RQP[T/S]LH and NADFDGDE) were used for detecting the corresponding gene of fish lymphocystis disease virus (FLCDV), a member of the family Iridoviridae, which replicates in the cytoplasm of infected cells of flatfish. The gene coding for the largest subunit of the DdRP was identified using a PCR-derived probe. The screening of the complete EcoRI gene library of the viral genome led to the identification of the gene locus of the largest subunit of the DdRP within the EcoRI DNA fragment B (12.4 kbp, 0.034 to 0.165 map units). The nucleotide sequence of a part (8334 bp) of the EcoRI DNA fragment B was determined and a large ORF on the lower strand (ATG = 5787; TAA = 2190) was detected which encodes a protein of 1199 amino acids. Comparison of the amino acid sequences of the largest subunits of the DdRP (RPO1) of FLCDV and Chilo iridescent virus (CIV) revealed a dramatic difference in their domain organization. Unlike the 1051 aa RPO1 of CIV, which lacks the C-terminal domain conserved in eukaryotic, eubacterial and other viral RNA polymerases, the 1199 aa RPO1 of FLCDV is fully collinear with its cellular and viral homologues. Despite this difference, comparative analysis of the amino acid sequences of viral and cellular RNA polymerases suggests a common origin for the largest RNA polymerase subunits of FLCDV and CIV.

Amino Acid Sequence↗

PubMed2000

Comparative maps of human 19p13.3 and mouse chromosome 10 allow identification of sequences at evolutionary breakpoints.

A cosmid/bacterial artificial chromosome (BAC) contiguous (contig) map of human chromosome (HSA) 19p13.3 has been constructed, and over 50 genes have been localized to the contig. Genes and anonymous ESTs from approximately 4000 kb of human 19p13.3 were placed on the central mouse chromosome 10 map by genetic mapping and pulsed-field gel electrophoresis (PFGE) analysis. A region of approximately 2500 kb of HSA 19p13.3 is collinear to mouse chromosome (MMU) 10. In contrast, the adjacent approximately 1200 kb are inverted. Two genes are located in a 50-kb region after the inversion on MMU 10, followed by a region of homology to mouse chromosome 17. The synteny breakpoint and one of the inversion breakpoints has been localized to sequenced regions in human <5 kb in size. Both breakpoints are rich in simple tandem repeats, including (TCTG)n, (CT)n, and (GTCTCT)n, suggesting that simple repeat sequences may be involved in chromosome breaks during evolution. The overall size of the region in mouse is smaller, although no large regions are missing. Comparing the physical maps to the genetic maps showed that in contrast to the higher-than-average rate of genetic recombination in gene-rich telomeric region on HSA 19p13.3, the average rate of recombination is lower than expected in the homologous mouse region. This might indicate that a hot spot of recombination may have been lost in mouse or gained in human during evolution, or that the position of sequences along the chromosome (telomeric compared to the middle of a chromosome) is important for recombination rates.

Animals↗

PubMed1997

Frequent collinear long transfer of DNA inclusive of the whole binary vector during Agrobacterium-mediated transformation.

When Agrobacterium was used to transform Nicotiana plumbaginifolia protoplasts and Arabidopsis thaliana roots and seedlings, a large number of plants were found in which not only the T-region defined by the border repeat sequences but the entire binary vector was integrated, as determined by both PCR and Southern analysis techniques. N. plumbaginifolia protoplast co-cultivation experiments yielded 3 out of 5 transformants with collinear sequence past the left border. In Arabidopsis root transformation experiments, 33% (6/18) of the transformants had T-DNA which exceeded the left border repeat. Vacuum infiltration of Arabidopsis seedlings produced even a greater percentage of transformants with sequences outside the left border repeat (62%, 39/63). The long transfer DNA cosegregated with the T-region encoded hygromycin resistance in the T2 progeny eliminating the possibility that long transfer DNA was of extrachromosomal or Agrobacterium origin. The high frequency of long transfer after vacuum infiltration of A. thaliana needs to be considered when analyzing T-DNA tagged mutants.

Arabidopsis↗

PubMed2026

Structural and functional characterization of peanut expansin proteins identifies AhEXPA3 as a stress-responsive regulator of seed germination.

Expansins are cell wall-associated proteins that play important roles in plant growth, development, and environmental responses, yet their structural features and functional significance in peanut remain insufficiently understood. Here, we performed a genome-wide identification and characterization of 70 expansin proteins in cultivated peanut. Phylogenetic analysis classified these genes into four subfamilies (EXPA, EXPB, EXLA, and EXLB), with conserved motif patterns and subgroup-specific exon-intron structures. Collinearity and evolutionary analyses revealed that segmental duplication mainly drove peanut expansin family expansion, with most duplicated gene pairs subsequently undergoing purifying selection. Promoter analysis identified abundant cis-regulatory elements associated with light responses, hormone signaling, and stress responses. Expression profiling indicated that many AhEXP genes were differentially expressed during seed germination and in response to abscisic acid (ABA), salt, and osmotic stresses. Among them, AhEXPA3 was identified as a stress-responsive expansin protein with marked transcriptional induction under abiotic stress conditions. Subcellular localization analysis suggested that AhEXPA3 exhibits an endoplasmic reticulum-associated localization pattern. Functional assays further demonstrated that heterologous expression of AhEXPA3 inhibited seed germination and early seedling establishment under stress conditions in both Arabidopsis thaliana and rice. These findings support a negative regulatory role of AhEXPA3 in stress-responsive seed germination and broaden current understanding of expansin protein function in legumes.

Germination↗