Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/422170

Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1

Azlan, A.·Obeidat, S. M.·Yunus, M. A.·Azzam, G.
View original source ↗Export metadata ↓

Abstract

Dengue virus (DENV) is a single-stranded, positive-strand RNA virus that belongs to the family of Flaviviridae, and it is mainly transmitted by the mosquito Aedes aegypti (Ae. aegypti). Understanding the interaction of the virus with mosquito vector is vital for devising new strategies for preventing virus transmission. Although protein-coding genes have been the central focus, many reports indicated that long non-coding RNAs (lncRNAs) were also involved in virus-host interaction. Recently, the latest version of Ae. aegypti genome (AaegL5) was released, and the assembly was up to chromosome level. This prompted us to perform lncRNA identification and characterization using the latest genome release as reference. In this study, we investigated the transcriptome profiles of both protein-coding and lncRNA genes in Aedes aegypti cells upon DENV infection. By combining RNA-seq libraries generated in this study with publicly available datasets, we identified a total of 7,221 novel lncRNA transcripts, of which 3,052 and 3,620 were intronic and intergenic respectively, while 549 were antisense to the reference genes. A total of 2,435 differentially expressed transcripts, of which 956 of them were lncRNAs. Overall, the distribution of lncRNA expression and fold change upon virus infection were lower than that of protein-coding genes. We found that the expression of immune-related genes involved in IMD and MAPK signaling pathways were altered. In addition, the expression of major genes involved in RNA-interference (RNAi) pathway that confers antiviral resistance in mosquitoes were found to be unchanged upon DENV infection. Gene ontology analysis suggests that differentially expressed transcripts, either upregulated or downregulated, generally belong to the same functional categories or working in similar signaling pathways. Taken together, besides providing a new set of lncRNA repertoire, the outcomes of our study offer better understanding of Ae. aegypti responses to DENV infection at gene level.\n\nAuthor SummaryDengue virus (DENV), a single-stranded and positive-strand RNA virus of the family Flaviviridae, is primarily transmitted by Aedes aegypti (Ae. aegypti) mosquitoes. There are four closely related but antigenically different serotypes of dengue virus namely DENV1-4. Our understanding on the interaction of each serotype of DENV with its mosquito vector is still very limited. Since vector-borne viruses pose significant burden to public health, knowledge on the virus-host interaction at the molecular level is essential, especially in developing effective strategies to control virus transmission. In this study, we embarked on investigating the transcriptional response of long non-coding RNAs (lncRNAs) and protein-coding genes upon dengue virus serotype 1 (DENV1) infection. Besides, we also generate a comprehensive list of novel lncRNAs identified from the latest and improved genome version of Ae. aegypti. Similar to protein-coding genes, we discovered that the overall expression of lncRNA was significantly altered, suggesting that lncRNAs were involved in virus-host interaction. The results of this study provide basic understanding on the interaction between DENV1 and Ae. aegypti vector at the transcriptional level.

Explore related subjects

geneticsPreprint

Keep this discovery

BibTeXRIS

Azlan, A., Obeidat, S. M., Yunus, M. A., Azzam, G.. 2018-09-19. Transcriptome profiles and novel lncRNA identification of Aedes aegypti cells in response to dengue virus serotype 1. https://doi.org/10.1101/422170

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The histone demethylase Kdm5 and the ARGONAUTE proteins Piwi and Aubergine regulate female abdominal pigmentation in Drosophila melanogaster

