scholarly journals MicroRNAs expression dynamics reveal post-transcriptional mechanisms regulating seed development in Phaseolus vulgaris L.

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
José Ricardo Parreira ◽  
Michela Cappuccio ◽  
Alma Balestrazzi ◽  
Pedro Fevereiro ◽  
Susana de Sousa Araújo
Keyword(s):  
Phaseolus Vulgaris ◽  
Seed Development ◽  
Developmental Stages ◽  
Production Systems ◽  
Expression Profiles ◽  
Target Prediction ◽  
Grain Legumes ◽  
Developing Seeds ◽  
Expression Of Genes ◽  
Post Transcriptional Regulation

AbstractThe knowledge on post-transcriptional regulation mechanisms implicated in seed development (SD) is still limited, particularly in one of the most consumed grain legumes, Phaseolus vulgaris L. We explore for the first time the miRNA expression dynamics in P. vulgaris developing seeds. Seventy-two known and 39 new miRNAs were found expressed in P. vulgaris developing seeds. Most of the miRNAs identified were more abundant at 10 and 40 days after anthesis, suggesting that late embryogenesis/early filling and desiccation were SD stages in which miRNA action is more pronounced. Degradome analysis and target prediction identified targets for 77 expressed miRNAs. While several known miRNAs were predicted to target HD-ZIP, ARF, SPL, and NF-Y transcription factors families, most of the predicted targets for new miRNAs encode for functional proteins. MiRNAs-targets expression profiles evidenced that these miRNAs could tune distinct seed developmental stages. MiRNAs more accumulated at early SD stages were implicated in regulating the end of embryogenesis, postponing the seed maturation program, storage compound synthesis and allocation. MiRNAs more accumulated at late SD stages could be implicated in seed quiescence, desiccation tolerance, and longevity with still uncovered roles in germination. The miRNAs herein described represent novel P. vulgaris resources with potential application in future biotechnological approaches to modulate the expression of genes implicated in legume seed traits with impact in horticultural production systems.

scholarly journals Fasulyede Büyüme ve Gelişme Dönemleri

2014 ◽  
Vol 3 (2) ◽  
pp. 84 ◽  
Author(s):  
Ramazan İlhan Aytekin ◽  
Sevgi Çalışkan
Keyword(s):  
Phaseolus Vulgaris ◽  
Seed Development ◽  
Plant Development ◽  
Developmental Stages ◽  
Bean Plant ◽  
Main Stem ◽  
Vegetative Stage ◽  
Biological Cycle ◽  
Phaseolus Vulgaris L ◽  
Pod Development

Uniform description of developmental stages in crops improve communication among producers, researchers and others. A standardized, accurate, and easy system is needed to describe bean (Phaseolus vulgaris L.) plant development. The objective of this study was to develop and describe stages of bean plant development in a manner which is simple but accurate. The biological cycle of the bean plant is divided into two successive phases: the vegetative stage (V) and the reproductive stage (R). Vegetative stages are determined by counting the number of trifoliolate leaves (V1 to VN) on the main stem beginning above the unifoliate leaf. Reproductive stages R1 and R2 are based on flowering, R3 and R4 on pod development, R5 and R6 on seed development, and R7, R8 and R9 on maturation.

scholarly journals Dynamic Clustering of Gene Expression

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Lingling An ◽  
R. W. Doerge
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Optimal Number ◽  
Sequential Data ◽  
Dynamic Clustering ◽  
Biological Processes ◽  
Time Frequency ◽  
Expression Of Genes

It is well accepted that genes are simultaneously involved in multiple biological processes and that genes are coordinated over the duration of such events. Unfortunately, clustering methodologies that group genes for the purpose of novel gene discovery fail to acknowledge the dynamic nature of biological processes and provide static clusters, even when the expression of genes is assessed across time or developmental stages. By taking advantage of techniques and theories from time frequency analysis, periodic gene expression profiles are dynamically clustered based on the assumption that different spectral frequencies characterize different biological processes. A two-step cluster validation approach is proposed to statistically estimate both the optimal number of clusters and to distinguish significant clusters from noise. The resulting clusters reveal coordinated coexpressed genes. This novel dynamic clustering approach has broad applicability to a vast range of sequential data scenarios where the order of the series is of interest.

scholarly journals Fatty Acid and Transcript Profiling in Developing Seeds of Three Brassica napus Cultivars

2015 ◽  
Vol 72 (1) ◽  
pp. 3-32
Author(s):  
Mariana Petkova ◽  
Wun S. Chao ◽  
Leonard Cook ◽  
Mark West ◽  
Mukhlesur Rahman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Seed Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Eicosenoic Acid ◽  
Expression Of Genes ◽  
Spring Canola

