scholarly journals Medicago ABI3 Splicing Isoforms Regulate the Expression of Different Gene Clusters to Orchestrate Seed Maturation

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1710
Author(s):  
David Lalanne ◽  
Jaiana Malabarba ◽  
Joseph Ly Vu ◽  
Michaela Hundertmark ◽  
Julien Delahaie ◽  
...  
Keyword(s):  
Seed Development ◽  
Desiccation Tolerance ◽  
Expression Patterns ◽  
Seed Viability ◽  
Gene Clusters ◽  
Seed Maturation ◽  
Specific Gene ◽  
Seed Color ◽  
Loss Of Function ◽  
Model Legume

Seed maturation comprises important developmental processes, such as seed filling and the acquisition of seed germination capacity, desiccation tolerance, longevity, and dormancy. The molecular regulation of these processes is tightly controlled by the LAFL transcription factors, among which ABSCISIC ACID INSENSITIVE 3 (ABI3) was shown to be involved in most of these seed maturation processes. Here, we studied the ABI3 gene from Medicago truncatula, a model legume plant for seed studies. With the transcriptomes of two loss-of-function Medicago abi3 mutants, we were able to show that many gene classes were impacted by the abi3 mutation at different stages of early, middle, and late seed maturation. We also discovered three MtABI3 expression isoforms, which present contrasting expression patterns during seed development. Moreover, by ectopically expressing these isoforms in Medicago hairy roots generated from the abi3 mutant line background, we showed that each isoform regulated specific gene clusters, suggesting divergent molecular functions. Furthermore, we complemented the Arabidopsis abi3 mutant with each of the three MtABI3 isoforms and concluded that all isoforms were capable of restoring seed viability and desiccation tolerance phenotypes even if not all isoforms complemented the seed color phenotype. Taken together, our results allow a better understanding of the ABI3 network in Medicago during seed development, as well as the discovery of commonly regulated genes from the three MtABI3 isoforms, which can give us new insights into how desiccation tolerance and seed viability are regulated.

scholarly journals Transcriptome Profiling Reveals Spatial-temporal Dynamics of Gene Expression Essential for Soybean Seed Development

2020 ◽  
Author(s):  
Hengyou Zhang ◽  
Zhenbin Hu ◽  
Yuming Yang ◽  
Xiaoqian Liu ◽  
Haiyan Lv ◽  
...  
Keyword(s):  
Seed Development ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Soybean Seed ◽  
Transcriptome Profiling ◽  
Transcript Abundance ◽  
Specific Gene ◽  
Oilseed Crop ◽  
Seed Formation ◽  
Developing Seeds

Abstract Background: Seeds are the economic basis of oilseed crops, especially for soybean, thus far the most widely cultivated oilseed crop worldwide. Seed development is accompanied with a multitude of diverse cellular processes and revealing the underlying regulatory activities is critical for seed improvement. Results: Here, we profiled transcriptomes of developing seeds (20, 25, 30, 40 days after flowering) representing key points of seed development from early to full development. We identified a set of highly-abundant genes and highlighted the importance of these genes to support nutrient accumulation and transcriptional regulation in developing seeds. We identified 8,925 differentially expressed genes that exhibited temporal expression patterns over the course and had expression specificities in distinct tissues including seeds and non-seed tissues (roots, stems, leaves). Genes with specificities to non-seed tissues have tissue-specialized roles while remain relatively low transcript abundance in developing seeds, exhibiting their supportive roles spatially for seed development. Co-expression network analysis identified several under-explored genes in soybean that bridge tissue-specific gene modules. Conclusions: Our study provides a global view of gene activities and biological processes critical for seed formation in soybean and prioritizes a set of genes for further study. The results shed insight into the mechanism controlling seed development and storage reserves.

Identification of tissue-specific gene clusters and orthologues of nodulation-related genes in Vigna angularis

2014 ◽  
Vol 12 (S1) ◽  
pp. S21-S26 ◽  
Author(s):  
Yang Jae Kang ◽  
Jayern Lee ◽  
Yong Hwan Kim ◽  
Suk-Ha Lee
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Lotus Japonicus ◽  
Gene Clusters ◽  
Specific Gene ◽  
Vigna Angularis ◽  
Model Legume ◽  
Tissue Specific ◽  
Autoregulation Of Nodulation ◽  
Species Specific

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.

