scholarly journals Reference Transcriptome Data in Silkworm Bombyx mori

Insects ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 519
Author(s):  
Kakeru Yokoi ◽  
Takuya Tsubota ◽  
Akiya Jouraku ◽  
Hideki Sezutsu ◽  
Hidemasa Bono
Keyword(s):  
Expression Profiles ◽  
Complex Structure ◽  
Complete Sequence ◽  
Silk Gland ◽  
Transcriptome Data ◽  
Silkworm Larvae ◽  
Tandem Gene Duplication ◽  
Reference Transcriptome ◽  
Basic Studies ◽  
Entomological Research

Herein, we performed RNA-seq analysis of ten major tissues/subparts of silkworm larvae. The sequences were mapped onto the reference genome assembly and the reference transcriptome data were successfully constructed. The reference data provided a nearly complete sequence for sericin-1, a major silk gene with a complex structure. We also markedly improved the gene model for other genes. The transcriptomic expression was investigated in each tissue and a number of transcripts were identified that were exclusively expressed in tissues such as the testis. Transcripts strongly expressed in the midgut formed tight genomic clusters, suggesting that they originated from tandem gene duplication. Transcriptional factor genes expressed in specific tissues or the silk gland subparts were also identified. We successfully constructed reference transcriptome data in the silkworm and found that a number of transcripts showed unique expression profiles. These results will facilitate basic studies on the silkworm and accelerate its applications, which will contribute to further advances in lepidopteran and entomological research as well as the practical use of these insects.

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 Introduction of a precocious metamorphosis BmNPV infection in the latter half of the fifth instar silkworm larvae

2020 ◽  
Author(s):  
Pingzhen Xu ◽  
Meirong Zhang ◽  
Xueyang Wang ◽  
Yangchun Wu
Keyword(s):  
Bombyx Mori ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Transcriptome Data ◽  
Silkworm Larvae ◽  
Early Maturation ◽  
Prothoracic Glands ◽  
Physiology And Biochemistry ◽  
New Perspective ◽  
Complete Metamorphosis

AbstractThe silkworm, Bombyx mori, is a complete metamorphosis insect, the model to study insect physiology and biochemistry. Bombyx mori nucleopolyhedrovirus (BmNPV) is a principal pathogen of the silkworm and its host range is restricted to silkworm larvae, requiring interaction with larvae to accomplish virus replication. Prothoracic glands (PGs) are a model for synthetic ecdysone with regulating insect growth and development. This study performed a transcriptome analysis of silkworm PGs after BmNPV infection. Transcriptome data were annotated with KEGG, GO, and shown to be of high quality by RT-qPCR. The spatial expression profiles of BmJing and BmAryl indicate that they may be specifically expressed in silkworm PGs. The RT-qPCR results of the DEGs in the PGs of BmNPV-infected larvae at 24, 48, and 72 h and at the developmental stages of days-6 and 7, comparing to day-3, reveal that the DEGs may be related to the BmNPV infection via promoting early maturation in the latter half of the silkworm fifth instar. This study is the first report on the identification of possible genes in PGs correlating with the precocious molting and metamorphosis of silkworm larvae under BmNPV infection in the latter half of the fifth instar. Our findings will help to address the interactions between BmNPV infection and host developmental response. This work provides a new perspective on BmNPV infection and host developmental response, as well as suggesting candidate genes for further research.

Changes in H+-translocating vacuolar-type ATPase in the anterior silk gland cell of Bombyx mori during metamorphosis.

1998 ◽  
Vol 201 (4) ◽  
pp. 479-486
Author(s):  
M Azuma ◽  
Y Ohta
Keyword(s):  
Bombyx Mori ◽  
Gland Cell ◽  
Specific Inhibitor ◽  
Instar Larva ◽  
Silk Gland ◽  
Ultrastructural Changes ◽  
Immunocytochemical Staining ◽  
Apical Plasma Membrane ◽  
Apical Surface ◽  
Silkworm Larvae

