scholarly journals Association of the phenylpropanoid pathway with dormancy and adaptive trait variation in apricot (Prunus armeniaca)

2019 ◽  
Vol 39 (7) ◽  
pp. 1136-1148 ◽  
Author(s):  
Anna O Conrad ◽  
Jiali Yu ◽  
Margaret E Staton ◽  
Jean-Marc Audergon ◽  
Guillaume Roch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Phenylpropanoid Pathway ◽  
Prunus Armeniaca ◽  
Trait Variation ◽  
Adaptive Trait ◽  
Improvement Programs ◽  
Floral Bud

Abstract Trees use many mechanisms to adapt and respond to stressful conditions. The phenylpropanoid pathway in particular is known to be associated with a diverse suite of plant stress responses. In this study, we explored the relationship between the phenylpropanoid pathway metabolite production, gene expression and adaptive trait variation associated with floral bud reactivation during and following dormancy in Prunus armeniaca L. (apricot). Concentrations of eight phenylpropanoid metabolites were measured during chill accumulation and at developmental stages corresponding to the emergence of sepals and petals in floral buds of varieties that differ phenotypically in bloom date (BD). A significant interaction effect of chill hours and BD phenotype on the concentration of each of the compounds was observed (mixed analysis of variance, P < 0.05), with the concentration of most phenylpropanoid metabolites dropping precipitously when sepals and petals emerged. While phenylpropanoid biosynthetic gene expression patterns were more variable in general, expression changed over time and was impacted, although to a lesser degree, by BD phenotype. Furthermore, separation of BD phenotypic groups was most pronounced when early and late BD varieties were at different developmental stages, i.e., 800 chill hours. Taken together, these results suggest that the phenylpropanoid pathway is associated with floral bud reactivation in apricot. Furthermore, we show that the phenylpropanoid pathway is also impacted by phenological trait variation associated with dormancy. A better understanding of how apricot and other perennial tree species respond and adapt to environmental perturbations will be critical for improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.

scholarly journals A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aliki Xanthopoulou ◽  
Javier Montero-Pau ◽  
Belén Picó ◽  
Panagiotis Boumpas ◽  
Eleni Tsaliki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cucurbita Pepo ◽  
Developmental Stages ◽  
Lateral Roots ◽  
Expression Patterns ◽  
Male Flower ◽  
Differentially Expressed ◽  
Gene Expression Atlas ◽  
Summer Squash ◽  
Expression Atlas

Abstract Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

scholarly journals Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

2019 ◽  
Vol 144 (2) ◽  
pp. 79-91 ◽  
Author(s):  
Zhigang Ouyang ◽  
Huihui Duan ◽  
Lanfang Mi ◽  
Wei Hu ◽  
Jianmei Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Messenger Rna ◽  
Citrus Sinensis ◽  
Rna Binding ◽  
Developmental Stages ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genome Wide ◽  
Yth Domain

In eukaryotic systems, messenger RNA regulations, including splicing, 3′-end formation, editing, localization, and translation, are achieved by different RNA-binding proteins and noncoding RNAs. The YTH domain is a newly identified RNA-binding domain that was identified by comparing its sequence with that of splicing factor YT521-B. Previous study showed that the YTH gene plays an important role in plant resistance to abiotic and biotic stress. In this study, 211 YTH genes were identified in 26 species that represent four major plant lineages. Phylogenetic analysis revealed that these genes could be divided into eight subgroups. All of the YTH genes contain a YT521 domain and have different structures. Ten YTH genes were identified in navel orange (Citrus sinensis). The expression profiles of these CitYTH genes were analyzed in different tissues and at different fruit developmental stages, and CitYTH genes displayed distinct expression patterns under heat, cold, salt, and drought stress. Furthermore, expression of the CitYTH genes in response to exogenous hormones was measured. Nuclear localization was also confirmed for five of the proteins encoded by these genes after transient expression in Nicotiana benthamiana cells. This study provides valuable information on the role of CitYTHs in the signaling pathways involved in environmental stress responses in Citrus.

scholarly journals Identification and Expression Analysis of the NAC Gene Family in Coffea canephora

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 670 ◽  
Author(s):  
Dong ◽  
Jiang ◽  
Yang ◽  
Xiao ◽  
Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Stress Responses ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Coffea Canephora ◽  
Coffee Bean ◽  
Systematic Analysis ◽  
Nac Gene Family ◽  
Basic Features

The NAC gene family is one of the largest families of transcriptional regulators in plants, and it plays important roles in the regulation of growth and development as well as in stress responses. Genome-wide analyses have been performed in diverse plant species, but there is still no systematic analysis of the NAC genes of Coffea canephora Pierre ex A. Froehner. In this study, we identified 63 NAC genes from the genome of C. canephora. The basic features and comparison analysis indicated that the NAC gene members increased via duplication events during the evolution of the plant. Phylogenetic analysis divided the NAC proteins from C. canephora, Arabidopsis and rice into 16 subgroups. Analysis of the expression patterns of CocNACs under cold stress and coffee bean development indicated that 38 CocNACs were differentially expressed under cold stress; six genes may play important roles in the process of cold acclimation, and four genes among 54 CocNACs showing a variety of expression patterns during different developmental stages of coffee beans may be positively related to the bean development. This study can expand our understanding of the functions of the CocNAC gene family in cold responses and bean development, thereby potentially intensifying the molecular breeding programs of Coffea spp. plants.

