scholarly journals Identification and Analysis of the SET-Domain Family in Silkworm,Bombyx mori

2015 ◽  
Vol 2015 ◽  
pp. 1-11
Author(s):  
Hailong Zhao ◽  
Chunqin Zheng ◽  
Hongjuan Cui
Keyword(s):  
Bombyx Mori ◽  
Expression Profiles ◽  
Model Organism ◽  
Set Domain ◽  
Domain Family ◽  
Catalytic Core ◽  
Nonhistone Proteins ◽  
Lepidopteran Insect ◽  
Evolutionary Features ◽  
Set Domains

As an important economic insect,Bombyx moriis also a useful model organism for lepidopteran insect. SET-domain-containing proteins belong to a group of enzymes named after a common domain that utilizes the cofactor S-adenosyl-L-methionine (SAM) to achieve methylation of its substrates. Many SET-domain-containing proteins have been shown to display catalytic activity towards particular lysine residues on histones, but emerging evidence also indicates that various nonhistone proteins are specifically targeted by this clade of enzymes. To explore their diverse functions of SET-domain superfamily in insect, we identified, cloned, and analyzed the SET-domains proteins in silkworm,Bombyx mori. Firstly, 24 genes containing SET domain from silkworm genome were characterized and 17 of them belonged to six subfamilies of SUV39, SET1, SET2, SUV4-20, EZ, and SMYD. Secondly, SET domains of silkworm SET-domain family were intraspecifically and interspecifically conserved, especially for the catalytic core “NHSC” motif, substrate binding site, and catalytic site in the SET domain. Lastly, further analyses indicated that silkworm SET-domain gene BmSu(var)3-9 owned different characterization and expression profiles compared to other invertebrates. Overall, our results provide a new insight into the functional and evolutionary features of SET-domain family.

scholarly journals Applicability of Honey on Silkworms (Bombyx mori) and Quality Improvement of Its Biomaterials

2021 ◽  
Vol 11 (10) ◽  
pp. 4613
Author(s):  
Gabriela-Maria Baci ◽  
Alexandra-Antonia Cucu ◽  
Adela Ramona Moise ◽  
Daniel Severus Dezmirean
Keyword(s):  
Quality Improvement ◽  
Bombyx Mori ◽  
Human Health ◽  
Recombinant Proteins ◽  
Therapeutic Agent ◽  
Life Sciences ◽  
Model Organism ◽  
Medical Field ◽  
Wide Range ◽  
Ancient Times

Since ancient times, honey has been considered one of the most illustrious and esteemed natural products. Honey plays two key roles; specifically, it is an appreciated nutritional product, and also exhibits a wide range of beneficial properties for human health as a therapeutic agent. Furthermore, it has been shown that honey has valuable effects on the biological and physiological features of mulberry silkworms (Bombyx mori). Bombyx mori exhibits importance not only for the economy, but it also serves as an important biotechnological bioreactor for the production of recombinant proteins that have a great impact in the medical field and beyond. It also represents an important model organism for life sciences. In view of the fact that silk fibroin serves as a natural biopolymer that displays high biocompatibility with human organisms and due to honey’s various and remarkable properties for human health, the two elements are currently used together in order to develop ideal biomaterials for a wide range of purposes. In this review, by discussing the applicability of honey on Bombyx mori and beyond, the importance of honey for life sciences and related fields is spotlighted.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

scholarly journals Effects of Pyriproxyfen Exposure on Reproduction and Gene Expressions in Silkworm, Bombyx mori

Insects ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 467
Author(s):  
He-Ying Qian ◽  
Xiao Zhang ◽  
Guo-Dong Zhao ◽  
Hui-Min Guo ◽  
Gang Li ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Model Organism ◽  
Ovary Development ◽  
Control Group ◽  
Hatching Rate ◽  
Hormone Regulation ◽  
Concentration Effects ◽  
Gene Expressions ◽  
Silkworm Larvae ◽  
Silkworm Bombyx Mori

The silkworm, Bombyx mori Linnaeus, is an important economic insect and a representative model organism of Lepidoptera, which has been widely used in the study of reproduction and development. The development of the silkworm’s reproductive gland is easily affected by many external factors, such as chemical insecticides. After the silkworm larvae were treated with different concentrations of pyriproxyfen, the results showed that the number of eggs and hatching rate of eggs in the silkworm can be reduced by pyriproxyfen, and the concentration effects were displayed. Pyriproxyfen exposure could affect the normal development of the ovary tissue by reducing the number of oocytes and oogonia in the ovaries of silkworm fed with pyriproxyfen. We employed qRT-PCR, to detect the expressions of genes related to ovary development (Vg, Ovo, Otu, Sxl-S and Sxl-L) and hormone regulation (EcR and JHBP2) in silkworm. Our study showed that the transcription levels of Vg, Ovo, Otu, Sxl-S and Sxl-L in the treatment group were lower than those in the control group (6.08%, 61.99%, 83.51%, 99.31% and 71.95%, respectively). The transcription level of ECR was 70.22% for the control group, while that of JHBP2 was upregulated by 3.92-fold. Changes of transcription levels of these genes caused by pyriproxyfen exposure ultimately affect the absorption of nutrients, energy metabolism, ovary development and egg formation of the silkworm, thus leading to reproductive disorders of the silkworm. In general, our study revealed the response of silkworm reproduction to pyriproxyfen exposure and provided a certain reference value for the metabolism of the silkworm to pyriproxyfen.