Insect pigmentation is an ecologically critical trait influencing many physiological processes. In Drosophila melanogaster, abdominal pigmentation is sexually dimorphic: males have fully pigmented posterior segments, while females exhibit a posterior melanin stripe. Pigmentation relies on the expression of pigmentation genes that encode enzymes involved in pigment synthesis. These genes are tightly regulated during pupal and young adult stages. To expand the gene regulatory network of pigmentation genes, we conducted an RNAi screen using the yellow-Gal4 driver, expressed during the pupal stage in abdominal epidermis. One of the candidates from this screen, Kdm5, encodes a histone demethylase erasing the H3K4me3 histone mark catalyzed by the histone methyl-transferase Trithorax (Trx). We show that Kdm5 down-regulation reduces abdominal pigmentation, mimicking trx down-regulation. Kdm5 activates melanin production through regulation of the pigmentation gene tan. Transcriptomic analyses reveal that Kdm5 and Trx share many targets in pupal abdominal epidermis, including piRNA pathway components such as piwi and aubergine. These piRNA components, originally associated with transposon silencing in the germline, also function in some somatic tissues such as the nervous system, the fat body or the gut. We demonstrate that Piwi and Aubergine participate in female abdominal pigmentation establishment, without evident piRNA production. We also show that Kdm5 and Piwi act not only in pupal abdominal epidermis but also in pupal fat body. This study therefore expands the regulatory network of pigmentation genes. It identifies a new somatic function for Kdm5 and Piwi and reveals a role for pupal fat body in female abdominal pigmentation regulation.

genetics↗
bioRxiv2026

Genetic diversity within and between polyploid sugarcane (Saccharum spp.) families obtained via caryopsis using microsatellite markers and multicategory model

Genetic diversity analyses are essential for sugarcane (Saccharum spp.) breeding programs. Crossbreeding, based on genetic distances between parental plants, is a tool used to increase genetic variability and enhance plant selection; however, quantifying variation in highly polyploid species remains a challenge. The present study aimed to evaluate the diversity within and between 12 families of sugarcane derived from caryopses, analyzing 120 individual seedlings arranged in an augmented block design. Genotyping was performed using primers for 16 microsatellite loci, five simple sequence repeat (SSR) loci, and 11 expressed sequence tag-SSR (EST-SSR) loci. To accurately account for polyploidy, similarity calculations were performed using Bruvos distances among individuals and RST distances among the families. Analysis of molecular variance (AMOVA) indicated that most of the genetic variability was within families (72%), with only 28% found between them. This high level of intra-family variation demonstrates that a significant reservoir of genetic diversity remains available within the crosses. The highest genetic similarity was observed between the families RB986952 x RB986960 and RB036122 x RB03611, whereas the lowest genetic similarity was observed between the families RB97319 x RB966928 and RB106802 x RB855036. Although the evaluated families shared high genetic similarity, the pronounced genetic variation within them demonstrates a robust recombination potential, indicating that the genetic basis of sugarcane can be better explored using the high variability that already exists in the selection of desirable morpho-agronomic characteristics within the families. Furthermore, this study highlights the importance of using appropriate distances for diversity studies with codominant markers, such as microsatellites, in polyploid species.

genetics↗
bioRxiv2026

Optimizing DNA extraction from environmentally degraded bone samples for molecular identification of cetacean species

Molecular identification of cetacean bone remains can be limited by DNA degradation and the presence of PCR inhibitors. Here, we present an optimized DNA extraction protocol based on a total demineralization method for environmentally exposed cetacean bones. The protocol uses 100 mg of bone powder, 24 h digestion with EDTA, N-lauroylsarcosine, and proteinase K, followed by a modified silica-column purification. Nine environmentally degraded bone samples representing eight individuals were processed. DNA concentrations ranged from 7.3 to 57.1 ng/uL (mean SD = 25.91- 13.91 ng/uL). The mitochondrial cytochrome b gene was successfully amplified from all samples using conventional PCR, and five samples (55.6%) yielded sequences suitable for downstream analysis. BLASTn identified Balaenoptera physalus as the closest database match for all recovered sequences, and phylogenetic analysis further supported their association with B. physalus reference sequences. These results demonstrate that the proposed protocol provides a practical approach for recovering amplifiable and molecularly informative mitochondrial DNA from environmentally degraded cetacean bone material, facilitating molecular identification from challenging skeletal remains.

genetics↗