scholarly journals A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

2019 ◽  
Author(s):  
Stewart TG Burgess ◽  
Edward J Marr ◽  
Kathryn Bartley ◽  
Francesca G Nunn ◽  
Rachel E Down ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Specific Gene ◽  
Multigene Families ◽  
Psoroptes Ovis ◽  
Specific Expression ◽  
Development Of Resistance

ABSTRACTPsoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources. Building on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.

scholarly journals Varying intolerance of gene pathways to mutational classes explain genetic convergence across neuropsychiatric disorders

2016 ◽  
Author(s):  
Shahar Shohat ◽  
Eyal Ben-David ◽  
Sagiv Shifman
Keyword(s):  
Gene Expression ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Expression Patterns ◽  
Neuropsychiatric Disorders ◽  
Autism Spectrum ◽  
Specific Gene ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Brain Gene Expression

AbstractGenetic susceptibility to Intellectual disability (ID), autism spectrum disorder (ASD) and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes with de novo mutations in the three disorders and genes implicated by SCZ genome-wide association study (GWAS). Using biological annotations and brain gene expression, we show that mutation class explains enrichment patterns more than specific disorder. Genes with loss of function mutations and genes with missense mutations were enriched with different pathways, shared with genes intolerant to mutations. Specific gene expression patterns were found for each disorder. ID genes were preferentially expressed in fetal cortex, ASD genes also in fetal cerebellum and striatum, and genes associated with SCZ were most significantly enriched in adolescent cortex. Our study suggests that convergence across neuropsychiatric disorders stems from vulnerable pathways to genetic variations, but spatiotemporal activity of genes contributes to specific phenotypes.

scholarly journals Changes in Proline Levels during Seed Development of Orthodox and Recalcitrant Seeds of Genus Acer in a Climate Change Scenario

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1362
Author(s):  
Joanna Kijowska-Oberc ◽  
Aleksandra M. Staszak ◽  
Mikołaj K. Wawrzyniak ◽  
Ewelina Ratajczak
Keyword(s):  
Climate Change ◽  
Seed Development ◽  
Desiccation Tolerance ◽  
Seed Viability ◽  
Climatic Conditions ◽  
Proline Content ◽  
Change Scenario ◽  
Acer Pseudoplatanus ◽  
Recalcitrant Seeds ◽  
Seed Desiccation

In the present study, we examined the utility of proline usage as a biochemical indicator of metabolic changes caused by climate change (mean temperature and precipitation) during seed development of two Acer species differing in desiccation tolerance: Norway maple (Acer platanoides L.—desiccation tolerant—orthodox) and sycamore (Acer pseudoplatanus L.—desiccation sensitive—recalcitrant). In plants, proline is an element of the antioxidant system, which has a role in response to water loss and high temperatures. Our study considered whether proline could be treated as an indicator of tree seed viability, crucial for genetic resources conservation. Proline content was measured biweekly in developing seeds (between 11 and 23 weeks after flowering) collected in consecutive years (2017, 2018, and 2019). We showed that proline concentrations in recalcitrant seeds were positively correlated with mean two-week temperature. In contrast, in orthodox seeds no such relationship was found. Proline content proved to be sensitive to thermal-moisture conditions changes, which makes it a promising biochemical marker of seed desiccation tolerance in different climatic conditions.

scholarly journals Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hengyou Zhang ◽  
Zhenbin Hu ◽  
Yuming Yang ◽  
Xiaoqian Liu ◽  
Haiyan Lv ◽  
...  
Keyword(s):  
Seed Development ◽  
Temporal Dynamics ◽  
Expression Patterns ◽  
Critical Time ◽  
Soybean Seed ◽  
Transcript Abundance ◽  
Specific Gene ◽  
Oilseed Crop ◽  
Seed Formation ◽  
Developing Seeds

Abstract Background Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. Results In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. Conclusions Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.

scholarly journals A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Edward J. Marr ◽  
Kathryn Bartley ◽  
Francesca G. Nunn ◽  
Rachel E. Down ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Specific Gene ◽  
Multigene Families ◽  
Psoroptes Ovis ◽  
Specific Expression ◽  
Development Of Resistance

Abstract Background Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources. Results Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression. Conclusions The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome.

scholarly journals Characterization and analysis of the transcriptome in Arapaima gigas using multi-tissue RNA-sequencing

2020 ◽  
Author(s):  
Danilo L. Martins ◽  
Leonardo R. S. Campos ◽  
André M. Ribeiro-dos-Santos ◽  
Ana Carolina M. F. Coelho ◽  
Renata L. Dantas ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Molecular Networks ◽  
Specific Gene ◽  
Protein Coding ◽  
Tissue Specific ◽  
Functional Studies ◽  
A Genome ◽  
Arapaima Gigas

