scholarly journals Genome-wide survey and characterization of transcription factors in the silk gland of the silkworm, Bombyx mori

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259870
Author(s):  
Yan Ma ◽  
Qiwei Sun ◽  
Lihua Huang ◽  
Qin Luo ◽  
Wenhui Zeng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Bombyx Mori ◽  
Large Scale ◽  
Expression Patterns ◽  
Silk Gland ◽  
Cellular Functions ◽  
Chromosomal Distribution ◽  
Genome Data ◽  
Silkworm Genome ◽  
Full Length Transcript

Transcription factors (TFs) are key proteins that modulate gene transcription and thereby lead to changes in the gene expression profile and the subsequent alteration of cellular functions. In the silk gland (SG) of silkworm Bombyx mori, an important silk-producing insect, TFs are of vital importance in the regulation of silk protein synthesis in this organ. However, which TFs exist and express in the SG remains largely unknown. Here, we report the large-scale identification of TFs in the SG based on available full-length transcript sequences and the most recent version of silkworm genome data. In total, 348 candidate TFs were identified by strict filtration and were classified into 56 TF families. Chromosomal distribution, motif composition, and phylogenetic relationship analyses revealed the typical characteristics of these TFs. In addition, the expression patterns of 348 TFs in various tissues of B. mori, especially the SG of fourth-molt (4LM) and day-3 and day-4 fifth-instar (5L3D and 5L4D) larvae, were investigated based on public RNA-seq data and gene microarray data, followed by spatiotemporal verification of TF expression levels by quantitative real-time PCR (qRT-PCR). This report describes the first comprehensive analysis of TFs in the B. mori SG. The results can serve as a baseline for further studies of the roles of TFs in the B. mori SG.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in  ginger: evolution and expression profiles during rhizome and inflorescence development

2021 ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
Yun Ren ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Whole Genome Sequence ◽  
Chromosomal Distribution ◽  
Inflorescence Development ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Erf Transcription Factors

Abstract Background:AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis (Arabidopsis thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of ginger (Zingiber officinale), which is an important edible and medicinal horticultural plant. The recently published whole genome sequence of ginger allowed us to study the tissue and expression profiles of AP2/ERF genes in ginger on a genome-wide basis.Results:In this study, 163 AP2/ERF genes of ginger (ZoAP2/ERF) were identified and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic analysis, namely, AP2 (35 members), ERF (125 members) and RAV (3 members). A total of 10 motifs were detected in ginger AP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes.Conclusion:A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and rhizome development stages by transcriptom sequence and quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of ZoAP2/ERF genes and improvement of ginger.

scholarly journals Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome

2020 ◽  
Vol 21 (2) ◽  
pp. 138-154
Author(s):  
Vinay Singh ◽  
Neeraj Kumar ◽  
Anuj K. Dwivedi ◽  
Rita Sharma ◽  
Manoj K. Sharma
Keyword(s):  
Transcription Factors ◽  
Large Scale ◽  
Agronomic Traits ◽  
Expression Patterns ◽  
Biomass Composition ◽  
Phylogenomic Analysis ◽  
Myb Transcription Factors ◽  
Myb Genes ◽  
R2r3 Myb ◽  
R2r3 Myb Transcription Factors

Background : Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods: We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used inhouse generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results: We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum. Conclusion: The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.

scholarly journals Transgenic Ectopic Overexpression of Broad Complex (BrC-Z2) in the Silk Gland Inhibits the Expression of Silk Fibroin Genes of Bombyx mori

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 374
Author(s):  
Jiangshan Cong ◽  
Cuicui Tao ◽  
Xuan Zhang ◽  
Hui Zhang ◽  
Tingcai Cheng ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Silk Gland ◽  
Silk Protein ◽  
Regulation Mechanism ◽  
Wild Type ◽  
Transgenic Lines ◽  
In The Wild ◽  
Broad Complex