Abstract Fatty acid levels and gene expression profiles for selected genes associated with the synthesis of fatty acids (FA), triacylglycerol, and oil body proteins were examined in three oilseed rape (Brassica napus) cultivars that have utility for cultivar development in our spring canola breeding program. The seed oil content of Bronowski, Q2, and Westar was 39.0, 40.1, and 40.6%, respectively at 40 days after flowering (DAF). During the 20 to 40 day period of seed development, cultivars had varying levels of palmitic, stearic, oleic, linoleic, α-linolenic, eicosenoic, and erucic acid. In general, the percentage of each FA was similar among the cultivars during seed development. However, the level of oleic acid was lower and the levels of eicosenoic acid and erucic acid were higher in Bronowski than in Q2 and Westar seeds; linoleic acid also tended to be lower in Bronowski. Gene expression among the cultivars was similar from 10 to 40 DAF. The few exceptions were that expression of KAS1 and SAD were higher in Westar and Q2 than in Bronowski at 25 DAF, SAD was highest in Q2, intermediate in Westar, and lowest in Bronowski at 35 DAF, FAD2 was higher in Q2 than in Bronowski at 35 DAF, FAD3 was higher in Q2 than in Bronowski at 15 DAF and Q2 and Westar at 25 and 30 DAF, and FAE1 was higher in Westar and Q2 than in Bronowski at 30 DAF. Correlation analysis for gene expression against DAF for each genotype supported a common trend in gene expression among the three cultivars with gene expression tending to decrease over time; except for LPAAT, which tended to increase. The correlation between the level of FAs and expression of genes by genotype indicated no general trend; rather correlations seem to depend on the genotype.

scholarly journals Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301

Genes ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 686 ◽  
Author(s):  
Li ◽  
Jiao ◽  
He ◽  
Sun ◽  
Xu ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Triticum Aestivum L ◽  
Differentially Expressed ◽  
High Yield ◽  
Differentially Expressed Mirnas ◽  
Key Events ◽  
Post Transcriptional Regulation

Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA–mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA–mRNA regulatory networks during tillering and early spike differentiating were established.

scholarly journals miRTil: An Extensive Repository for Nile Tilapia microRNA Next Generation Sequencing Data

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1752
Author(s):  
Luiz Augusto Bovolenta ◽  
Danillo Pinhal ◽  
Marcio Luis Acencio ◽  
Arthur Casulli de Oliveira ◽  
Simon Moxon ◽  
...  
Keyword(s):  
Nile Tilapia ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Interaction Network ◽  
Mature Mirnas ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Genomic Context ◽  
Protein Coding ◽  
Post Transcriptional Regulation

Nile tilapia is the third most cultivated fish worldwide and a novel model species for evolutionary studies. Aiming to improve productivity and contribute to the selection of traits of economic impact, biotechnological approaches have been intensively applied to species enhancement. In this sense, recent studies have focused on the multiple roles played by microRNAs (miRNAs) in the post-transcriptional regulation of protein-coding genes involved in the emergence of phenotypes with relevance for aquaculture. However, there is still a growing demand for a reference resource dedicated to integrating Nile Tilapia miRNA information, obtained from both experimental and in silico approaches, and facilitating the analysis and interpretation of RNA sequencing data. Here, we present an open repository dedicated to Nile Tilapia miRNAs: the “miRTil database”. The database stores data on 734 mature miRNAs identified in 11 distinct tissues and five key developmental stages. The database provides detailed information about miRNA structure, genomic context, predicted targets, expression profiles, and relative 5p/3p arm usage. Additionally, miRTil also includes a comprehensive pre-computed miRNA-target interaction network containing 4936 targets and 19,580 interactions.

Differential expression of genes during legume seed development

1986 ◽  
Vol 314 (1166) ◽  
pp. 367-384 ◽  
Keyword(s):  
Gene Expression ◽  
Seed Development ◽  
Seed Protein ◽  
Practical Significance ◽  
Specific Expression ◽  
Control Of Gene Expression ◽  
Developing Seeds ◽  
Expression Of Genes ◽  
Seed Protein Genes ◽  
Developmental Programme