AbstractArapaima gigas is a giant bony tongue air-breathing fish, and a promising species for aquaculture due to its particular features. However, there is still a lack of information on its biology and few transcriptome studies are available. Our aim was to characterize the transcriptome of arapaima in order to shed light on molecular networks contributing to its unique traits. Through RNA-sequencing, we generated a transcriptome from eight tissues (brain, pituitary, heart, muscle, kidney, lung, ovary, and testis) collected from arapaima adults specimens. Using a genome-guided strategy associated with homologous protein evidence, 57,706 transcripts were assembled, which aligned to 23,353 high confidence protein-coding genes. The analysis revealed a global view of expression patterns, as well as it allowed us to identify tissue-specific gene clusters, transcription factors within the clusters, and to compare expression patterns between male and female. These analyses has generated tissue-specific and sex-biased transcriptome profiles, which will be helpful to understand its molecular biology, evolution, and also guide future functional studies of the arapaima.

scholarly journals Medicago truncatulaFerroportin2 mediates iron import into nodule symbiosomes

2019 ◽  
Author(s):  
Viviana Escudero ◽  
Isidro Abreu ◽  
Manuel Tejada-Jiménez ◽  
Elena Rosa-Núñez ◽  
Julia Quintana ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Symbiotic Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Specific Gene ◽  
Nitrogen Fixing ◽  
Loss Of Function ◽  
Model Legume ◽  
Endosymbiotic Bacteria ◽  
Signal Transduction Proteins ◽  
Iron Delivery

ABSTRACTIron is an essential cofactor for symbiotic nitrogen fixation. It is required by many of the enzymes facilitating the conversion of N2into NH4+by endosymbiotic bacteria living within root nodule cells, including signal transduction proteins, O2homeostasis systems, and nitrogenase itself. Consequently, host plants have developed a transport network to deliver essential iron to nitrogen-fixing nodule cells. Model legumeMedicago truncatula Ferroportin2(MtFPN2) is a nodule-specific gene that encodes an iron-efflux protein. MtFPN2 is located in intracellular membranes in the nodule vasculature, and in the symbiosome membranes that contain the nitrogen-fixing bacteria in the differentiation and early-fixation zones of the nodules. Loss-of-function ofMtFPN2leads to altered iron distribution and speciation in nodules, which causes a reduction in nitrogenase activity and in biomass production. Using promoters with different tissular activity to driveMtFPN2expression inMtFPN2mutants, we determined that MtFPN2-facilitated iron delivery across symbiosomes is essential for symbiotic nitrogen fixation, while its presence in the vasculature does not seem to play a major role in in the conditions tested.

Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation

2021 ◽  
Author(s):  
Debamalya Chatterjee ◽  
Kameron Wittmeyer ◽  
Tzuu-fen Lee ◽  
Jin Cui ◽  
Neela H Yennawar ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Ectopic Expression ◽  
Cell Types ◽  
Endosperm Development ◽  
Adjacent Cell ◽  
Specific Gene ◽  
Loss Of Function ◽  
Wall Ingrowth ◽  
Wide Range ◽  
The Impact

Abstract Maize (Zea mays L.) Ufo1-1 is a spontaneous dominant mutation of the unstable factor for orange1 (ufo1). We recently cloned ufo1, which is a Poaceae specific gene expressed solely during seed development in maize. Here we have characterized Ufo1-1 and a loss-of-function Ds insertion allele (ufo1-Dsg) to decipher the role of ufo1 in maize. We found that both ufo1 mutant alleles impact sugars and hormones, and have defects in the basal endosperm transfer layer (BETL) and adjacent cell types. The Ufo1-1 BETL had reduced cell elongation and cell wall ingrowth, resulting in cuboidal shaped transfer cells. In contrast, the ufo1-Dsg BETL cells showed a reduced overall size with abnormal wall ingrowth. Expression analysis identified the impact of ufo1 on several genes essential for BETL development. The overexpression of Ufo1-1 in various tissues leads to ectopic phenotypes, including abnormal cell organization and stomata subsidiary cell defects. Interestingly, pericarp and leaf transcriptomes also showed that as compared to wild type, Ufo1-1 had ectopic expression of endosperm development-specific genes. This study shows that Ufo1-1 impacts the expression patterns of a wide range of genes involved in various developmental processes.

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