A proton-translocating vacuolar-type ATPase (V-ATPase) was identified and characterized in the anterior silk gland of Bombyx mori. By incubating the intact tissue with the fluorescent dye Acridine Orange, the acidified compartment was detected at the apical pole of the epithelial cells. This was observed throughout the feeding period of the fifth-instar larva until the onset of spinning. Acidification was prevented completely and reversibly by 0.8 micromol l-1 bafilomycin A1, a specific inhibitor of V-ATPase. The presence of V-ATPase in a microsomal fraction was verified by immunoblots using an antiserum to the V-ATPase holoenzyme from Manduca sexta midgut. The antiserum localized the V-ATPase to the apical plasma membrane of the anterior silk gland cells, suggesting that the enzyme is functionally active in pumping protons out of the cell towards the glandular lumen of feeding silkworm larvae. In spinning larvae, the acidification produced by the V-ATPase appears to cease, because acidic compartments were seen rarely and only in the periphery of basal cytoplasm, and because immunocytochemical staining for the V-ATPase was greatly reduced at the apical surface. The metamorphic changes in relation to the occurrence of V-ATPase corresponded well with the ultrastructural changes in the anterior silk gland cell of Bombyx mori larvae.

scholarly journals Precocious Metamorphosis of Silkworm Larvae Infected by BmNPV in the Latter Half of the Fifth Instar

2021 ◽  
Vol 12 ◽  
Author(s):  
Ping-Zhen Xu ◽  
Mei-Rong Zhang ◽  
Xue-Yang Wang ◽  
Yang-Chun Wu
Keyword(s):  
Growth And Development ◽  
Model Organism ◽  
Maturation Process ◽  
Transcriptome Data ◽  
Regulatory Effect ◽  
Rna Seq ◽  
Control Groups ◽  
Silkworm Larvae ◽  
Prothoracic Glands ◽  
Mulberry Silkworm

The mulberry silkworm (Bombyx mori) is a model organism, and BmNPV is a typical baculovirus. Together, these organisms form a useful model to investigate host–baculovirus interactions. Prothoracic glands (PGs) are also model organs, used to investigate the regulatory effect of synthetic ecdysone on insect growth and development. In this study, day-4 fifth instar silkworm larvae were infected with BmNPV. Wandering silkworms appeared in the infected groups 12 h earlier than in the control groups, and the ecdysone titer in infected larvae was significantly higher than that of the control larvae. We then used RNA sequencing (RNA-seq) to analyze silkworm PGs 48 h after BmNPV infection. We identified 15 differentially expressed genes (DEGs) that were classified as mainly being involved in metabolic processes and pathways. All 15 DEGs were expressed in the PGs, of which Novel01674, BmJing, and BmAryl were specifically expressed in the PGs. The transcripts of BmNGDN, BmTrypsin-1, BmACSS3, and BmJing were significantly increased, and BmPyd3, BmTitin, BmIGc2, Novel01674, and BmAryl were significantly decreased from 24 to 72 h in the PGs after BmNPV infection. The changes in the transcription of these nine genes were generally consistent with the transcriptome data. The upregulation of BmTrypsin-1 and BmACSS3 indicate that these DEGs may be involved in the maturation process in the latter half of the fifth instar of silkworm larvae. These findings further our understanding of silkworm larval development, the interaction between BmNPV infection and the host developmental response, and host–baculovirus interactions in general.

scholarly journals De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

2020 ◽  
Author(s):  
Ercha Hu ◽  
Yuan Meng ◽  
Ying Ma ◽  
Ruiqi Song ◽  
Zhengxiang Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Blood Feeding ◽  
Differentially Expressed ◽  
Whole Body ◽  
Sequence Information ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Dermacentor Marginatus

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly one third of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood-feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

Isolation of dehydration-responsive genes in a drought tolerant common bean cultivar and expression of a group 3 late embryogenesis abundant mRNA in tolerant and susceptible bean cultivars

2007 ◽  
Vol 34 (4) ◽  
pp. 368 ◽  
Author(s):  
Blanca E. Barrera-Figueroa ◽  
Julián M. Peña-Castro ◽  
Jorge A. Acosta-Gallegos ◽  
Roberto Ruiz-Medrano ◽  
Beatriz Xoconostle-Cázares
Keyword(s):  
Common Bean ◽  
Expression Profiles ◽  
Sugar Metabolism ◽  
Complete Sequence ◽  
Late Embryogenesis Abundant ◽  
Suppression Subtractive Hybridisation ◽  
Cellular Protection ◽  
Drought Tolerant ◽  
Late Embryogenesis ◽  
Group 3