The accumulation of certain proteins specific to those tissues in the developing seeds of legumes represents a system of academic and practical significance in the study of differential gene expression. Besides the simple distinction between ‘seed-specific’ and ‘non-seed-specific’ expression of genes, further controls are present in determining the level of expression of a particular gene, and the variations in its expression with cell type, developmental stage and environmental perturbation. There are also genetic factors that lead to variations in the expression of homologous genes between lines or species. Gene expression can be assayed at the levels of synthesis of specific proteins, level of mRNA species, and transcription of specific genes, and the results of all these assays lead to a broad correlation between events at the level of the gene and protein deposition in the developing seed. This correlation is strong at earlier stages of seed development, but is weaker at later stages. Evidence is presented that control of gene expression occurs both at transcription and by post-transcriptional processes. Seed protein genes have conserved sequences in their 5' flanking regions that are specific to gene families, and these are suggested to be involved in transcriptional control of the expression of these genes. Although such sequences are unlikely to be solely responsible for transcription control, there is no strong evidence for changes in DNA methylation or in chromatin conformation being causally related to expression of seed protein genes. Control of gene expression in developing seeds is considered in terms of a genetically determined, conserved developmental programme, the aim of which is to produce a viable embryo. This programme will allow considerable plasticity in gene expression within constraints prescribed by seed viability. Although it may be possible to understand the immediate controls of seed protein gene expression, present systems are not adequate to study the genes that control the developmental programme. More fundamental investigations will be assisted by mutants that possess altered seed development patterns.

scholarly journals Gene expression profile during coffee fruit development and identification of candidate markers for phenological stages

2012 ◽  
Vol 47 (7) ◽  
pp. 972-982 ◽  
Author(s):  
Cristiana de Gaspari-Pezzopane ◽  
Nemailla Bonturi ◽  
Oliveiro Guerreiro Filho ◽  
José Laércio Favarin ◽  
Mirian Perez Maluf
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Profile ◽  
Fruit Development ◽  
Developmental Stages ◽  
Isocitrate Lyase ◽  
Expression Profiles ◽  
Phenological Stages ◽  
Caffeine Synthase ◽  
Expression Of Genes

The objective of this work was to identify genes that could be used as suitable markers for molecular recognition of phenological stages during coffee (Coffea arabica) fruit development. Four cultivars were evaluated as to their differential expression of genes associated to fruit development and maturation processes. Gene expression was characterized by both semi-quantitative and quantitative RT-PCR, in fruit harvested at seven different developmental stages, during three different seasons. No size polymorphisms or differential expression were observed among the cultivars for the evaluated genes; however, distinct expression profiles along fruit development were determined for each gene. Four out of the 28 evaluated genes exhibited a regular expression profile in all cultivars and harvest seasons, and, therefore, they were validated as candidate phenological markers of coffee fruit. The gene α-galactosidase can be used as a marker of green stage, caffeine synthase as a marker of transition to green and yellowish-green stages, and isocitrate lyase and ethylene receptor 3 as markers of late maturation.

scholarly journals Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ngoot-Chin Ting ◽  
Katrina Sherbina ◽  
Jia-Shiun Khoo ◽  
Katialisa Kamaruddin ◽  
Pek-Lan Chan ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Oil Palm ◽  
Interspecific Hybrids ◽  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Transcriptome Data ◽  
Triacylglycerol Synthesis ◽  
Expression Of Genes ◽  
Genes Encoding

Abstract Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.

scholarly journals Maintaining Genome Integrity during Seed Development in Phaseolus vulgaris L.: Evidence from a Transcriptomic Profiling Study

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 463 ◽  
Author(s):  
José Parreira ◽  
Alma Balestrazzi ◽  
Pedro Fevereiro ◽  
Susana Araújo
Keyword(s):  
Dna Damage ◽  
Phaseolus Vulgaris ◽  
Seed Development ◽  
Chromatin Remodeling ◽  
Dna Damage Response ◽  
Genome Integrity ◽  
Phaseolus Vulgaris L ◽  
Expression Of Genes ◽  
Late Embryogenesis ◽  
Damage Response

The maintenance of genome integrity is crucial in seeds, due to the constant challenge of several endogenous and exogenous factors. The knowledge concerning DNA damage response and chromatin remodeling during seed development is still scarce, especially in Phaseolus vulgaris L. A transcriptomic profiling of the expression of genes related to DNA damage response/chromatin remodeling mechanisms was performed in P. vulgaris seeds at four distinct developmental stages, spanning from late embryogenesis to seed desiccation. Of the 14,001 expressed genes identified using massive analysis of cDNA ends, 301 belong to the DNA MapMan category. In late embryogenesis, a high expression of genes related to DNA damage sensing and repair suggests there is a tight control of DNA integrity. At the end of filling and the onset of seed dehydration, the upregulation of genes implicated in sensing of DNA double-strand breaks suggests that genome integrity is challenged. The expression of chromatin remodelers seems to imply a concomitant action of chromatin remodeling with DNA repair machinery, maintaining genome stability. The expression of genes related to nucleotide excision repair and chromatin structure is evidenced during the desiccation stage. An overview of the genes involved in DNA damage response and chromatin remodeling during P. vulgaris seed development is presented, providing insights into the mechanisms used by developing seeds to cope with DNA damage.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

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