scholarly journals Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Gracia Zabala ◽  
Anupreet Kour ◽  
Lila O. Vodkin
Keyword(s):  
Seed Coat ◽  
Developmental Stages ◽  
Sequence Data ◽  
Acc Oxidase ◽  
Germplasm Collection ◽  
Cdna Libraries ◽  
Small Ring ◽  
Recurrent Parent ◽  
Expression Of Genes ◽  
Hormone Balance

Abstract Background To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region. Results RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10–25, 25–50 and 50–100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, iiR t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, iiR T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes. Conclusions We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.

scholarly journals Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

2005 ◽  
Vol 18 (3) ◽  
pp. 229-243 ◽  
Author(s):  
Thomas A. Randall ◽  
Rex A. Dwyer ◽  
Edgar Huitema ◽  
Katinka Beyer ◽  
Cristina Cvitanich ◽  
...  
Keyword(s):  
Phytophthora Infestans ◽  
Stress Responses ◽  
Large Scale ◽  
Developmental Stages ◽  
Sequence Data ◽  
Growth Conditions ◽  
Gene Content ◽  
Cdna Libraries ◽  
Class Iii ◽  
Genes Encoding

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coveragethe P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.

scholarly journals Diversity of metabolite accumulation patterns in inner and outer seed coats of pomegranate: exploring their relationship with genetic mechanisms of seed coat development

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Gaihua Qin ◽  
Chunyan Liu ◽  
Jiyu Li ◽  
Yongjie Qi ◽  
Zhenghui Gao ◽  
...  
Keyword(s):  
Seed Coat ◽  
Developmental Stages ◽  
Morphological Differentiation ◽  
Expression Of Genes ◽  
Monolignol Biosynthesis ◽  
Genes Encoding ◽  
Genetic Mechanisms ◽  
Sensory Qualities ◽  
Pomegranate Seeds ◽  
Seed Coats

AbstractThe expanded outer seed coat and the rigid inner seed coat of pomegranate seeds, both affect the sensory qualities of the fruit and its acceptability to consumers. Pomegranate seeds are also an appealing model for the study of seed coat differentiation and development. We conducted nontarget metabolic profiling to detect metabolites that contribute to the morphological differentiation of the seed coats along with transcriptomic profiling to unravel the genetic mechanisms underlying this process. Comparisons of metabolites in the lignin biosynthetic pathway accumulating in seed coat layers at different developmental stages revealed that monolignols, including coniferyl alcohol and sinapyl alcohol, greatly accumulated in inner seed coats and monolignol glucosides greatly accumulated in outer seed coats. Strong expression of genes involved in monolignol biosynthesis and transport might explain the spatial patterns of biosynthesis and accumulation of these metabolites. Hemicellulose constituents and flavonoids in particular accumulated in the inner seed coat, and candidate genes that might be involved in their accumulation were also identified. Genes encoding transcription factors regulating monolignol, cellulose, and hemicellulose metabolism were chosen by coexpression analysis. These results provide insights into metabolic factors influencing seed coat differentiation and a reference for studying seed coat developmental biology and pomegranate genetic improvement.

scholarly journals Anatomy and Histochemistry of Seed Coat Development of Wild (Pisum sativum subsp. elatius (M. Bieb.) Asch. et Graebn. and Domesticated Pea (Pisum sativum subsp. sativum L.)

2021 ◽  
Vol 22 (9) ◽  
pp. 4602
Author(s):  
Lenka Zablatzká ◽  
Jana Balarynová ◽  
Barbora Klčová ◽  
Pavel Kopecký ◽  
Petr Smýkal
Keyword(s):  
Pisum Sativum ◽  
Seed Coat ◽  
Developmental Stages ◽  
Histochemical Staining ◽  
Ruthenium Red ◽  
Detailed Knowledge ◽  
Maternal Plant ◽  
Wild Progenitor ◽  
Strong Signal ◽  
Biochemical Studies

