Changes in Transcriptome and Gene Expression in Sogatella furcifera (Hemiptera: Delphacidae) in Response to Cycloxaprid

2020 ◽  
Author(s):  
Jian-Xue Jin ◽  
Zhao-Chun Ye ◽  
Dao-Chao Jin ◽  
Feng-Liang Li ◽  
Wen-Hong Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Virus Transmission ◽  
Resistance Mechanisms ◽  
Amino Acid Sequences ◽  
Coding Region ◽  
Sogatella Furcifera ◽  
Neonicotinoid Insecticide

Abstract The white-backed planthopper, Sogatella furcifera (Horváth), causes substantial damage to crops by direct feeding or virus transmission, especially southern rice black-streaked dwarf virus, which poses a serious threat to rice production. Cycloxaprid, a novel cis-nitromethylene neonicotinoid insecticide, has high efficacy against rice planthoppers, including imidacloprid-resistant populations. However, information about the influence of cycloxaprid on S. furcifera (Hemiptera: Delphacidae) at the molecular level is limited. Here, by de novo transcriptome sequencing and assembly, we constructed two transcriptomes of S. furcifera and profiled the changes in gene expression in response to cycloxaprid at the transcription level. We identified 157,906,456 nucleotides and 131,601 unigenes using the Illumina technology from cycloxaprid-treated and untreated S. furcifera. In total, 38,534 unigenes matched known proteins in at least one database, accounting for 29.28% of the total unigenes. The number of coding DNA sequences was 28,546 and that of amino acid sequences in the coding region was 22,299. In total, 15,868 simple sequence repeats (SSRs) were identified. The trinucleotide repeats accounted for 45.1% (7,157) of the total SSRs and (AAG/CTT)n were the most frequent motif. There were 359 differentially expressed genes that might have been induced by cycloxaprid. There were 131 upregulated and 228 downregulated genes. Twenty-two unigenes might be involved in resistance against cycloxaprid, such as cytochrome P450, glutathione S-transferase (GST), acid phosphatase (ACP), and cadherin. Our study provides vital information on cycloxaprid-induced resistance mechanisms, which will be useful to analyze the molecular mechanisms of cycloxaprid resistance and may lead to the development of novel strategies to manage S. furcifera.

scholarly journals Transcriptome and expression analysis of Sogatella furcifera (Horváth) (Hemiptera: Delphacidae) in response to cycloxaprid

2019 ◽  
Author(s):  
Jin Jian Xue ◽  
Ye Zhao-Chun ◽  
Cheng Ying ◽  
Li Feng-Liang ◽  
Li Wen-Hong ◽  
...  
Keyword(s):  
High Efficiency ◽  
De Novo ◽  
Crop Protection ◽  
Resistance Mechanism ◽  
Plant Viruses ◽  
Transcriptional Level ◽  
Coding Region ◽  
Sogatella Furcifera ◽  
Glutathione S Transferase ◽  
Neonicotinoid Insecticide

Abstract Background The white backed planthopper, Sogatella furcifera (Horváth), causes substantial damage to many crops by direct feeding or transmitting plant viruses, especially southern rice black-streaked dwarf virus (SRBSDV) that has become a great threat to rice production in East Asia. Cycloxaprid, a novel cis-nitromethylene neonicotinoid insecticide, has good industrialization prospects because of its high efficiency against rice planthoppers, including imidacloprid-resistant populations. This chemical would be used extensively in future. However, very little is known about the influence on S. furcifera after cycloxaprid application at the molecular level. We sequenced S. furcifera transcriptome of female adult of S. furcifera using the Illumina sequencing. Results By de novo transcriptome assembling and massive parallel pyrosequencing, we constructed two transcriptomes of S. furcifera and profiled the alternation of gene expression in response to cycloxaprid treatment in transcriptional level. Over 157,906,456 nucleotides and 131,601 different unigenes were generated using Illumina technology from both cycloxaprid-treatment and no-treatment S. furcifera. And a total of 38,534 unigenes matched known proteins in at least one database, accounting for 29.28% in total unigenes. The number of Coding DNA Sequence (CDS) were 28,546 and that of the amino acid sequence of coding region were 22,299. A total 15,868 simple sequence repeats (SSRs) were identified. The trinucleotide repeats accounted for 45.1% (7,157) in total SSRs and the (AAG/CTT)n was the most frequent motif. There were 359 differentially expressed genes (DEGs) that might be induced by cycloxaprid. There were 131 genes up-regulated and 228 down-regulated. 22 unigenes may take participate in the resistance to cycloxaprid, such as cytochrome P450, Glutathione-s transferase (GST), Acid phosphatase (ACP), cadherin, etc. Conclusions Our study will provide a splendid database for future investigations of the resistance mechanism induced by cycloxaprid and will provide new strategies for pest management and crop protection.

