VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms

Giraldo-Calderón, Gloria I.; Harb, Omar S.; Kelly, Sarah; Rund, Samuel S. C.; Roos, David S.; McDowell, Mary Ann

doi:10.1016/j.cois.2021.11.008

Cited by 41 publications

(25 citation statements)

References 53 publications

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“…gambiae male reproductive organs (consisted of testes and MAGs) and female reproductive organs (consisted of ovaries and common oviduct) [ 40 ]. The normalized expression values for these experiments were taken from the VectorBase [ 41 ] ( Table S4 , Figure 3 ). Both microarray and RNA-seq data showed a similar pattern in sex-biased expression ( Figure 3 and Table S4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Interestingly, a positive selection was found for AGAP011684 (dN/dS = 1.283). According to the VectorBase [ 41 ] annotation, it was an aryl hydrocarbon receptor-interacting protein, a binding partner of transcription factor IRF7, which plays antiviral roles [ 54 ]. Consistent with a previous study [ 51 ], we found signals of positive selection based on branch-site model analyses in AGAP010423 (STAT-B), which is involved in resistance to bacteria and Plasmodium parasites.…”

Section: Resultsmentioning

confidence: 99%

“…gambiae , sex-tissues including male reproductive organs (consisted of testis and accessory glands) and female reproductive organs (consisted of ovaries and common oviduct) were analyzed and the expression levels were normalized with mean transcript abundance in transcripts per million (TPM + 10 −3 ). Both microarray and RNA-seq raw data were downloaded from VectorBase ( ; February 2022; [ 41 ]). The raw data of germline stages of spermatogenesis RNA-seq expression was retrieved from [ 28 ] and normalized here with ln(FPKM + 1), which is the average of the natural logarithmic treatment of FPKM expression values.…”

Section: Methodsmentioning

confidence: 99%

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Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes

Miller

Chen

Liang

et al. 2022

Genes

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Genes that originate during evolution are an important source of novel biological functions. Retrogenes are functional copies of genes produced by retroduplication and as such are located in different genomic positions. To investigate retroposition patterns and retrogene expression, we computationally identified interchromosomal retroduplication events in nine portions of the phylogenetic history of malaria mosquitoes, making use of species that do or do not have classical sex chromosomes to test the roles of sex-linkage. We found 40 interchromosomal events and a significant excess of retroduplications from the X chromosome to autosomes among a set of young retrogenes. These young retroposition events occurred within the last 100 million years in lineages where all species possessed differentiated sex chromosomes. An analysis of available microarray and RNA-seq expression data for Anopheles gambiae showed that many of the young retrogenes evolved male-biased expression in the reproductive organs. Young autosomal retrogenes with increased meiotic or postmeiotic expression in the testes tend to be male biased. In contrast, older retrogenes, i.e., in lineages with undifferentiated sex chromosomes, do not show this particular chromosomal bias and are enriched for female-biased expression in reproductive organs. Our reverse-transcription PCR data indicates that most of the youngest retrogenes, which originated within the last 47.6 million years in the subgenus Cellia, evolved non-uniform expression patterns across body parts in the males and females of An. coluzzii. Finally, gene annotation revealed that mitochondrial function is a prominent feature of the young autosomal retrogenes. We conclude that mRNA-mediated gene duplication has produced a set of genes that contribute to mosquito reproductive functions and that different biases are revealed after the sex chromosomes evolve. Overall, these results suggest potential roles for the evolution of meiotic sex chromosome inactivation in males and of sexually antagonistic conflict related to mitochondrial energy function as the main selective pressures for X-to-autosome gene reduplication and testis-biased expression in these mosquito lineages.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes

Miller

Chen

Liang

et al. 2022

Genes

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“…aegypti transcriptome or the An. gambiae transcriptome Aedes aegypti LVP_AGWG Aaeg L5.2 and Anopheles gambiae PEST Agam P4.12, VectorBase, https://www.vectorbase.org/ ( Giraldo-Calderón et al, 2022 ) using Salmon version 0.9.1 with default parameters. Salmon’s transcript-level quantifications were then aggregated to the gene level for gene-level differential expression analysis with the “tximport” package on the R version 3.5.…”

Section: Methodsmentioning

confidence: 99%

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females

Hixson

Bing

Yang

et al. 2022

eLife

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Mosquito vectors transmit numerous pathogens, but large gaps remain in our understanding of their physiology. To facilitate future explorations of mosquito biology, with specific attention to the major vector Aedes aegypti, we have created Aegypti-Atlas (http://aegyptiatlas.buchonlab.com/), an online resource hosting RNAseq profiles of Ae. aegypti body parts (head, thorax, abdomen, gut, Malpighian tubules, and ovaries), gut regions (crop, proventriculus, anterior and posterior midgut, and hindgut), and a time course of blood meal digestion in the gut. Using Aegypti-Atlas, we provide new insights into the regionalization of gut function, blood feeding response, and immune defenses. We find that the anterior and posterior regions of the mosquito midgut possess clearly delineated digestive specializations which are preserved in the blood-fed state. Blood feeding initiates the sequential transcriptional induction and repression/depletion of multiple cohorts of peptidases throughout blood meal digestion. With respect to defense, immune signaling components, but not recognition or effector molecules, show enrichment in ovaries. Basal expression of antimicrobial peptides is dominated by two genes, holotricin and gambicin, that are expressed in the carcass and the digestive tissues, respectively, in a near mutually exclusive manner. In the midgut, gambicin and other immune effector genes are almost exclusively expressed in the anterior regions, while the posterior midgut exhibits the hallmarks of immune tolerance. Finally, in a cross-species comparison between the midguts of Ae. aegypti and Anopheles gambiae (s.l.), we observe that regional digestive and immune specializations are closely conserved, indicating that our data may yield inferences that are broadly relevant to multiple mosquito vector species. We further demonstrate that the expression of orthologous genes is highly correlated, with the exception of a ‘species signature’ comprising a small number of highly/disparately expressed genes. With this work, we show the potential of Aegypti-Atlas to unlock a more complete understanding of mosquito biology.

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“…Mota et al [ 21 ] also did not identify a 53BP1 ortholog in Ae. aegypti , however this may be due to an overly stringent similarity cutoff, as there is one protein [ 41 ] which appears to contain both the p53-binding protein-1 Tudor domain (Interpro ID: IPR015125) and BRCT domain superfamily (Interpro ID: IPR036420), making this gene a strong candidate for consideration as the Ae. aegypti 53BP1 ortholog.…”

Section: Modified Nuclease Systems To Bias For Hdr Only At Targeted Dsbsmentioning

confidence: 99%

Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local

Finney

Romanowski

Adelman

2022

Virol J

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Programmable gene editing systems such as CRISPR-Cas have made mosquito genome engineering more practical and accessible, catalyzing the development of cutting-edge genetic methods of disease vector control. This progress, however, has been limited by the low efficiency of homology-directed repair (HDR)-based sequence integration at DNA double-strand breaks (DSBs) and a lack of understanding about DSB repair in mosquitoes. Innovative efforts to optimize HDR sequence integration by inhibiting non-homologous end joining or promoting HDR have been performed in mammalian systems, however many of these approaches have not been applied to mosquitoes. Here, we review some of the most relevant steps of DNA DSB repair choice and highlight promising approaches that influence this choice to enhance HDR in the context of mosquito gene editing.

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VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms

Cited by 41 publications

References 53 publications

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes

Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes

A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females

Strategies to improve homology-based repair outcomes following CRISPR-based gene editing in mosquitoes: lessons in how to keep any repair disruptions local

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