scholarly journals PML Regulates the Epidermal Differentiation Complex and Skin Morphogenesis during Mouse Embryogenesis

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1130
Author(s):  
Anna Połeć ◽  
Alexander D. Rowe ◽  
Pernille Blicher ◽  
Rajikala Suganthan ◽  
Magnar Bjørås ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Growth Control ◽  
Wild Type Mouse ◽  
Global Gene Expression ◽  
Mouse Embryos ◽  
Epidermal Differentiation ◽  
Envelope Gene ◽  
Epidermal Differentiation Complex

The promyelocytic leukemia (PML) protein is an essential component of nuclear compartments called PML bodies. This protein participates in several cellular processes, including growth control, senescence, apoptosis, and differentiation. Previous studies have suggested that PML regulates gene expression at a subset of loci through a function in chromatin remodeling. Here we have studied global gene expression patterns in mouse embryonic skin derived from Pml depleted and wild type mouse embryos. Differential gene expression analysis at different developmental stages revealed a key role of PML in regulating genes involved in epidermal stratification. In particular, we observed dysregulation of the late cornified envelope gene cluster, which is a sub-region of the epidermal differentiation complex. In agreement with these data, PML body numbers are elevated in basal keratinocytes during embryogenesis, and we observed reduced epidermal thickness and defective hair follicle development in PML depleted mouse embryos.

scholarly journals The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression

2020 ◽  
Vol 21 (24) ◽  
pp. 9719
Author(s):  
Marco Spreafico ◽  
Eleonora Mangano ◽  
Mara Mazzola ◽  
Clarissa Consolandi ◽  
Roberta Bordoni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
System Development ◽  
Expression Patterns ◽  
Nervous System Development ◽  
Zebrafish Embryos ◽  
Loss Of Function ◽  
Zebrafish Model ◽  
Genome Wide ◽  
Transcriptional Effect

Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.

Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum

Genome ◽  
2015 ◽  
Vol 58 (6) ◽  
pp. 305-313 ◽  
Author(s):  
Jagesh Kumar Tiwari ◽  
Sapna Devi ◽  
S. Sundaresha ◽  
Poonam Chandel ◽  
Nilofer Ali ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Microarray Analysis ◽  
Somatic Hybrid ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Gene Expression Patterns ◽  
Potato Tuberization ◽  
Solanum Etuberosum

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.

Photosynthetic Gene Expression in Amaranth, an NAD-ME Type C4 Dicot

1997 ◽  
Vol 24 (4) ◽  
pp. 423 ◽  
Author(s):  
James O. Berry ◽  
Dennis J. McCormac ◽  
John J. Long ◽  
Joseph Boinski ◽  
Amy C. Corey
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Metabolic Enzyme ◽  
Gene Expression Patterns ◽  
Control Mechanisms ◽  
Multiple Control ◽  
Amaranthus Hypochondriacus ◽  
Specific Accumulation ◽  
Post Transcriptional Regulation

Post-transcriptional regulation determines initial C4 gene expression patterns in developing leaves of Amaranthus hypochondriacus, an NAD-ME type C4 dicot. RuBPCase, PEPCase, and PPdK mRNAs are abundant in meristems and in leaf primordia, but are utilised only during specific developmental stages. While each enzyme shows independent patterns of initial mRNA and polypeptide accumulation, cell-specific localisation of the polypeptides occurs prior to cell-specific localisation of the mRNAs. In mature three-coloured leaves of A. tricolor, loss of photosynthetic activity correlates with reductions in the transcription rates of some plastid-encoded genes, reduction and loss of coordination in the translation of RuBPCase polypeptides, and loss of cell-specific accumulation of RuBPCase mRNAs (but not the polypeptides). The mitochondrial NAD-dependent malic enzyme (NAD-ME) provides an example of a basic metabolic enzyme that has acquired specialised gene expression patterns allowing it to function in the C4 pathway. NAD-ME occurs preferentially in photosynthetic tissues, and is specific to bundle sheath cells throughout development. NAD-ME synthesis is regulated by light and development at transcriptional and post-transcriptional levels. The findings summarised here indicate that C4 genes are independently regulated by multiple control mechanisms in response to developmental, environmental, and metabolic signals.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals Evolution of gene expression across species and specialized zooids in Siphonophora

2021 ◽  
Author(s):  
Catriona Munro ◽  
Felipe Zapata ◽  
Mark Howison ◽  
Stefan Siebert ◽  
Casey W Dunn
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Gene Trees ◽  
Species Trees ◽  
Examine Gene Expression ◽  
Specialized Tissue ◽  
Species Specific

Background: Siphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. Results: Within and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. Conclusions: Our findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

Sign in / Sign up

Export Citation Format

Share Document