Multiple calmodulin mRNA species are derived from two distinct genes

1987 ◽  
Vol 7 (5) ◽  
pp. 1873-1880
Author(s):  
H Nojima ◽  
K Kishi ◽  
H Sokabe
Keyword(s):  
Dna Sequences ◽  
Northern Blotting ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Rat Tissues ◽  
Coding Region ◽  
Genomic Libraries ◽  
Mrna Species ◽  
Nuclease Mapping ◽  
Rat Genome

We have observed three calmodulin mRNA species in rat tissues. In order to know from how many expressed genes they are derived, we have investigated the genomic organization of calmodulin genes in the rat genome. From a rat brain cDNA library, we obtained two kinds of cDNAs (pRCM1 and pRCM3) encoding authentic calmodulin. DNA sequence analysis of these cDNA clones revealed substitutions of nucleotides at 73 positions of 450 nucleotides in the coding region, although the amino acid sequences of these calmodulins are exactly the same. DNA sequences in the 5' and 3' noncoding regions are quite different between these two cDNAs. From these results, we conclude that they are derived from two distinct bona fide calmodulin genes, CaMI (pRCM1) and CaMII (pRCM3). Total genomic Southern hybridization suggested four distinct calmodulin-related genes in the rat genome. By cloning and sequencing the calmodulin-related genes from rat genomic libraries, we demonstrated that the other two genes are processed pseudogenes generated from the CaMI (lambda SC9) and CaMII (lambda SC8) genes, respectively, through an mRNA-mediated process of insertions. Northern blotting showed that the CaMI gene is transcribed in liver, muscle, and brain in similar amounts, whereas the CaMII gene is transcribed mainly in brain. S1 nuclease mapping indicated that the CaMI gene produced two mRNA species (1.7 and 4 kilobases), whereas the CaMII gene expressed a single mRNA species (1.4 kilobases).

scholarly journals Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Íria Gabriela Dias dos Santos ◽  
Tiago Antônio de Oliveira Mendes ◽  
Gerluza Aparecida Borges Silva ◽  
Amanda Maria Sena Reis ◽  
Cláudia Barros Monteiro-Vitorello ◽  
...  
Keyword(s):  
Animal Model ◽  
Limb Development ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Development And Differentiation ◽  
Marsupial Species ◽  
Scientific Questions ◽  
Didelphis Albiventris

Abstract Background The white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development. Results The D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at 5 days of age (P5) and at 10 days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development. Conclusions The elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.

Tissue Microarray Is a Useful Tool in the Evaluation of Genes Implicated in Transformation of Follicular Lymphoma.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2267-2267 ◽  
Author(s):  
Abigail Lee ◽  
Andrew Davies ◽  
Andrew Clear ◽  
Maria Calaminici ◽  
Janet Matthews ◽  
...  
Keyword(s):  
Gene Expression ◽  
Follicular Lymphoma ◽  
Tissue Microarray ◽  
Molecular Mechanisms ◽  
De Novo ◽  
B Cell Lymphoma ◽  
Follicular Dendritic Cell ◽  
Response To Therapy ◽  
Aurora Kinase B ◽  
General Response

