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.

scholarly journals De novo characterization of the Lycium ruthenicum transcriptome and analysis of its digital gene expression profiles during fruit development and ripening

2017 ◽  
Vol 69 (1) ◽  
pp. 181-190 ◽  
Author(s):  
Yong Peng ◽  
Huiqin Ma ◽  
Shangwu Chen
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
De Novo ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Digital Gene Expression ◽  
Orthologous Group ◽  
Functional Studies ◽  
Lycium Ruthenicum

Lycium ruthenicum Murr., which belongs to the family Solanaceae, is a resource plant for Chinese traditional medicine and nutraceutical foods. In this study, RNA sequencing was applied to obtain raw reads of L. ruthenicum fruit at different stages of ripening, and a de novo assembly of its sequence was performed. Approximately 52.45 million 100-bp paired-end raw reads were generated from the samples by deep RNA-seq analysis. These short reads were assembled to obtain 164814 contigs, and the contigs were assembled into 84968 non-redundant unigenes using the Trinity method. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group and KEGG (Kyoto Encyclopedia of Genes and Genomes)pathway terms. Digital gene expression analysis was applied to compare gene-expression patterns at different fruit developmental stages. These results contribute to existing sequence resources for Lycium spp. during the fruit-ripening stages, which is valuable for further functional studies of genes involved in L. ruthenicum fruit nutraceutical quality.

scholarly journals De Novo Transcriptome Assembly of Isatis indigotica at Reproductive Stages and Identification of Candidate Genes Associated with Flowering Pathways

2018 ◽  
Vol 143 (1) ◽  
pp. 56-66
Author(s):  
Yu Bai ◽  
Ying Zhou ◽  
Xiaoqing Tang ◽  
Yu Wang ◽  
Fangquan Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Rna Seq ◽  
Isatis Indigotica ◽  
Regulatory Pathways ◽  
Kegg Pathways ◽  
Bolting And Flowering

The appropriate timing of bolting and flowering is one of the keys to the reproductive success of Isatis indigotica. Several flowering regulatory pathways have been reported in plant species, but we know little about flowering regulatory in I. indigotica. In the present study, we performed RNA-seq and annotated I. indigotica transcriptome using RNA from five tissues (leaves, roots, flowers, fruit, and stems). Illumina sequencing generated 149,907,857 high-quality clean reads and 124,508 unigenes were assembled from the sequenced reads. Of these unigenes, 88,064 were functionally annotated by BLAST searches against the public protein databases. Functional classification and annotation assigned 55,991 and 23,072 unigenes to 52 gene ontology (GO) terms and 25 clusters of orthologous group (COG) categories, respectively. A total of 19,927 unigenes were assigned to 124 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 80 candidate genes related to plant circadian rhythm were identified. We also identified a number of differentially expressed genes (DEG) and 91 potential bolting and flowering-related genes from the RNA-seq data. This study is the first to identify bolting and flowering-related genes based on transcriptome sequencing and assembly in I. indigotica. The results provide foundations for the exploration of flowering pathways in I. indigotica and investigations of the molecular mechanisms of bolting and flowering in Brassicaceae plants.

scholarly journals De novo Transcriptome Assembly and Comprehensive Annotation of Two Tree Tomato Cultivars (Solanum betaceum Cav.) with Different Fruit Color

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 431
Author(s):  
Juan Pacheco ◽  
Santiago Vilanova ◽  
Rubén Grillo-Risco ◽  
Francisco Garcia-Garcia ◽  
Jaime Prohens ◽  
...  
Keyword(s):  
De Novo ◽  
Average Length ◽  
Transcriptome Assembly ◽  
Orthologous Group ◽  
Significant Similarity ◽  
Single Nucleotide ◽  
Kegg Pathways ◽  
Tomato Cultivars ◽  
Solanum Betaceum ◽  
Tree Tomato

The tree tomato (Solanum betaceum Cav.) is an underutilized fruit crop native to the Andean region and phylogenetically related to the tomato and potato. Tree tomato fruits have a high amount of nutrients and bioactive compounds. However, so far there are no studies at the genome or transcriptome level for this species. We performed a de novo assembly and transcriptome annotation for purple-fruited (A21) and an orange-fruited (A23) accessions. A total of 174,252 (A21) and 194,417 (A23) transcripts were assembled with an average length of 851 and 849 bp. A total of 34,636 (A21) and 36,224 (A23) transcripts showed a significant similarity to known proteins. Among the annotated unigenes, 22,096 (A21) and 23,095 (A23) were assigned to the Gene Ontology (GO) term and 14,035 (A21) and 14,540 (A23) were found to have Clusters of Orthologous Group (COG) term classifications. Furthermore, 22,096 (A21) and 23,095 (A23) transcripts were assigned to 155 and 161 (A23) KEGG pathways. The carotenoid biosynthetic process GO terms were significantly enriched in the purple-fruited accession A21. Finally, 68,647 intraspecific single-nucleotide variations (SNVs) and almost 2 million interspecific SNVs were identified. The results of this study provide a wealth of genomic data for the genetic improvement of the tree tomato.

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.

scholarly journals Initial virome characterization of the common cnidarian lab model Nematostella vectensis

2020 ◽  
Author(s):  
Magda Lewandowska ◽  
Yael Hazan ◽  
Yehu Moran
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Artemia Salina ◽  
Model Organisms ◽  
Nematostella Vectensis ◽  
Virus Identification ◽  
Functional Studies ◽  
Powerful Approach ◽  
Viral Communities ◽  
Viral Sequences

AbstractThe role of viruses in forming a stable holobiont has been a subject of extensive research in the recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed almost complete lack of viruses in the samples from the early developmental stages which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for functional studies of viruses and antiviral systems in this lab model cnidarian.

