Biology subjects

Gomez-Diaz, E.

Publications and source records attributed to Gomez-Diaz, E..

5 recordsLinked to original sources

bioRxiv2025

The dynamic transcriptome of Plasmodium malariae in the mosquito

To survive and multiply in different host niches, malaria parasites require sets of proteins that are expressed during the life cycle in a timely manner. Plasmodium malariae is a human malaria parasite that is present in most malaria-endemic regions. However, this species remains enigmatic because it is very challenging to culture, its low parasitaemia in human infections, and frequent co-infection with other malarias. We investigate the transcriptome of P. malariae during transmission in the vector by analyzing RNA-seq data from midgut and salivary gland parasite stages obtained in two experimental mosquito infections with field P. malariae isolates. Our analysis resulted in 3,699 expressed genes, of which 263 are developmentally regulated and 1,338 are P. malariae specific, including genes with unknown functions and without orthologs in other Plasmodium. We detected unique expression patterns of the ApiAP2 family of transcription factors, many of which appear to function as master regulators during sporogony. We found expressed several members of multigene families, like PIR, PHIST, fam-l, and described new families potentially showing transcriptional heterogeneity. Our findings point to the uniqueness of the P. malariae transcriptome, probably related to different transmission traits in the vector, and the lower pathogenicity and virulence in the human.

microbiology↗

bioRxiv2023

Alternative splicing and its regulation in the malaria vector Anopheles gambiae

Alternative splicing (AS) is a highly conserved mechanism that allows to expand the coding capacity of the genome, by modifying how multiple isoforms are expressed or used to generate different phenotypes. Despite its importance in physiology and disease, genome-wide studies of AS are lacking in most insects, including mosquitoes. Even for model organisms, chromatin associated processes involved in the regulation AS are poorly known. In this study, we investigated AS in the mosquito Anopheles gambiae in the context of tissue-specific gene expression and mosquito responses to a Plasmodium falciparum infection, as well as the relationship between patterns of differential isoform expression and usage with chromatin accessibility changes. For this, we combined RNA-seq and ATAC-seq data from A. gambiae midguts and salivary glands, and from infected and non-infected midguts. We report differences between tissues in the expression of 456 isoforms and in the use of 211 isoforms. Secondly, we find a clear and significant association between chromatin accessibility states and tissue-specific patterns of AS. The analysis of differential accessible regions located at splicing sites permitted the identification of several motifs resembling the binding sites of Drosophila transcription factors. Finally, the genome-wide analysis of tissue-dependent enhancer activity revealed that approximately 20% of A. gambiae transcriptional enhancers annotate to a differentially expressed or used isoform and that their activation status is linked to AS differences between tissues. This research illuminates the role of AS in gene expression in vector mosquitoes, and identifies regulatory regions potentially involved in AS regulation, which could reveal novel strategies for vector control.

genomics↗

bioRxiv2021

From contigs to chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Although there is a promise of long read technologies to obtain "perfect genomes", the number of contigs often exceeds the number of chromosomes by far, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented the ILRA pipeline to correct long read-based assemblies, so contigs are reordered, renamed, merged, circularized, or filtered if erroneous or contaminated, and Illumina reads are used to correct homopolymer errors. We successfully tested our approach by improving the genomes of Trypanosoma brucei and Leptosphaeria spp, and generated four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seems to be required to correct larger numbers of sequencing errors. In summary, we described and compared the performance of our new tool, which improved the quality of novel long read assemblies of genomes up to 1Gbp. AvailabilityThe tool is available at GitHub: https://github.com/ThomasDOtto/ILRA.

bioinformatics↗

bioRxiv2020

The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression

Anopheles gambiae mosquitoes are primary human malaria vectors, but we know very little about mechanisms of transcriptional regulation. We profiled chromatin accessibility by ATAC-seq in laboratory-reared An. gambiae mosquitoes experimentally infected with the human malaria parasite Plasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that annotate to mosquito immune-response genes. This study is important not only for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information is of great potential for developing new mosquito-control and anti-malaria strategies.

genomics↗

bioRxiv2018

Chromatin changes induced by a Plasmodium falciparum infection in Anopheles gambiae

Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso. We report 15,916 regions containing differential histone modification enrichment, of which 8,339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection responsive genes showing differential enrichment in various histone modifications, such as CLIP pro-teases, anti-microbial peptides encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways. The analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to a P. falciparum infection but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.

molecular biology↗