Abstract A subset of patients (pts.) with follicular lymphoma (FL) will transform to a more aggressive histological sub-type, most typically diffuse large B-cell lymphoma (DLBCL). In general response to therapy is poor and survival short. Paired analysis of samples pre- and post transformation suggest that the molecular mechanisms underlying transformation (Tx) are heterogeneous. In order to independently validate recurring changes in gene/protein expression at transformation (GC phenotype of TxDLBCL, Davies et al., 2002; loss of follicular dendritic Cell (FDC) markers, Shiozawa et al., 2003) a Tx-tissue microarray (Tx-TMA) was created comprising serial samples from 35 pts. (median age 54yrs (22–81) at the time of transformation). In these pts. transformation occurred a median of 3.1years from diagnosis (range 0–15.4) and for each pt. ‘set’ at least 1 pre-Tx FL sample (1–3; n=56), and 1 (1–4; n=44) post transformation sample were represented on the array. To ensure that the Tx-TMA cores accurately represented the corresponding full tissue sections a panel of routine immunohistochemical (IHC) diagnostic markers (n=9) were scored. The concordance between Tx-TMA and full sections (n=10) was >90%. The Tx-TMA was then used to investigate the phenotype of transformed DLBCL, according to the germinal centre (GC)/non-GC like model of de novo DLBCL. Using CD10, BCL6 and MUM1 expression to discriminate between the two subclasses of DLBCL the methodology was first validated on a de novo DLBCL TMA (n=31; 20/31 (65%) non-GC, 11/31 (35%) GC phenotype; 5-yr survival for non-GC pts. 51% and for GC pts., 73%). IHC confirmed the results of gene expression profiling indicating that in 31/35 (89%) pts. transformed DLBCL was of GC phenotype (28/35 (80%) CD10+ and 3/35 (9%) CD10-, BCL6+, MUM1-). Of the remainder, 4/35 were CD10-, BCL6+, of which 3/4 were MUM1+ (3/35 (9%) non-GC phenotype; 1/4 MUM1 was not assessable). Similarly the Tx-TMA confirmed loss of FDC markers (CD21 and CD23) on transformation. Samples from 28 pts were evaluable for CD21 and CD23 IHC expression. In 71% (20/28) of pts. the FDC meshwork was lost or became more sparse on transformation (CD21 loss 15/28 (54%); CD23 loss 17/28 (61%)). The most discriminating changes in gene expression on transformation are now being assessed by IHC. Aurora kinase B (ARKB) is an attractive therapeutic target given that disruption of ARK function results in the induction of apoptosis in RL, a t(14:18) positive DLBCL cell line (Harrington et al. 2004). The observed elevation in ARKB transcription on transformation was confirmed by IHC in this series. The Tx-TMA showed ARKB expression increased on Tx in 13/33 (40%) pts., potentially defining a subset of pts. who might be considered for ARKB directed therapies. Expression of ARKB was low throughout in 18/33 (55%) pts and decreased in 2/33 (6%) pts.; difference in ARKB expression was not significantly associated with survival. These preliminary studies suggest that the availability of TMA of serial biopsies from pts. with transformed FL will provide a powerful means of assessing the relevance of gene expression, both within the tumour and the microenvironment while facilitating the selection of patients most likely to benefit from directed therapeutic approaches.

scholarly journals Didelphis albiventris: an overview of an unprecedented transcriptome sequencing of the white-eared opossum

2019 ◽  
Author(s):  
Íria Gabriela Dias dos Santos ◽  
Tiago Antônio de Oliveira Mendes ◽  
Gerluza Aparecida Borges Silva ◽  
Amanda Maria Sena Reis ◽  
Cláudia Barros Monteiro Vitorello ◽  
...  
Keyword(s):  
Animal Model ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Mammalian Species ◽  
Amino Acid Sequences ◽  
Rna Seq ◽  
Development And Differentiation ◽  
Marsupial Species ◽  
Scientific Questions ◽  
Didelphis Albiventris

Abstract BackgroundThe white-eared opossum (Didelphis albiventris) is widely distributed throughout Brazil and South America. It has been used as an animal model for studying different scientific questions ranging from the restoration of degraded green areas to medical aspects of Chagas disease, leishmaniasis and resistance against snake venom. As a marsupial, D. albiventris can also contribute to the understanding of the molecular mechanisms that govern the different stages of organogenesis. Opossum joeys are born after only 13 days, and the final stages of organogenesis occur when the neonates are inside the pouch, depending on lactation. As neither the genome of this opossum species nor its transcriptome has been completely sequenced, the use of D. albiventris as an animal model is limited. In this work, we sequenced the D. albiventris transcriptome by RNA-seq to obtain the first catalogue of differentially expressed (DE) genes and gene ontology (GO) annotations during the neonatal stages of marsupial development.ResultsThe D. albiventris transcriptome was obtained from whole neonates harvested at birth (P0), at five days of age (P5) and at ten days of age (P10). The de novo assembly of these transcripts generated 85,338 transcripts. Approximately 30% of these transcripts could be mapped against the amino acid sequences of M. domestica, the evolutionarily closest relative of D. albiventris to be sequenced thus far. Among the expressed transcripts, 2,077 were found to be DE between P0 and P5, 13,780 between P0 and P10, and 1,453 between P5 and P10. The enriched GO terms were mainly related to the immune system, blood tissue development and differentiation, vision, hearing, digestion, the CNS and limb development.ConclusionsThe elucidation of opossum transcriptomes provides an out-group for better understanding the distinct characteristics associated with the evolution of mammalian species. This study provides the first transcriptome sequences and catalogue of genes for a marsupial species at different neonatal stages, allowing the study of the mechanisms involved in organogenesis.