In angiosperms, the mature seed consists of embryo, endosperm, and a maternal plant-derived seed coat (SC). The SC plays a role in seed filling, protects the embryo, mediates dormancy and germination, and facilitates the dispersal of seeds. SC properties have been modified during the domestication process, resulting in the removal of dormancy, mediated by SC impermeability. This study compares the SC anatomy and histochemistry of two wild (JI64 and JI1794) and two domesticated (cv. Cameor and JI92) pea genotypes. Histochemical staining of five developmental stages: 13, 21, 27, 30 days after anthesis (DAA), and mature dry seeds revealed clear differences between both pea types. SC thickness is established early in the development (13 DAA) and is primarily governed by macrosclereid cells. Polyanionic staining by Ruthenium Red indicated non homogeneity of the SC, with a strong signal in the hilum, the micropyle, and the upper parts of the macrosclereids. High peroxidase activity was detected in both wild and cultivated genotypes and increased over the development peaking prior to desiccation. The detailed knowledge of SC anatomy is important for any molecular or biochemical studies, including gene expression and proteomic analysis, especially when comparing different genotypes and treatments. Analysis is useful for other crop-to-wild-progenitor comparisons of economically important legume crops.

scholarly journals Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽  
2009 ◽  
Vol 136 (5) ◽  
pp. 469-485 ◽  
Author(s):  
A. S. TAFT ◽  
J. J. VERMEIRE ◽  
J. BERNIER ◽  
S. R. BIRKELAND ◽  
M. J. CIPRIANO ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sequence Data ◽  
Subsequent Development ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Expression ◽  
Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

scholarly journals Aminoethoxyvinylglycine Inhibits Fruit Abscission Induced by Naphthaleneacetic Acid and Associated Relationships with Expression of Genes for Ethylene Biosynthesis, Perception, and Cell Wall Degradation in ‘Delicious’ Apples

2008 ◽  
Vol 133 (6) ◽  
pp. 727-734 ◽  
Author(s):  
Hong Zhu ◽  
Eric P. Beers ◽  
Rongcai Yuan
Keyword(s):  
Cell Wall ◽  
Ethylene Production ◽  
Acc Oxidase ◽  
Ethylene Biosynthesis ◽  
Naphthaleneacetic Acid ◽  
Cell Wall Degradation ◽  
Oxidase Gene ◽  
Young Fruit ◽  
Fruit Abscission ◽  
Expression Of Genes

Effects of naphthaleneacetic acid (NAA) and aminoethoxyvinylglycine (AVG) on young fruit abscission, leaf and fruit ethylene production, and expression of genes related to ethylene biosynthesis and cell wall degradation were examined in ‘Delicious’ apples (Malus ×domestica Borkh.). NAA at 15 mg·L−1 increased fruit abscission and ethylene production of leaves and fruit when applied at the 11-mm stage of fruit development, whereas AVG, an inhibitor of ethylene biosynthesis, at 250 mg·L−1 reduced NAA-induced fruit abscission and ethylene production of leaves and fruit. NAA also increased expression of 1-aminocyclopropane-1-carboxylate (ACC) synthase genes (MdACS5A and MdACS5B), ACC oxidase gene (MdACO1), and ethylene receptor genes (MdETR1a, MdETR1b, MdETR2, MdERS1, and MdERS2) in fruit cortex and fruit abscission zones. However, AVG reduced NAA-induced expression of these genes except for MdERS2 in fruit abscission zones. NAA increased expression of the polygalacturonase gene MdPG2 in fruit abscission zones but not in fruit cortex, whereas AVG reduced NAA-enhanced expression of MdPG2 in fruit abscission zones. The expression of β-1,4-glucanase gene MdCel1 in fruit abscission zones was decreased by NAA but was unaffected by AVG. Our results suggest that ethylene biosynthesis, ethylene perception, and the MdPG2 gene are involved in young fruit abscission caused by NAA.

scholarly journals Sucrose Metabolism in Plants under Drought Stress Condition: A Review

2021 ◽  
Author(s):  
Anie Thomas ◽  
R. Beena
Keyword(s):  
Drought Stress ◽  
Developmental Stages ◽  
Sucrose Concentration ◽  
Turgor Pressure ◽  
Biomass Accumulation ◽  
Sucrose Metabolism ◽  
Drought Condition ◽  
Expression Of Genes ◽  
Source To Sink ◽  
Root Shoot Ratio