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.

scholarly journals Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae)

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Xiao-Rong Zhou ◽  
Yan-Min Shan ◽  
Yao Tan ◽  
Zhuo-Ran Zhang ◽  
Bao-Ping Pang
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Low Temperatures ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Glucose Dehydrogenase ◽  
Insect Pest ◽  
Cuticle Protein

Abstract Galeruca daurica (Joannis) has become a new insect pest in the Inner Mongolia grasslands since 2009, and its larvae and eggs have strong cold tolerance. To get a deeper insight into its molecular mechanisms of cold stress responses, we performed de novo transcriptome assembly for G. daurica by RNA-Seq and compared the transcriptomes of its larvae exposed to five different temperature treatments (−10, −5, 0, 5, and 25°C for 1 h and then recovered at 25°C for 1 h), respectively. Compared with the control (25°C), the numbers of differentially expressed genes (DEGs) decreased from 1,821 to 882, with the temperature declining from 5 to −10°C. Moreover, we obtained 323 coregulated DEGs under different low temperatures. Under four low temperatures (−10, −5, 0, and 5°C), a large number of genes were commonly upregulated during recovery from cold stresses, including those related to cuticle protein, followed by cytochrome P450, clock protein, fatty acid synthase, and fatty acyl-CoA reductase; meanwhile, lots of genes encoding cuticle protein, RNA replication protein, RNA-directed DNA polymerase, and glucose dehydrogenase were commonly downregulated. Our findings provide important clues for further investigations of key genes and molecular mechanisms involved in the adaptation of G. daurica to harsh environments.

scholarly journals Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Fahad Al-Qurainy ◽  
Aref Alshameri ◽  
Abdel-Rhman Gaafar ◽  
Salim Khan ◽  
Mohammad Nadeem ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Annotation ◽  
Transcriptome Assembly ◽  
Average Frequency ◽  
Cyamopsis Tetragonoloba ◽  
Metabolic Pathway Analysis ◽  
Illumina Hiseq ◽  
Forage Crop ◽  
Kegg Pathways ◽  
Advanced Analysis

The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity. A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level. Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies. RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C. tetragonoloba under normal, heat, drought, and salinity conditions. Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers. A total of 218.2 million paired-end raw reads (~44 Gbp) were generated. Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes. There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta. Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated. A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected. Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively. The transcriptome was associated with 985 enzymes and 156 KEGG pathways. A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts. This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.

scholarly journals De novo transcriptome assembly of Premnotrypes vorax (Coleoptera: Curculionidae)

2020 ◽  
Author(s):  
Luisa-Fernanda Velásquez C. ◽  
Pablo Emiliano Canton ◽  
Alejandro Sánchez-Flores ◽  
Alejandra Bravo ◽  
Jairo Cerón
Keyword(s):  
Biological Control ◽  
Control Strategy ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Insect Pest ◽  
Illumina Hiseq ◽  
Tissue Samples ◽  
Cry Toxin ◽  
Illumina Hiseq Platform ◽  
Potato Crops

Abstract Objective: Premnotrypes vorax (P. vorax) is an insect pest that causes significant losses to potato crops in Colombia. Currently, the insect control is mainly done by using highly toxic chemical insecticides and there are no reports of any commercial biological control strategy against this pest. Hence, the objective of this study was to characterize the insect genetic expression to search for genes that could codify for Bacillus thuringiensis Cry toxin receptors. Using an RNA-seq approach, we sequenced the mRNA from the insect tissue, performed a de novo assembly and analyzed the reconstructed transcriptome of P. vorax. To our knowledge, this is the first genetic report of this endemic insect which will set the basis of a possible biological control strategy.Results: The transcriptome data was obtained from dissected midgut tissue samples of P. vorax larvae. The isolated RNA was isolated and sequenced using the Illumina HiSeq platform with a configuration of 2x150pb reads. A total of 383,552,246 reads were obtained and subsequently a quality and cleaning process was performed through FastQC and Trimmomatic software, respectively. A novo assembly was done using the Trinity software, obtaining a transcriptome assembly with 25,631 genes that showed at least one annotation record, resulting in 74,984 transcript isoforms.

scholarly journals De novo Transcriptome Assembly of Myllocerinus aurolineatus Voss in Tea Plants

2021 ◽  
Vol 5 ◽  
Author(s):  
Xin Xie ◽  
Junmei Jiang ◽  
Meiqing Chen ◽  
Maoxi Huang ◽  
Linhong Jin ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Single Nucleotide ◽  
Functional Studies ◽  
Myllocerinus Aurolineatus ◽  
Tea Plants ◽  
The Trinity ◽  
Simple Sequence

Myllocerinus aurolineatus Voss is a species of the insecta class in the arthropod. In this study, we first observed and identified M. aurolineatus Voss in tea plants in Guizhou, China, where it caused severe quantity and quality losses in tea plants. Knowledge on M. aurolineatus Voss genome is inadequate, especially for biological or functional research. We performed the first transcriptome sequencing by using the Illumina Hiseq™ technique on M. aurolineatus Voss. Over 55.9 million high-quality paired-end reads were generated and assembled into 69,439 unigenes using the Trinity short read software, resulting in a cluster of 1,207 bp of the N50 length. A total of 69,439 genes were predicted by BLAST to known proteins in the NCBI database and were distributed into Gene Ontology (20,190), eukaryotic complete genomes (12,488), and the Kyoto Encyclopedia of Genes and Genomes (3,170). We also identified 96,790 single-nucleotide polymorphisms and 13,121 simple sequence repeats in these unigenes. Our transcriptome data provide a useful resource for future functional studies of M. aurolineatus Voss for dispersal control in tea plants.

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