Transposable Elements in Anopheles Species: Refining Annotation Strategies Towards Population Genomics Analyses

Vargas-Chávez, Carlos; González, Josefa

doi:10.1007/13836_2020_86

Cited by 2 publications

(4 citation statements)

References 102 publications

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“…We also assessed the phylogenetic distribution of the 64 new TE families in 15 species of the Anopheles genus, including the eight members of the An. gambiae complex, two more distantly related mosquitoes species (Culex quinquefasciatus, Aedes aegypti) and Drosophila melanogaster (Additional file 1: Table S3) (36,59,60). We found that the new families were unevenly distributed among the members of the Anopheles genus (Figure 2C and Additional file 3: Figure S2C).…”

Section: New Anopheline Te Families Discovered In An Coluzziimentioning

confidence: 87%

“…This suggests that there are possibly other characteristics of each genome that affect the identification of high-quality TE families, such as biases in the location of the TE insertions given that TE families are challenging to identify in regions with low complexity or with numerous nested TEs. Nonetheless, the identification of TE families is dependent on the methodology used to perform TE annotations, therefore different annotation strategies could lead to the discovery of still undescribed families (60).…”

Section: Discussionmentioning

confidence: 99%

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Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vectorAnopheles coluzzii

Vargas-Chávez

Pendy

Nsango

et al. 2020

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BackgroundAnopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has colonized the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments is partly due to an increased tolerance to organic pollution and insecticides. While some of the molecular mechanisms for ecological adaptation, including chromosome rearrangements and introgressions, are known, the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet.ResultsTo better understand 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 the complete set of TEs and identified 64 previously undescribed families. TEs were non-randomly 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. Moreover, we identified several TE insertions providing promoter and transcription factor binding sites to insecticide resistance and immune-related genes.ConclusionsThe analysis of multiple genomes sequenced using long-read technologies allowed us to generate the most comprehensive TE annotations in this species to date. We found that TEs have an impact in both the genome architecture and the regulation of functionally relevant genes in An. coluzzii. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.

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Section: New Anopheline Te Families Discovered In An Coluzziimentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vectorAnopheles coluzzii

Vargas-Chávez

Pendy

Nsango

et al. 2020

Preprint

Self Cite

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show abstract

“…This suggests that there are possibly other characteristics of each genome that affected the identification of high-quality TE families, such as biases in the location of the TE insertions, given that TE families are challenging to identify in regions with low complexity or with numerous nested TEs. Nonetheless, the identification of TE families is dependent on the methodology used to perform TE annotations; therefore, other annotation strategies could lead to the discovery of still undescribed families ( Vargas-Chávez and González 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…Although TE insertions have been annotated genome-wide in several anopheline species including An. coluzzii , most studies to date have characterized the TE repertoire in a single genome for each species (for review, see Vargas-Chávez and González 2020 ). To capture the full extent of TE natural variation and the potential consequences of TE insertions, it is necessary to evaluate multiple genomes to comprehensively assess diversity within a species ( Yang et al 2019 ; Bayer et al 2020 ; Weissensteiner et al 2020 ).…”

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confidence: 99%

Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii

et al. 2021

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Anophelescoluzzii 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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Transposable Elements in Anopheles Species: Refining Annotation Strategies Towards Population Genomics Analyses

Cited by 2 publications

References 102 publications

Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vectorAnopheles coluzzii

Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vectorAnopheles coluzzii

Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii

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