Drought stress reduces photosynthetic rate and leading to depletion of the energy source and lowers the yield. Under drought stress, reduced turgor pressure cause inhibition of cell elongation and impaired mitosis leads to reduction in growth rate. Role of sucrose metabolism under drought adaptation and response of plants to stress in different tissues and at different developmental stages. Cytoplasmic sucrose synthesis is more under drought condition and there is differential expression in tolerant and susceptible cultivars. Under drought condition, plant start consuming its own sink for its survival thus reducing sucrose concentration. But reduction in sucrose concentration is less in drought tolerant plants. Drought stress induced an increase of the root/shoot ratio, which was due to the increased inhibition of biomass accumulation of shoots compared to roots. Drought stress enhanced the activities of sucrose metabolic enzymes and up-regulated the expression of genes such as SPS, SuSy and INV. In addition, drought stress up-regulated the expression levels of SWEET and SUC and promoted the transport of sucrose from source to sink.

scholarly journals Transcriptome dynamics underlying flower color in marigold (Tagetes erecta L.)

2019 ◽  
Author(s):  
Huali Zhang ◽  
Shiya Zhang ◽  
Hua Zhang ◽  
Xi Chen ◽  
Fang Liang ◽  
...  
Keyword(s):  
Inbred Line ◽  
Developmental Stages ◽  
De Novo ◽  
Flower Color ◽  
Carotenoid Biosynthesis ◽  
Cdna Libraries ◽  
Carotenoid Content ◽  
Tagetes Erecta ◽  
Tagetes Erecta L ◽  
Carotenoid Degradation

Abstract Background: Marigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of flower colors. Despite its economic value, few biochemical and molecular studies have explored the generation of flower color in this species. Results: To study the mechanism underlying marigold petal color, we performed a metabolomics analysis and de novo cDNA sequencing on the inbred line ‘V-01’ and its petal color mutant ‘V-01M’ at four flower developmental stages. A total of 49,217 unigenes were identified from 24 cDNA libraries. Based on our transcriptomic and metabolomic analyses, we present an overview of carotenoid biosynthesis, degradation, and accumulation in marigold flowers. The carotenoid content of the yellow mutant ‘V-01M’ was higher than that of the orange inbred line ‘V-01’, and the abundances of the yellow compounds lutein, neoxanthin, violaxanthin, zeaxanthin, and antheraxanthin were significantly higher in the mutant. During flower development, the carotenoid biosynthesis genes were upregulated in both ‘V-01’ and ‘V-01M’, with no significant differences between the two lines. By contrast, the carotenoid degradation genes were dramatically downregulated in the yellow mutant ‘V-01M’. Conclusions: We therefore speculate that the carotenoid degradation genes are the key factors regulating the carotenoid content of marigold flowers. Our research provides a large amount of transcriptomic data and insights into the marigold color metabolome.

Single pass cDNA sequencing - a powerful tool to analyse gene expression in preparasitic juveniles of the southern root-knot nematode Meloidogyne incognita

Nematology ◽  
2001 ◽  
Vol 3 (2) ◽  
pp. 129-139 ◽  
Author(s):  
Jaap Bakker ◽  
Fred Gommers ◽  
Geert Smant ◽  
Pierre Abad ◽  
Marie-Noëlle Rosso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cdna Library ◽  
Meloidogyne Incognita ◽  
Sequence Data ◽  
Homo Sapiens ◽  
Large Fraction ◽  
Nematode Species ◽  
Cdna Libraries ◽  
Parasitic Nematodes ◽  
Root Knot Nematode

AbstractExpressed sequence tags (EST) have been widely used to assist in gene discovery in various organisms (e.g., Arabidopsis thaliana, Caenorhabditis elegans, Mus musculus, and Homo sapiens). In this paper we describe an EST project, which aims to investigate gene expression in Meloidogyne incognita at the onset of parasitism. Approximately 1000 5′-end sequence tags were produced from a cDNA library made of freshly hatched preparasitic second stage juveniles (J2). The EST were identified in the primary transformants of the cDNA library, and assigned to nine different functional groups, including (candidate) parasitism genes. A large fraction of the EST (45%) did not have a putative homologue in public databases. Sixty five percent of the EST that could be clustered into a functional group had putative homologues in other nematode species. EST were found for virtually all parasitism related genes that have been cloned from M. incognita to date. In addition, several novel genes were tagged, including a xylanase and a chitinase gene. The efficiency of EST projects, which produce sequence data for thousands of genes in months time without any difficult pre-selections of mRNA pools, makes random sequencing cDNA libraries a superior method to identify candidates for parasitism related genes in plant-parasitic nematodes. The sequences in this paper are retrievable from Genbank with the accession numbers BE191640 to BE191741, BE217592 to BE217720, BE225324 to BE225598, BE238852 to BE239221, and BE240829 to BE240865.

