scholarly journals Transcriptome analysis of developmental stages of cocoa pod borer, Conopomorpha cramerella: A polyphagous insect pest of economic importance in Southeast Asia.

2021 ◽  
Author(s):  
Chia Lock Tan ◽  
Rosmin Kasran ◽  
Wei Wei Lee ◽  
Wai Mun Leong
Keyword(s):  
Southeast Asia ◽  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Homology Search ◽  
General Function ◽  
Protein Coding ◽  
Pod Borer ◽  
Three Stages ◽  
Polyphagous Insect

The cocoa pod borer, Conopomorpha cramerella (Snellen) is a serious pest in cocoa plantations in Southeast Asia.  It causes significant losses in the crop.  Unfortunately, genetic resources for this insect is extremely scarce.  To improve these resources, we sequenced the transcriptome of C. cramerella representing the three stages of development, larva, pupa and adult moth using Illumina NovaSeq6000.  Transcriptome assembly was performed by Trinity for all the samples.  A total number of 147,356,088 high quality reads were obtained.  Of these, 285,882 contigs were assembled.  The mean contig size was 374 bp.  Protein coding sequence (CDS) was extracted from the reconstructed transcripts by TransDecoder.  Subsequently, BlastX and InterProScan were applied for homology search to make a prediction of the function of CDS in unigene.  Additionally, we identified a number of genes that are involved in reproduction and development such as genes involved in general function processes in the insect.  Genes found to be involved in reproduction such as porin, dsx, bol and fruitless were associated with sex determination, spermatogenesis and pheromone binding.  Furthermore, transcriptome changes during development were analysed.  There were 2,843 differentially expressed genes (DEG) detected between the larva and pupa samples.  A total of 2,861 DEG were detected between adult and larva stage whereas between adult and pupa stage, 1,953 DEG were found.  In conclusion, the transcriptomes could be a valuable genetic resource for identification of genes in C. cramerella and the study will provide putative targets for RNAi pest control.

Transcriptome Analysis Reveals Candidate Genes During the Prepupal-pupal Transition in the Oriental Armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2020 ◽  
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Pupal Stage ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Rna Seq ◽  
Mythimna Separata ◽  
Expression Levels ◽  
Lepidoptera Noctuidae

Abstract Background Metamorphosis ensures the transformation of a larva of the holometabolous insects into a reproductive adult through a transitory pupal stage. Understanding how changes in expression levels of genes during the prepupal-pupal transition will inform us of how the metamorphosis arises. Results In this study, mature larvae (ML), wandering (W), 1 day (P1), 5 days (P5), and 10 days (P10) after pupation of the Mythimna separata (Walker), a notorious migratory pest of agricultural crops, were selected, forming five groups. RNA-Seq revealed that the draft transcriptome assembly contained 140562 contigs, and more than half (74,059) were similar to sequence at NCBI (e value < e− 3), including 22884, 23534, 26643, and 33238 differentially expressed genes (DEGs) in ML vs W, W vs P1, P1 vs P5, and P5-vs-P10, respectively. Comparative transcriptomics revealed the enrichment of biological processes related to the membrane and integral component of membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, enabled us to delineate and partially validate the metabolic pathway in M. separata. Of these DEGs, 33 CP, 18 20E, and 7 JH genes were differentially expressed across the developmental stages. Correlation analysis uncovered that the relative expression levels of 10 selected CP, 20E, and JH-related genes obtained by real-time PCR quantitative (RT-qPCR) matched well with their FPKM values derived from RNA-seq. Conclusions The data gave here represent an important first step to uncover the molecular mechanism of metamorphosis in M. separata, which also provide valuable information for manipulation of insect development and metamorphosis using the obtained DEGs as targets and broaden the applications of available tools for insect pest control.

scholarly journals The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 7
Author(s):  
Nur Lina Rahmat ◽  
Anis Nadyra Zifruddin ◽  
Cik Mohd Rizuan Zainal Abidin ◽  
Nor-Azlan Nor Muhammad ◽  
Maizom Hassan
Keyword(s):  
Oil Palm ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Instar Larva ◽  
Orthologous Group ◽  
Kegg Pathways ◽  
Developmental Gene Expression ◽  
Functional Studies

Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These datasets add valuable transcriptomic resources for further study of developmental gene expression, transcriptional regulations and functional gene activities involved in the development of M. plana. Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an RNAi-mediated pest control management by targeting certain pathways, and functional studies of the genes in M. plana.

Infectivity of entomopathogenic nematodes against the legume pod-borer, Maruca vitrata Fabricius, infesting pigeon pea

2021 ◽  
Vol 95 ◽  
Author(s):  
R. Pervez ◽  
U. Rao
Keyword(s):  
Entomopathogenic Nematodes ◽  
Agricultural Research ◽  
Insect Pest ◽  
Indian Agricultural Research Institute ◽  
Pigeon Pea ◽  
Fourth Instar ◽  
Maruca Vitrata ◽  
Pod Borer ◽  
Legume Pod Borer ◽  
Maximum Penetration

