TitleHidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly.
Publication TypeJournal Article
Year of Publication2021
AuthorsChakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LThanh, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ
JournalBMC Biol
Date Published2021 Feb 10
KeywordsAnimals, Anopheles, Female, Gene Expression, Gene Expression Profiling, Genome, Insecticide Resistance, Malaria, Male, Mosquito Vectors

BACKGROUND: The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution.

RESULTS: To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role.

CONCLUSION: Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.

Alternate JournalBMC Biol
PubMed ID33568145
PubMed Central IDPMC7876825
Grant ListK99 GM129411 / GM / NIGMS NIH HHS / United States
R01 GM117321 / GM / NIGMS NIH HHS / United States
R01 GM123303 / GM / NIGMS NIH HHS / United States