Characterization and Expression of Genes Encoding Superoxide Dismutase in the Oriental Armyworm, Mythimna separata (Lepidoptera: Noctuidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2381-2388 ◽  
Author(s):  
Hong-Bo Li ◽  
Chang-Geng Dai ◽  
Yong-Fu He ◽  
Yang Hu
Keyword(s):  
Superoxide Dismutase ◽  
Population Density ◽  
Developmental Stages ◽  
Mythimna Separata ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Key Factor ◽  
Important Pest ◽  
Oriental Armyworm

Abstract Superoxide dismutase (SOD) is an antioxidant metalloenzyme that catalyzes the dismutation of the superoxide anion O2− to O2 and H2O2. Many studies have focused on the role of SOD in response to abiotic stress, but its role during biotic stress, such as changes in organismal population density, has rarely been investigated. The oriental armyworm, Mythimna separata, is an economically important pest that exhibits phenotypic changes in response to population density. Solitary and gregarious phases occur at low and high population density, respectively. To examine the role of SODs in response to population density stress, we cloned two genes encoding SOD, MsCuZnSOD and MsMnSOD, and compared their expression in solitary and gregarious phases of M. separata. The MsCuZnSOD and MsMnSOD ORFs were 480 and 651 bp and encoded predicted protein products of 159 and 216 amino acids, respectively. The two SODs contained motifs that are typical of orthologous proteins. Real-time PCR indicated that the two SOD genes were expressed throughout developmental stages and were significantly upregulated in more mature stages of gregarious M. separata. Expression of the two SOD genes in various tissues of sixth-instar larvae was higher in gregarious versus solitary insects. Furthermore, expression of the SOD genes was significantly upregulated in response to crowding in solitary individuals, but suppressed in gregarious insects subjected to isolation. Collectively, these results suggest that population density may be key factor in the induction of SOD genes in M. separata.

scholarly journals Distinct Patterns of Gene Expression Associated with Development of Fluconazole Resistance in Serial Candida albicansIsolates from Human Immunodeficiency Virus-Infected Patients with Oropharyngeal Candidiasis

1998 ◽  
Vol 42 (11) ◽  
pp. 2932-2937 ◽  
Author(s):  
Jose L. Lopez-Ribot ◽  
Robert K. McAtee ◽  
Linda N. Lee ◽  
William R. Kirkpatrick ◽  
Theodore C. White ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Immunodeficiency Virus ◽  
Sequence Data ◽  
Point Mutations ◽  
Oropharyngeal Candidiasis ◽  
Fluconazole Resistance ◽  
Expression Of Genes ◽  
Immunodeficiency Virus ◽  
Major Facilitator ◽  
Abc Transporter Genes

ABSTRACT Resistance to fluconazole is becoming an increasing problem in the management of oropharyngeal candidiasis in human immunodeficiency virus-infected patients. Strains obtained from five patients developed decreased fluconazole susceptibility over time. DNA strain typing confirmed the high degree of relatedness among isolates from one patient and the variability among isolates from different patients. Expression of genes involved in development of fluconazole resistance was monitored in each isolate using probes specific for ERG11 (lanosterol 14α-demethylase), MDR1 (a major facilitator), andCDR (ATP-binding cassette or ABC transporter) genes. Increased expression of CDR genes was detected in the series of isolates from two patients. Isolates from one of the two patients also demonstrated increased ERG11 expression, whereas isolates from the other patient did not. Increased levels ofMDR1 mRNA correlated with increased resistance in sequential isolates from another patient. Initial overexpression ofMDR1 with subsequent overexpression of CDRgenes and a final isolate again overexpressing MDR1 were detected in serial isolates from another patient. In another patient, overexpression of these genes was not detected despite an eightfold increase in fluconazole MIC. In this patient, sequence data of theERG11 gene revealed no point mutations associated with decreased susceptibility. Five different patterns of gene expression were observed in isolates recovered from five patients who developed resistance. Therefore, these experiments demonstrate that a variety of mechanisms or combinations of mechanisms are associated with the development of fluconazole drug resistance. Additional studies are needed to estimate the frequency and clinical impact of these mechanisms of resistance.

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