Abstract The legume pod-borer, Maruca vitrata Fabricius (Lepidoptera: Crambidae) (LPB), is an important insect pest of pigeon pea. Chemical pesticides are generally employed to manage this pest, but because of the soil residue issues and other environmental hazards associated with their use, biopesticides are also in demand. Another benign alternative is to use entomopathogenic nematodes (EPNs) to manage this vital pest. In the present study, the infectivity of ten native EPNs was evaluated against LPB by assessing their penetration and production in the LPB. The effectiveness of the promising EPNs against second-, third- and fourth-instar LPB larvae was also studied. Heterorhabditis sp. (Indian Agricultural Research Institute-Entomopathogenic Nematodes Rashid Pervez (IARI-EPN RP) 06) and Oscheius sp. (IARI-EPN RP 08) were found to be most pathogenic to LPB, resulting in about 100% mortality within 72 h, followed by Steinernema sp. (IARI-EPN RP 03 and 09). Oscheius sp. (IARI-EPN RP 04) was found to be the least pathogenic to LPB larva with 67% mortality. Maximum penetration was exhibited by Heterorhabditis sp. (IARI-EPN RP 06) followed by Oscheius sp. (IARI-EPN RP 08), whereas the lowest rate of penetration was exhibited by Oscheius sp. (IARI-EPN RP 01). The highest rate of production was observed with Oscheius sp. (IARI-EPN RP 08), followed by Oscheius sp. (IARI-EPN RP 04 and 10). Among the tested instars of the LPB larvae, second-instar larvae were more susceptible to EPNs, followed by third- and fourth-instar larvae. The results indicate that Heterorhabditis sp. (IARI-EPN RP 06) and Oscheius sp. (IARI-EPN RP 08) have a good potential to the manage LPB.

Effects of insecticides chlorpyrifos, emamectin benzoate and fipronil on Spodoptera litura might be mediated by OBPs and CSPs

2017 ◽  
Vol 108 (5) ◽  
pp. 658-666 ◽  
Author(s):  
X. Lin ◽  
Y. Jiang ◽  
L. Zhang ◽  
Y. Cai
Keyword(s):  
Spodoptera Litura ◽  
Quantitative Polymerase Chain Reaction ◽  
Insect Pest ◽  
Survival Rates ◽  
Gene Families ◽  
Cross Resistance ◽  
Emamectin Benzoate ◽  
Insecticide Exposure ◽  
Polyphagous Insect ◽  
Related Proteins

AbstractSpodoptera litura is a widespread polyphagous insect pest that can develop resistance and cross-resistance to insecticides, making it difficult to control. Insecticide exposure has previously been linked with induction of specific olfactory-related proteins, including some chemosensory proteins (CSPs) and odorant-binding proteins (OPBs), which may disrupt detection of environmental factors and reduce fitness. However, functional evidence supporting insecticide and OBPs/CSPs mediation remains unknown. Here we fed male S. litura moths with sucrose water containing one of three insecticides, chlorpyrifos, emamectin benzoate or fipronil, and used real-time quantitative polymerase chain reaction and RNAi to investigate OBPs and CSPs expression and their correlations with survival. Chlorpyrifos and emamectin benzoate increased expression of 78% of OBPs, plus 63 and 56% of CSP genes, respectively, indicating a major impact on these gene families. RNAi knockdown of SlituCSP18, followed by feeding with chlorpyrifos or fipronil, decreased survival rates of male moths significantly compared with controls. Survival rate also decreased significantly with the downregulation of SlituOBP9 followed by feeding with chlorpyrifos. Thus, although these three insecticides had different effects on OBP and CSP gene expression, we hypothesize that SlituOBPs and SlituCSPs might mediate their effects by increasing their expression levels to improve survival. Moreover, the differential response of S. litura male moths to the three insecticides indicated the potential specificity of chlorpyrifos affect SlituCSP18 and SlituOBP9 expression.

scholarly journals Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages

Insects ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 226
Author(s):  
Siying Fu ◽  
Yujie Duan ◽  
Siqi Wang ◽  
Yipeng Ren ◽  
Wenjun Bu
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Economic Losses ◽  
Future Research ◽  
Economic Damage ◽  
Wing Formation ◽  
Riptortus Pedestris

Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.

scholarly journals An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq

2019 ◽  
Author(s):  
Thomas F. Martinez ◽  
Qian Chu ◽  
Cynthia Donaldson ◽  
Dan Tan ◽  
Maxim N. Shokhirev ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Human Leukocyte ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Proteomics Data ◽  
Protein Coding ◽  
Leukocyte Antigen ◽  
Human Genes ◽  
Small Open Reading Frames

Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs, providing an approach to select smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

Alternative RNA splicing that is spatially regulated: generation of transcripts from the Antennapedia gene of Drosophila melanogaster with different protein-coding regions

1988 ◽  
Vol 8 (10) ◽  
pp. 4143-4154
Author(s):  
V L Stroeher ◽  
J C Gaiser ◽  
R L Garber
Keyword(s):  
Alternative Splicing ◽  
Rna Splicing ◽  
Developmental Stages ◽  
Molecular Evidence ◽  
Rnase Protection ◽  
Protein Coding ◽  
Spatial Regulation ◽  
Coding Regions ◽  
Imaginal Disks ◽  
Isolated Tissues

We have shown previously that transcription of the Drosophila homeotic gene Antennapedia results in four major RNA species which differ in long 5'- and 3'-untranslated sequences. The protein-coding portion of these transcripts, however, is located in exons common to all. Using RNase protection assays and further cDNA clone isolation, we have now detected two alternative splicing events between exons of this region. These result in four RNA variations which, if translated, would encode a family of Antennapedia proteins. By analyzing transcripts from various developmental stages and isolated tissues, we show that alternative splicing is under strict temporal and spatial regulation. For example, while similar patterns of splicing were found for all wild-type thoracic imaginal disks examined, these differed distinctly from the patterns observed in neural tissues. Our results suggest that individual RNAs may be associated with different biological roles, and provide molecular evidence that the Antennapedia gene is involved in multiple functions.

scholarly journals Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages

2019 ◽  
Vol 10 (2) ◽  
pp. 443-454
Author(s):  
Chang Liu ◽  
Cornelius Tlotliso Sello ◽  
Yujian Sui ◽  
Jingtao Hu ◽  
Shaokang Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Receptor Interaction ◽  
Keratinocyte Proliferation ◽  
Skin Development

In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.

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