scholarly journals Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii

2019 ◽  
Vol 32 (1) ◽  
pp. 81-99 ◽  
Author(s):  
Sabyasachi Mandal ◽  
Wangming Ji ◽  
Thomas D. McKnight
Keyword(s):  
Plant Defense ◽  
Candidate Gene ◽  
Gene Networks ◽  
Solanum Pennellii ◽  
Wild Tomato

scholarly journals Candidate Gene Networks for Acylsugar Metabolism and Plant Defense in Wild Tomato Solanum pennellii

2018 ◽  
Author(s):  
Sabyasachi Mandal ◽  
Wangming Ji ◽  
Thomas D. McKnight
Keyword(s):  
Fatty Acids ◽  
Plant Defense ◽  
Candidate Genes ◽  
Gene Networks ◽  
Solanum Pennellii ◽  
Biosynthetic Genes ◽  
Defense Proteins ◽  
Metabolic Genes ◽  
Branched Chain ◽  
Chain Fatty Acids

ABSTRACTMany plants in the Solanaceae family secrete acylsugars, which are branched-chain and straight-chain fatty acids esterified to glucose or sucrose. These compounds have important roles in plant defense and potential commercial applications. However, several acylsugar metabolic genes remain unidentified, and little is known about regulation of this pathway. We used comparative transcriptomic analysis between low- and high-acylsugar-producing accessions of Solanum pennellii and found that expression levels of most acylsugar metabolic genes, including known acylsucrose biosynthetic genes and novel candidate genes (putatively encoding a ketoacyl-ACP synthase IV/II-like enzyme, peroxisomal acyl-activating enzymes, ABC transporters, and central carbon metabolic enzymes), were positively correlated with acylsugar accumulation, except two acylglucose biosynthetic genes. Genes putatively encoding oxylipin metabolic proteins, subtilisin-like proteases, and other antimicrobial defense proteins were upregulated in low-acylsugar-producing accessions, possibly to compensate for diminished defense activities of acylsugars. Gene co-expression network analysis clustered most differentially expressed genes into two separate modules and identified genetic networks associated with acylsugar production and plant defense. Transcriptome analysis after inhibition of biosynthesis of branched-chain amino acids (precursors to branched-chain fatty acids) further supported the coordinated regulation of most acylsugar candidate genes and identified three putative AP2-family transcription factor genes that form a strong co-expression network with many acylsugar metabolic genes.

scholarly journals Integration of anatomy ontology data with protein–protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Pasan C. Fernando ◽  
Paula M. Mabee ◽  
Erliang Zeng
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Gene Networks ◽  
Prediction Accuracy ◽  
Gene Prediction ◽  
Anatomical Entity ◽  
Anatomy Ontology ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Entity Relationships

Abstract Background Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein–protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. Moreover, PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes. Therefore, we developed an integrative framework to improve the candidate gene prediction accuracy for anatomical entities by combining existing experimental knowledge about gene-anatomical entity relationships with PPI networks using anatomy ontology annotations. We hypothesized that this integration improves the quality of the PPI networks by reducing the number of false positive and false negative interactions and is better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomical entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These anatomy-based gene networks were semantic networks, as they were constructed based on the anatomy ontology annotations that were obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database and compared the performance of their network-based candidate gene predictions. Results According to evaluations of candidate gene prediction performance tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks, which were semantically improved PPI networks, showed better performances by having higher area under the curve values for receiver operating characteristic and precision-recall curves than PPI networks for both zebrafish and mouse. Conclusion Integration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improved the candidate gene prediction accuracy and optimized them for predicting candidate genes for anatomical entities.

scholarly journals Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0248607
Author(s):  
Amber N. Bible ◽  
Mang Chang ◽  
Jennifer L. Morrell-Falvey
Keyword(s):  
Candidate Gene ◽  
Gene Networks ◽  
Populus Deltoides ◽  
Inducible Promoter ◽  
Microbial Colonization ◽  
Plant Roots ◽  
Plant Colonization ◽  
Gene Products ◽  
Diguanylate Cyclase ◽  
Diguanylate Cyclases

Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the identities and functions of many of these gene products have yet to be discovered. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides, forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots. One of these diguanylate cyclases, DGC2884, localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate gene products that may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into the mechanisms of plant association as well as the activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.

scholarly journals Intraspecific genetic variation underlying postmating reproductive barriers between species in the wild tomato clade (Solanum sect. Lycopersicon)

2019 ◽  
Author(s):  
Cathleen P Jewell ◽  
Simo Zhang ◽  
Matthew J. S. Gibson ◽  
Alejandro Tovar-Méndez ◽  
Bruce McClure ◽  
...  
Keyword(s):  
Intraspecific Variation ◽  
Interspecific Cross ◽  
Female Reproductive Tract ◽  
Reproductive Barriers ◽  
Solanum Pennellii ◽  
Wild Tomato ◽  
Genetic Components ◽  
Standing Variation ◽  
Pollen Rejection ◽  
In The Wild

AbstractA goal of speciation genetics is to understand how the genetic components underlying interspecific reproductive barriers originate within species. Unilateral incompatibility (UI) is a postmating prezygotic barrier in which pollen rejection in the female reproductive tract (style) occurs in only one direction of an interspecific cross. Natural variation in the strength of UI has been observed among populations within species in the wild tomato clade. In some cases, molecular loci underlying self-incompatibility (SI) are associated with this variation in UI, but the mechanistic connection between these intra- and inter-specific pollen rejection behaviors is poorly understood in most instances. We generated an F2 population between SI and SC genotypes of a single species, Solanum pennellii, to examine the genetic basis of intraspecific variation in the strength of UI against other species, and to determine whether loci underlying SI are genetically associated with this variation. We found that F2 individuals vary in the rate at which UI rejection occurs. One large effect QTL detected for this trait co-localized with the SI-determining S-locus. Moreover, individuals that expressed S-RNase—the S-locus protein involved in SI pollen rejection—in their styles had much more rapid UI responses compared to those without S-RNase protein. Our analysis shows that intraspecific variation at mate choice loci—in this case at loci that prevent self-fertilization—can contribute to variation in the strength of interspecific isolation, including postmating prezygotic barriers. Understanding the nature of such standing variation can provide insight into the accumulation of these barriers between diverging lineages.

scholarly journals Characterization of 15-cis-ζ-Carotene Isomerase Z-ISO in Cultivated and Wild Tomato Species Differing in Ripe Fruit Pigmentation

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2365
Author(s):  
Gleb I. Efremov ◽  
Anna V. Shchennikova ◽  
Elena Z. Kochieva
Keyword(s):  
Regulatory Elements ◽  
Fruit Color ◽  
Carotenoid Content ◽  
Fleshy Fruit ◽  
Ripe Fruit ◽  
Solanum Pennellii ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
The Difference

Isomerization of 9,15,9′-tri-cis-ζ-carotene mediated by 15-cis-ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade (Solanum section Lycopersicon) comprises the cultivated tomato (Solanum lycopersicum) and 12 related wild species differing in fruit color and, thus, represents a good model for studying carotenogenesis in fleshy fruit. In this study, we identified homologous Z-ISO genes, including 5′-UTRs and promoter regions, in 12 S. lycopersicum cultivars and 5 wild tomato species (red-fruited Solanum pimpinellifolium, yellow-fruited Solanum cheesmaniae, and green-fruited Solanum chilense, Solanum habrochaites, and Solanum pennellii). Z-ISO homologs had a highly conserved structure, suggesting that Z-ISO performs a similar function in tomato species despite the difference in their fruit color. Z-ISO transcription levels positively correlated with the carotenoid content in ripe fruit of the tomatoes. An analysis of the Z-ISO promoter and 5′-UTR sequences revealed over 130 cis-regulatory elements involved in response to light, stresses, and hormones, and in the binding of transcription factors. Green- and red/yellow-fruited Solanum species differed in the number and position of cis-elements, indicating changes in the transcriptional regulation of Z-ISO expression during tomato evolution, which likely contribute to the difference in fruit color.