Bombyx mori silk protein genes are strictly turned on and off in different developmental stages under the hormone periodically change. The broad complex (BrC) is a transcription factor mediating 20-hydroxyecdysone action, which plays important roles during metamorphosis. Here, we observed that two isoforms of BmBrC (BmBrC-Z2 and BmBrC-Z4) exhibited contrasting expression patterns with fibroin genes (FibH, FibL and P25) in the posterior silk gland (PSG), suggesting that BmBrC may negatively regulate fibroin genes. Transgenic lines were constructed to ectopically overexpress BmBrC-Z2 in the PSG. The silk protein genes in the transgenic line were decreased to almost half of that in the wild type. The silk yield was decreased significantly. In addition, the expression levels of regulatory factors (BmKr-h1 and BmDimm) response to juvenile hormone (JH) signal were inhibited significantly. Then exogenous JH in the BmBrC-Z2 overexpressed lines can inhibit the expression of BmBrC-Z2 and activate the expression of silk protein genes and restore the silk yield to the level of the wild type. These results indicated that BmBrC may inhibit fibroin genes by repressing the JH signal pathway, which would assist in deciphering the comprehensive regulation mechanism of silk protein genes.

scholarly journals Reference transcriptome data in silkworm Bombyx mori

2019 ◽  
Author(s):  
Kakeru Yokoi ◽  
Takuya Tsubota ◽  
Jianqiang Sun ◽  
Akiya Jouraku ◽  
Hideki Sezutsu ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Reference Genome ◽  
Enrichment Analysis ◽  
Silk Gland ◽  
Transcriptome Data ◽  
Data Set ◽  
Reference Transcriptome ◽  
Genome Data ◽  
Silk Glands ◽  
Sequence Region

AbstractThe silkworm Bombyx mori has long been used in the silk industry and utilized in studies of physiology, genetics, molecular biology, and pathology. We recently reported high quality reference genome data for B. mori. In the present study, we constructed a reference transcriptome data set using the reference genome data and RNA-seq data of 10 tissues from P50T strain larvae. Reference transcriptome data contained 51,926 transcripts, with 39,619 having one or more coding sequence region. The abundance of each transcript in the 10 tissues as well as 5 tissues from other strain larvae was estimated, and hierarchical clustering was performed. The results obtained showed that data on abundance were highly reproducible and there here is a little difference of transcriptome abundance between the two strain larvae. New isoforms of silk-related genes were searched for in the reference transcriptomes, and the longest isoform of sericin-1 possessing a long exon was identified. We also extracted transcripts that were strongly expressed in one or more parts of the silk glands. An enrichment analysis performed using the functional annotation data of the transcripts provided novel insights into the functions of the silk gland parts. Therefore, the reference transcriptome data set obtained has extended B. mori genomic and transcriptomic insights and may contribute to advances in entomologic and vertebrate research, including that on humans.

scholarly journals Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

2018 ◽  
Author(s):  
Hamutal Arbel ◽  
William W. Fisher ◽  
Ann S. Hammonds ◽  
Kenneth H. Wan ◽  
Soo Park ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Large Scale ◽  
Scale Validation ◽  
Expression Patterns ◽  
Prediction Method ◽  
High Accuracy ◽  
Enhancer Activity ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Scan

AbstractIdentifying functional enhancers elements in metazoan systems is a major challenge. For example, large-scale validation of enhancers predicted by ENCODE reveal false positive rates of at least 70%. Here we use the pregrastrula patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held out data results from heterogeneity of functional signatures in enhancer elements. We show that two classes of enhancer are active during early Drosophila embryogenesis and that by focusing on a single, relatively homogeneous class of elements, over 98% prediction accuracy can be achieved in a balanced, completely held-out test set. The class of well predicted elements is composed predominantly of enhancers driving multi-stage, segmentation patterns, which we designate segmentation driving enhancers (SDE). Prediction is driven by the DNA occupancy of early developmental transcription factors, with almost no additional power derived from histone modifications. We further show that improved accuracy is not a property of a particular prediction method: after conditioning on the SDE set, naïve Bayes and logistic regression perform as well as more sophisticated tools. Applying this method to a genome-wide scan, we predict 1,640 SDEs that cover 1.6% of the genome, 916 of which are novel. An analysis of 32 novel SDEs using wholemount embryonic imaging of stably integrated reporter constructs chosen throughout our prediction rank-list showed >90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.Significance StatementWe demonstrate a high accuracy method for predicting enhancers genome wide with > 85% precision as validated by transgenic reporter assays in Drosophila embryos. This is the first time such accuracy has been achieved in a metazoan system, allowing us to predict with high-confidence 1640 enhancers, 916 of which are novel. The predicted enhancers are demarcated by heterogeneous collections of epigenetic marks; many strong enhancers are free from classical indicators of activity, including H3K27ac, but are bound by key transcription factors. H3K27ac, often used as a one-dimensional predictor of enhancer activity, is an uninformative parameter in our data.