Drought is one of the main constraints for common bean (Phaseolus vulgaris L.) production in Latin America. The aim of this work was to identify upregulated genes in the drought-tolerant common bean cv. Pinto Villa, grown under water-deficit conditions. Twenty-eight cDNAs representing differentially-expressed mRNAs in roots and/or leaves were isolated via suppression subtractive hybridisation. Their expression profiles in plants under intermediate and severe dehydration stress were tested. Three cDNAs corresponded to genes already described as associated to drought stress in P. vulgaris, 12 were known P. vulgaris sequences without previous association with drought response, and 13 were new P. vulgaris sequences. Analysis of the deduced proteins encoded by the cDNAs revealed putative functions in cellular protection, sugar metabolism, and protein synthesis, folding and turnover. Additionally, a new member of group 3 late embryogenesis abundant (LEA) genes (PvLEA3) was cloned and its complete sequence was obtained. Given the lack of reports comparing expression of dehydration-responsive genes in bean cultivars with different response to drought, the expression of PvLEA3 transcript in five bean cultivars from different origin was analysed. The induction of PvLEA3 was directly associated with the level of drought tolerance in the cultivars studied.

scholarly journals A gene-based association method for mapping traits using reference transcriptome data

2015 ◽  
Vol 47 (9) ◽  
pp. 1091-1098 ◽  
Author(s):  
Eric R Gamazon ◽  
◽  
Heather E Wheeler ◽  
Kaanan P Shah ◽  
Sahar V Mozaffari ◽  
...  
Keyword(s):  
Transcriptome Data ◽  
Reference Transcriptome ◽  
Association Method

scholarly journals Estrogen-Related Receptor Influences the Hemolymph Glucose Content by Regulating Midgut Trehalase Gene Expression in the Last Instar Larvae of Bombyx mori

2021 ◽  
Vol 22 (9) ◽  
pp. 4343
Author(s):  
Guanwang Shen ◽  
Jinxin Wu ◽  
Ying Lin ◽  
Xiaoting Hua ◽  
Qingyou Xia ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Silk Gland ◽  
Strongly Correlated ◽  
Cell Level ◽  
Silkworm Larvae ◽  
Glucose Content ◽  
Trehalose Metabolism ◽  
The Relationship ◽  
Glucose Supply ◽  
Estrogen Related Receptor

The expression of trehalase in the midgut of insects plays an important role in glucose supply to the hemolymph. Energy metabolism is usually regulated by the estrogen-related receptor (ERR). A decrease in ATP levels is caused by the ERR hindering glycolysis. However, the relationship between trehalose accumulation and ERR expression is still unclear. Here, we found that silkworm ERR (BmERR) is concentrated and BmERR expression is strongly correlated with trehalase in the midgut during the last instar silkworm larval stage. We cloned the promoter of the trehalase from Bombyx mori (BmTreh) and found that the ERR bound directly to the core response elements of the promoter. Cell level interference and the overexpression of ERR can reduce or enhance BmTreh transcription and promoter activity. Overexpressed transgenic BmERR can significantly increase the expression of BmTreh in the midgut of the last instar silkworm larvae, thereby hydrolyzing trehalose into glucose and releasing it into the hemolymph. Additionally, increased hemolymph glucose content reduces silkworm pupa weight but does not affect silk protein production from the silk gland. Our results suggest a novel function for BmERR through its involvement in BmTreh regulation and expand the understanding of ERR functions in insect trehalose metabolism.

scholarly journals AdRoit is an accurate and robust method to infer complex transcriptome composition

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Tao Yang ◽  
Nicole Alessandri-Haber ◽  
Wen Fury ◽  
Michael Schaner ◽  
Robert Breese ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
Adaptive Learning ◽  
Expression Profiles ◽  
Cell Types ◽  
Transcriptome Data ◽  
Robust Method ◽  
Gene Expressions ◽  
Tissue Organization

AbstractBulk RNA sequencing provides the opportunity to understand biology at the whole transcriptome level without the prohibitive cost of single cell profiling. Advances in spatial transcriptomics enable to dissect tissue organization and function by genome-wide gene expressions. However, the readout of both technologies is the overall gene expression across potentially many cell types without directly providing the information of cell type constitution. Although several in-silico approaches have been proposed to deconvolute RNA-Seq data composed of multiple cell types, many suffer a deterioration of performance in complex tissues. Here we present AdRoit, an accurate and robust method to infer the cell composition from transcriptome data of mixed cell types. AdRoit uses gene expression profiles obtained from single cell RNA sequencing as a reference. It employs an adaptive learning approach to alleviate the sequencing technique difference between the single cell and the bulk (or spatial) transcriptome data, enhancing cross-platform readout comparability. Our systematic benchmarking and applications, which include deconvoluting complex mixtures that encompass 30 cell types, demonstrate its preferable sensitivity and specificity compared to many existing methods as well as its utilities. In addition, AdRoit is computationally efficient and runs orders of magnitude faster than most methods.

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