Anopheles coluzzii, a new system to study how transposable elements may foster adaptation to urban environments
Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
Transposable elements (TEs) are mobile DNA sequences that can increase their copy number and move from one location to another within the genome . Because of their transposition dynamics, TEs constitute a significant fraction of eukaryotic genomes. TEs are also known to play an important functional role and a wealth of studies has now reported how TEs may influence single host traits [e.g. 2–4]. Given that TEs are more likely than classical point mutations to cause extreme changes in gene expression and phenotypes, they might therefore be especially prone to produce the raw diversity necessary for individuals to respond to challenging environments [5,6] such as the ones found in urban area.
In their study , Vargas et al. establish the foundation to investigate how TEs may help Anopheles coluzzii - the primary vectors of human malaria in sub-Saharan Africa - adapt to urban environments. To cover natural breeding sites in major Central Africa cities, they made use of the previously available An. coluzzii genome from Yaoundé (Cameroon) and sequenced with long-read technology six additional ones originating from Douala (Cameroon) and Libreville (Gabon). The de novo annotation of TEs in these genomes revealed 64 new anopheline TE families and allowed to identify seven active families. As a first step towards characterizing the potential role of TEs in the adaptation of An. coluzzii to urban environments, they further analyzed the distribution of TEs across the seven genomes. By doing so, they identified a significant number of polymorphic or fixed TE insertions located in the vicinity of genes involved in insecticide resistance and immune response genes.
The availability of seven An. coluzzii genomes allowed the authors to explore how TE diversity may affect genes functionally relevant for the adaptation to urban environments and provide ground for further functional validation studies. More and more studies have demonstrated the impact of TEs on adaptation and as such, the work of Vargas et al. contributes to fostering our understanding of the link between TEs and gain of function in a species facing strong anthropogenic pressures.
 Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, Paux E, SanMiguel P, Schulman AH (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8, 973–982. https://doi.org/10.1038/nrg2165
 van’t Hof AE, Campagne P, Rigden DJ, Yung CJ, Lingley J, Quail MA, Hall N, Darby AC, Saccheri IJ (2016) The industrial melanism mutation in British peppered moths is a transposable element. Nature, 534, 102–105. https://doi.org/10.1038/nature17951
 González J, Karasov TL, Messer PW, Petrov DA (2010) Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLOS Genetics, 6, e1000905. https://doi.org/10.1371/journal.pgen.1000905
 Lisch D (2013) How important are transposons for plant evolution? Nature Reviews Genetics, 14, 49–61. https://doi.org/10.1038/nrg3374
 Bonchev G, Parisod C (2013) Transposable elements and microevolutionary changes in natural populations. Molecular Ecology Resources, 13, 765–775. https://doi.org/10.1111/1755-0998.12133
 Casacuberta E, González J (2013) The impact of transposable elements in environmental adaptation. Molecular Ecology, 22, 1503–1517. https://doi.org/10.1111/mec.12170
 Vargas-Chavez C, Pendy NML, Nsango SE, Aguilera L, Ayala D, González J (2021). Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. bioRxiv, 2020.11.22.393231, ver. 3 peer-reviewed and recommended by Peer community in Genomics. https://doi.org/10.1101/2020.11.22.393231
Anne Roulin (2021) Anopheles coluzzii, a new system to study how transposable elements may foster adaptation to urban environments. Peer Community in Genomics, 100006. pci.genomics.100006
Evaluation round #1
DOI or URL of the preprint: 10.1101/2020.11.22.393231
Author's Reply, 17 Jun 2022
Decision by Anne Roulin, 27 Jan 2021
Dear Dr. Gonzalez,
Thank you for submitting your work entitled "Impact of transposable elements on the genome of the urban malaria vector Anopheles coluzzii" for consideration by PCI Genomics. Your article has been reviewed by 2 peer reviewers.
Based on these 2 reviews, I regret to inform you that your work can not be accepted for recommendation in PCI genomics as such. I would like nonetheless to invite you to revise your manuscript based on the reviewers comments.
While both reviewers acknowledge that the data produced are extremely valuable and open new avenues of research to study the adaptation of An. coluzzii, they also fear that the study does not demonstrate the role of TEs in this process per se and therefore remains descriptive. I understand that a functional validation is beyond the scope of the study but Reviewer1 suggested some analyses to include in order to sustain the claims you made. They have also made additional comments which I hope will help you to improve the manuscript.
Looking forward to reading a revised version of your manuscript