scholarly journals Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata

2021 ◽  
Vol 11 ◽  
Author(s):  
Rongrong Zhang ◽  
Zhenzhen Chen ◽  
Libing Zhang ◽  
Wei Yao ◽  
Zhichao Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factors ◽  
Alternative Splicing ◽  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Andrographis Paniculata ◽  
Wrky Transcription Factors ◽  
Chromosomal Distribution ◽  
Specific Expression ◽  
Go Annotation

Andrographolide, which is enriched in the leaves of Andrographis paniculata, has been known as “natural antibiotic” due to its pharmacological activities such as anti-inflammatory, antimicrobial and antioxidant effects. Several key enzymes in andrographolide biosynthetic pathway have been studied since the genome sequences were released, but its regulatory mechanism remains unknown. WRKY transcription factors proteins have been reported to regulate plant secondary metabolism, development as well as biotic and abiotic stresses. Here, WRKY transcription factors related to andrographolide biosynthesis were systematically identified, including sequences alignment, phylogenetic analysis, chromosomal distribution, gene structure, conserved motifs, synteny, alternative splicing event and Gene ontology (GO) annotation. A total of 58 WRKYs were identified in Chuanxinlian genome and phylogenetically classified into three groups. Moreover, nine WRKY genes underwent alternative splicing events. Furthermore, the combination of binding site prediction, gene-specific expression patterns, and phylogenetic analysis suggested that 7 WRKYs (ApWRKY01, ApWRKY08, ApWRKY12, ApWRKY14, ApWRKY19, ApWRKY20, and ApWRKY50) might regulate andrographolide biosynthesis. This study laid a foundation for understanding the regulatory mechanism of andrographolide biosynthesis and the improvement and breeding of Andrographis paniculata varieties.

Role of Bm30kc6 gene in cell apoptosis and the silk gland degradation signaling pathway in Bombyx mori L.

2020 ◽  
Vol 105 (3) ◽  
Author(s):  
Ying Xiao ◽  
Lei‐lei Li ◽  
Asma Bibi ◽  
Ning Zhang ◽  
Ting Chen ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Signaling Pathway ◽  
Cell Apoptosis ◽  
Silk Gland ◽  
Bombyx Mori L

scholarly journals Expression patterns of signalling molecules and transcription factors in the early rabbit embryo and their significance for modelling amniote axis formation

2021 ◽  
Author(s):  
Ruben Plöger ◽  
Christoph Viebahn
Keyword(s):  
Transcription Factors ◽  
Expression Patterns ◽  
In Situ Hybridisation ◽  
Body Plan ◽  
The Body ◽  
Anchor Point ◽  
Axis Formation ◽  
Point Model ◽  
Signalling Molecules ◽  
Rabbit Embryo

AbstractThe anterior-posterior axis is a central element of the body plan and, during amniote gastrulation, forms through several transient domains with specific morphogenetic activities. In the chick, experimentally proven activity of signalling molecules and transcription factors lead to the concept of a ‘global positioning system’ for initial axis formation whereas in the (mammotypical) rabbit embryo, a series of morphological or molecular domains are part of a putative ‘three-anchor-point model’. Because circular expression patterns of genes involved in axis formation exist in both amniote groups prior to, and during, gastrulation and may thus be suited to reconcile these models, the expression patterns of selected genes known in the chick, namely the ones coding for the transcription factors eomes and tbx6, the signalling molecule wnt3 and the wnt inhibitor pkdcc, were analysed in the rabbit embryonic disc using in situ hybridisation and placing emphasis on their germ layer location. Peripheral wnt3 and eomes expression in all layers is found initially to be complementary to central pkdcc expression in the hypoblast during early axis formation. Pkdcc then appears — together with a posterior-anterior gradient in wnt3 and eomes domains — in the epiblast posteriorly before the emerging primitive streak is marked by pkdcc and tbx6 at its anterior and posterior extremities, respectively. Conserved circular expression patterns deduced from some of this data may point to shared mechanisms in amniote axis formation while the reshaping of localised gene expression patterns is discussed as part of the ‘three-anchor-point model’ for establishing the mammalian body plan.

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