Genome-wide identification and analysis of JHBP-domain family members in the silkworm Bombyx mori

2016 ◽  
Vol 291 (6) ◽  
pp. 2159-2171 ◽  
Author(s):  
Wei Li ◽  
Tingcai Cheng ◽  
Wenbo Hu ◽  
Zhangchuan Peng ◽  
Chun Liu ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Family Members ◽  
Domain Family ◽  
Genome Wide ◽  
Silkworm Bombyx Mori

scholarly journals De novo genome assembly of the tobacco hornworm moth (Manduca sexta)

2021 ◽  
Vol 11 (1) ◽  
pp. 1-9
Author(s):  
Ariel Gershman ◽  
Tatiana G Romer ◽  
Yunfan Fan ◽  
Roham Razaghi ◽  
Wendy A Smith ◽  
...  
Keyword(s):  
Manduca Sexta ◽  
Reference Genome ◽  
De Novo ◽  
Model Organism ◽  
Tobacco Hornworm ◽  
Model System ◽  
Future Research ◽  
De Novo Genome Assembly ◽  
Lepidopteran Insect ◽  
Modern Technologies

Abstract The tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience, and immunity. However, current studies rely on the highly fragmented reference genome Msex_1.0, which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present a new reference genome for M. sexta, JHU_Msex_v1.0, applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly is 470 Mb and is ∼20× more continuous than the original assembly, with scaffold N50 > 14 Mb. We annotated the assembly by lifting over existing annotations and supplementing with additional supporting RNA-based data for a total of 25,256 genes. The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of the M. sexta genome improves resequencing studies and benefits future research on M. sexta as a model organism.

scholarly journals Genome rearrangements induce biofilm formation inEscherichia coliC – an old model organism with a new application in biofilm research

2019 ◽  
Author(s):  
Jarosław E. Król ◽  
Donald C. Hall ◽  
Sergey Balashov ◽  
Steven Pastor ◽  
Justin Siebert ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Insertion Sequence ◽  
Genomic Sequence ◽  
Expression Profiles ◽  
Model Organism ◽  
The Other ◽  
Start Codon ◽  
Bacterial Survival ◽  
E Coli ◽  
Full Genomic Sequence

AbstractEscherichia coliC forms more robust biofilms than the other laboratory strains. Biofilm formation and cell aggregation under a high shear force depends on temperature and salt concentrations. It is the last of fiveE. colistrains (C, K12, B, W, Crooks) designated as safe for laboratory purposes whose genome has not been sequenced. Here we present the complete genomic sequence of this strain in which we utilized both long-read PacBio-based sequencing and high resolution optical mapping to confirm a large inversion in comparison to the other laboratory strains. Notably, DNA sequence comparison revealed the absence of several genes thought to be involved in biofilm formation, including antigen 43,waaSBOJYZULfor LPS synthesis, andcpsBfor curli synthesis. The first main difference we identified that likely affects biofilm formation is the presence of an IS3-like insertion sequence in front of the carbon storage regulatorcsrAgene. This insertion is located 86 bp upstream of thecsrAstart codon inside the −35 region of P4 promoter and blocks the transcription from the sigma32and sigma70promoters P1-P3 located further upstream. The second is the presence of an IS5/IS1182 in front of thecsgDgene, which may drive its overexpression in biofilm. And finally,E. coliC encodes an additional sigma70subunit overexpressed in biofilm and driven by the same IS3-like insertion sequence. Promoter analyses using GFP gene fusions and total expression profiles using RNA-seq analyses comparing planktonic and biofilm envirovars provided insights into understanding this regulatory pathway inE. coli.IMPORTANCEBiofilms are crucial for bacterial survival, adaptation, and dissemination in natural, industrial, and medical environments. Most laboratory strains ofE. coligrown for decadesin vitrohave evolved and lost their ability to form biofilm, while environmental isolates that can cause infections and diseases are not safe to work with. Here, we show that the historic laboratory strain ofE. coliC produces a robust biofilm and can be used as a model organism for multicellular bacterial research. Furthermore, we ascertained the full genomic sequence as well as gene expression profiles of both the biofilm and planktonic envirovars of this classic strain, which provide for a base level of characterization and make it useful for many biofilm-based applications.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Yong Zou ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Gene Structure ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Profiles ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and 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 preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

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