scholarly journals DNA Microarrays of the Complex Human Cytomegalovirus Genome: Profiling Kinetic Class with Drug Sensitivity of Viral Gene Expression

1999 ◽  
Vol 73 (7) ◽  
pp. 5757-5766 ◽  
Author(s):  
James Chambers ◽  
Ana Angulo ◽  
Dhammika Amaratunga ◽  
Hongqing Guo ◽  
Ying Jiang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Cytomegalovirus ◽  
Dna Sequences ◽  
De Novo ◽  
Expression Profiles ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Viral Dna ◽  
Viral Protein Synthesis ◽  
Entire Genome

ABSTRACT We describe, for the first time, the generation of a viral DNA chip for simultaneous expression measurements of nearly all known open reading frames (ORFs) in the largest member of the herpesvirus family, human cytomegalovirus (HCMV). In this study, an HCMV chip was fabricated and used to characterize the temporal class of viral gene expression. The viral chip is composed of microarrays of viral DNA prepared by robotic deposition of oligonucleotides on glass for ORFs in the HCMV genome. Viral gene expression was monitored by hybridization to the oligonucleotide microarrays with fluorescently labelled cDNAs prepared from mock-infected or infected human foreskin fibroblast cells. By using cycloheximide and ganciclovir to block de novo viral protein synthesis and viral DNA replication, respectively, the kinetic classes of array elements were classified. The expression profiles of known ORFs and many previously uncharacterized ORFs provided a temporal map of immediate-early (α), early (β), early-late (γ1), and late (γ2) genes in the entire genome of HCMV. Sequence compositional analysis of the 5′ noncoding DNA sequences of the temporal classes, performed by using algorithms that automatically search for defined and recurring motifs in unaligned sequences, indicated the presence of potential regulatory motifs for β, γ1, and γ2 genes. In summary, these fabricated microarrays of viral DNA allow rapid and parallel analysis of gene expression at the whole viral genome level. The viral chip approach coupled with global biochemical and genetic strategies should greatly speed the functional analysis of established as well as newly discovered large viral genomes.

scholarly journals Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Jian Wang ◽  
Chengcheng Lu ◽  
Yifan Zhao ◽  
Zhijiao Tang ◽  
Jiakun Song ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Lateral Line ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Sensory Organs ◽  
Specific Expression ◽  
Voltage Gated ◽  
Voltage Gated Calcium Channels ◽  
Early Regeneration

Abstract Background The electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these two sensory organs have characteristic morphological and physiological differences. The molecular mechanisms for the specification of AOs and NMs are not clearly understood. Results We sequenced the transcriptome for neomycin treated sturgeon AOs and NMs in the early regeneration stages, and de novo assembled a sturgeon transcriptome. By comparing the gene expression differences among untreated AOs, NMs and general epithelia (EPs), we located some specific genes for these two sensory organs. In sturgeon lateral line, the voltage-gated calcium channels and voltage-gated potassium channels were predominant calcium and potassium channel subtypes, respectively. And by correlating gene expression with the regeneration process, we predicated several candidate key transcriptional regulation related genes might be involved in AOs and NMs regeneration. Conclusions Genes with specific expression in the two lateral line sensory organs suggests their important roles in mechanoreceptor and electroreceptor formation. The candidate transcriptional regulation related genes may be important for mechano- and electro- receptor specification, in a “dosage-related” manner. These results suggested the molecular basis for specification of these two sensory organs in sturgeon.

scholarly journals The growth hormone gene has evolved independently in African Pygmy Mouse Mus minutoides

2021 ◽  
Author(s):  
Sumito Matsuya ◽  
Hiroyuki Imai ◽  
Yasuo Kiso ◽  
Ken Takeshi Kusakabe ◽  
Kiyoshi Kano
Keyword(s):  
Gene Expression ◽  
Growth Hormone ◽  
Amino Acid Sequences ◽  
Growth Hormone Gene ◽  
Neighbor Joining ◽  
Coding Region ◽  
Transcriptional Regulatory ◽  
African Pygmy Mouse ◽  
Mus Minutoides ◽  
Gene Expression Levels