scholarly journals Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities

2020 ◽  
Author(s):  
Pasan Chinthana Fernando ◽  
Paula M Mabee ◽  
Erliang Zeng
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Protein Interaction ◽  
Gene Networks ◽  
Gene Prediction ◽  
Anatomy Ontology ◽  
Experimental Knowledge ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Network Quality

AbstractBackgroundIdentification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet-lab techniques used for this purpose, such as gene knockout, are high in resource and time consumption. Protein-protein interaction (PPI) networks are frequently used to predict disease genes for humans and gene candidates for molecular functions, but they are rarely used to predict genes for anatomical entities. This is because PPI networks suffer from network quality issues, which can be a limitation for their usage in predicting candidate genes for anatomical entities. We developed an integrative framework to predict candidate genes for anatomical entities by combining existing experimental knowledge about gene-anatomy relationships with PPI networks using anatomy ontology annotations. We expected this integration to improve the quality of the PPI networks and be better optimized to predict candidate genes for anatomical entities. We used existing Uberon anatomy entity annotations for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between the genes. These ‘anatomy-based gene networks’ are semantic networks, as they are constructed based on the Uberon anatomy ontology annotations that are obtained from the experimental data in the literature. We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retrieved from the STRING database, and we compared the performance of their network-based candidate gene predictions.ResultsAccording to candidate gene prediction performance evaluations tested under four different semantic similarity calculation methods (Lin, Resnik, Schlicker, and Wang), the integrated networks showed better receiver operating characteristic (ROC) and precision-recall curve performances than PPI networks for both zebrafish and mouse.ConclusionIntegration of existing experimental knowledge about gene-anatomical entity relationships with PPI networks via anatomy ontology improves the network quality, which makes them better optimized for predicting candidate genes for anatomical entities.

Identification and Expression Pattern of a ZPR1 Gene in Wild Tomato (Solanum Pennellii)

2012 ◽  
Vol 31 (2) ◽  
pp. 409-417 ◽  
Author(s):  
Jinhua Li ◽  
Wei Sima ◽  
Bo Ouyang ◽  
Zhidan Luo ◽  
Changxian Yang ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Solanum Pennellii ◽  
Wild Tomato

scholarly journals Evolution of metabolic novelty: A trichome-expressed invertase creates specialized metabolic diversity in wild tomato

2019 ◽  
Vol 5 (4) ◽  
pp. eaaw3754 ◽  
Author(s):  
Bryan J. Leong ◽  
Daniel B. Lybrand ◽  
Yann-Ru Lou ◽  
Pengxiang Fan ◽  
Anthony L. Schilmiller ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Gland Cell ◽  
Metabolic Enzyme ◽  
South American ◽  
Metabolic Diversity ◽  
Solanum Pennellii ◽  
Wild Tomato ◽  
Specialized Metabolites ◽  
New Class ◽  
In The Wild

Plants produce a myriad of taxonomically restricted specialized metabolites. This diversity—and our ability to correlate genotype with phenotype—makes the evolution of these ecologically and medicinally important compounds interesting and experimentally tractable. Trichomes of tomato and other nightshade family plants produce structurally diverse protective compounds termed acylsugars. While cultivated tomato (Solanum lycopersicum) strictly accumulates acylsucroses, the South American wild relative Solanum pennellii produces copious amounts of acylglucoses. Genetic, transgenic, and biochemical dissection of the S. pennellii acylglucose biosynthetic pathway identified a trichome gland cell–expressed invertase-like enzyme that hydrolyzes acylsucroses (Sopen03g040490). This enzyme acts on the pyranose ring–acylated acylsucroses found in the wild tomato but not on the furanose ring–decorated acylsucroses of cultivated tomato. These results show that modification of the core acylsucrose biosynthetic pathway leading to loss of furanose ring acylation set the stage for co-option of a general metabolic enzyme to produce a new class of protective compounds.

scholarly journals Schizophrenia Gene Networks and Pathways and Their Applications for Novel Candidate Gene Selection

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e11351 ◽  
Author(s):  
Jingchun Sun ◽  
Peilin Jia ◽  
Ayman H. Fanous ◽  
Edwin van den Oord ◽  
Xiangning Chen ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Gene Networks ◽  
Gene Selection
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