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Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
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Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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Sreenivasamurthy SK, Madugundu AK, Patil AH, Dey G, Mohanty AK, Kumar M, Patel K, Wang C, Kumar A, Pandey A, Prasad TSK. Mosquito-Borne Diseases and Omics: Tissue-Restricted Expression and Alternative Splicing Revealed by Transcriptome Profiling of Anopheles stephensi. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:488-497. [PMID: 28708456 DOI: 10.1089/omi.2017.0073] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Malaria is one of the most debilitating mosquito-borne diseases with high global health burdens. While much of the research on malaria and mosquito-borne diseases is focused on Africa, Southeast Asia accounts for a sizable portion of the global burden of malaria. Moreover, about 50% of the Asian malaria incidence and deaths have been from India. A promising development in this context is that the completion of genome sequence of Anopheles stephensi, a major malaria vector in Asia, offers new opportunities for global health innovation, including the progress in deciphering the vectorial ability of this mosquito species at a molecular level. Moving forward, tissue-based expression profiling would be the next obvious step in understanding gene functions of An. stephensi. We report in this article, to the best of our knowledge, the first in-depth study on tissue-based transcriptomic profile of four important organs (midgut, Malpighian tubules, fat body, and ovary) of adult female An. stephensi mosquitoes. In all, we identified over 20,000 transcripts corresponding to more than 12,000 gene loci from these four tissues. We present and discuss the tissue-based expression profiles of majority of annotated transcripts in An. stephensi genome, and the dynamics of their alternative splicing in these tissues, in this study. The domain-based Gene Ontology analysis of the differentially expressed transcripts in each of the mosquito tissue indicated enrichment of transcripts with proteolytic activity in midgut; transporter activity in Malpighian tubules; cell cycle, DNA replication, and repair activities in ovaries; and oxidoreductase activities in fat body. Tissue-based study of transcript expression and gene functions markedly enhances our understanding of this important malaria vector, and in turn, offers rationales for further studies on vectorial ability and identification of novel molecular targets to intercept malaria transmission.
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Affiliation(s)
| | - Anil K Madugundu
- 1 Institute of Bioinformatics , Bangalore, India .,3 Centre for Bioinformatics, Pondicherry University , Kalapet, India
| | - Arun H Patil
- 1 Institute of Bioinformatics , Bangalore, India .,4 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,5 School of Biotechnology, KIIT University , Bhubaneswar, India
| | - Gourav Dey
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Ajeet Kumar Mohanty
- 6 National Institute of Malaria Research , Field Station, Panjim, India .,7 Department of Zoology, Goa University , Taleigao Plateau, India
| | - Manish Kumar
- 1 Institute of Bioinformatics , Bangalore, India .,2 Manipal University , Manipal, India
| | - Krishna Patel
- 1 Institute of Bioinformatics , Bangalore, India .,8 Amrita School of Biotechnology , Amrita Vishwa Vidyapeetham, Kollam, India
| | - Charles Wang
- 9 Center for Genomics and Department of Basic Sciences, School of Medicine, Loma Linda University , Loma Linda, California
| | - Ashwani Kumar
- 6 National Institute of Malaria Research , Field Station, Panjim, India
| | - Akhilesh Pandey
- 1 Institute of Bioinformatics , Bangalore, India .,10 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,11 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Oncology, Johns Hopkins University School of Medicine , Baltimore, Maryland.,13 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland
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