AbstractMus minutoides (the African pygmy mouse) is one of the smallest mammals. We determined the nucleotide sequence of the growth hormone (Gh) gene and the sequence of the putative coding region in M. minutoides, where is predicted to be distinct in the functional and transcriptional regulatory regions between M. minutoides and Mus musculus (the House mouse). To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic tree based on the putative amino acid sequences of Gh in M. musculus and mammals by neighbor-joining method, suggesting that Gh diverged relatively earlier than other Mus genus and may have evolved independently in M. minutoides. Furthermore, analysis of Gh gene expression levels showed a tendency to be higher in M. minutoides than in M. musculus. Our results suggest that Gh may have evolved independently in M. minutoides and may have different functions and signaling in Mus genus.

scholarly journals Application of Genomics for Understanding Plant Virus-Insect Vector Interactions and Insect Vector Control

2016 ◽  
Vol 106 (10) ◽  
pp. 1213-1222 ◽  
Author(s):  
Navneet Kaur ◽  
Daniel K. Hasegawa ◽  
Kai-Shu Ling ◽  
William M. Wintermantel
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Virus Transmission ◽  
Plant Viruses ◽  
Significant Shift ◽  
Insect Vector ◽  
Insect Vectors ◽  
Genomic Technologies ◽  
Potential Applications ◽  
Generation Sequencing

The relationships between plant viruses and their vectors have evolved over the millennia, and yet, studies on viruses began <150 years ago and investigations into the virus and vector interactions even more recently. The advent of next generation sequencing, including rapid genome and transcriptome analysis, methods for evaluation of small RNAs, and the related disciplines of proteomics and metabolomics offer a significant shift in the ability to elucidate molecular mechanisms involved in virus infection and transmission by insect vectors. Genomic technologies offer an unprecedented opportunity to examine the response of insect vectors to the presence of ingested viruses through gene expression changes and altered biochemical pathways. This review focuses on the interactions between viruses and their whitefly or thrips vectors and on potential applications of genomics-driven control of the insect vectors. Recent studies have evaluated gene expression in vectors during feeding on plants infected with begomoviruses, criniviruses, and tospoviruses, which exhibit very different types of virus-vector interactions. These studies demonstrate the advantages of genomics and the potential complementary studies that rapidly advance our understanding of the biology of virus transmission by insect vectors and offer additional opportunities to design novel genetic strategies to manage insect vectors and the viruses they transmit.

scholarly journals Molecular Cloning and Bioinformatics Analysis of DQA Gene from Mink (Neovison vison)

2019 ◽  
Vol 20 (5) ◽  
pp. 1037
Author(s):  
Zhaobin Fan ◽  
Houfeng Zhang ◽  
Min Rong ◽  
Dongmei Meng ◽  
Zhenxing Yu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Molecular Mechanisms ◽  
Signal Sequence ◽  
Amino Acid Sequences ◽  
Neovison Vison ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Coding Region ◽  
Full Length Sequence

In the present study, we cloned, sequenced, and explored the structural and functional characteristics of the major histocompatibility complex (MHC)-DQA gene from mink (Neovison vison) for the first time. The full-length sequence of DQA gene was 1147-bp-long, contained a coding region of 768-bp, which was predicted to encoding 255 amino acid residues. The comparison between DQA from mink (Neovison vison) and other MHC-DQA molecules from different animal species showed that nucleotide and encoded amino acid sequences of the mink DQA gene exhibited high similarity with the ferret (Mustela pulourius furo). Phylogenetic analysis revealed that mink (Neovison vison) DQA is grouped with that of ferret (Mustela pulourius furo). The cloned sequence contained a 23-amino acid NH2-terminal signal sequence with the signal peptide cutting site located in amino acids 23–24, and had three Asn-Xaa-Ser/Thr sequons. Three cysteine residues were also identified (Cys-85, Cys-121, and Cys-138). The 218 to 240 amino acids were predicted to be the transmembrane domains. The prediction of the secondary structure revealed three α-helixes and fourteen β-sheets in Neovison vison DQA protein, while random coil was a major pattern. In this study, the whole CDS sequence of Neovison vison DQA gene was successfully cloned, which was valuable for exploring the function and antiviral molecular mechanisms underlying the molecule. The findings of the present study have laid the foundation for the disease resistance and breeding of mink.

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