Improved reference genome of Aedes aegypti informs arbovirus vector control

Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E.; Glassford, William J.; Herre, Margaret; Redmond, Seth; Rose, Noah H.; Weedall, Gareth D.; Wu, Yang; Batra, Sanjit Singh; Brito-Sierra, Carlos A; Buckingham, Steven D.; Campbell, Corey L.; Chan, Saki; Cox, Eric; Evans, Benjamin R.; Fansiri, Thanyalak; Filipović, Igor; Fontaine, Albin; Gloria‐Soria, Andrea; Hall, Richard J.; Joardar, Vinita; Jones, Andrew K.; Kay, Raissa G. G.; Kodali, Vamsi K.; Lee, Joyce; Lycett, Gareth; Mitchell, Sara N.; Muehling, Jill; Murphy, Michael R.; Omer, Arina D.; Partridge, Frederick A.; Peluso, Paul; Aiden, Aviva Presser; Ramasamy, Vidya; Rašić, Gordana; Roy, Sourav; Saavedra-Rodríguez, Karla; Sharan, Shruti; Sharma, Atashi; Smith, Melissa; Turner, Joe; Weakley, Allison M.; Zhao, Zhilei; Akbari, Omar S.; Black, William C.; Cao, Han; Darby, Alistair C.; Hill, Catherine A.; Johnston, J. Spencer; Murphy, Terence; Raikhel, Alexander S.; Sattelle, David B.; Sharakhov, Igor V.; White, Bradley J.; Zhao, Li; Aiden, E; Mann, Richard S.; Lambrechts, Louis; Powell, Jeffrey R.; Sharakhova, Maria V.; Tu, Zhijian; Robertson, Hugh M.; McBride, Carolyn S.; Hastie, Alex; Korlach, Jonas; Neafsey, Daniel E.; Phillippy, Adam M.; Vosshall, Leslie B.

doi:10.1038/s41586-018-0692-z

Cited by 495 publications

(672 citation statements)

References 85 publications

(138 reference statements)

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“…Although initially unexpected, white has been previously been descrbied as a sex-linked gene in Ae. aegypti (47), and recent genome sequencing has confirmed this linkage (54,55) as white is located in close proximaty to Nix (AAEL022912), a dominant male-determining factor (M-factor) on chromosome I (56,57). Therefore, depending on which chromosome the GDe initially integrated, the GDe and Nix were either linked, producing nearly all male progeny, which inherited both w GDe and Nix to exhibit male-biased inheritance, or the GDe was inherited separately from Nix (w GDe /w+) to exhibit female-biased inheritance ( Fig.…”

Section: Sex-biased Inheritance Of Gdementioning

confidence: 89%

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Development of a Confinable Gene-Drive System in the Human Disease Vector,Aedes aegypti

Li¹,

Yang²,

Kandul³

et al. 2019

Preprint

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Aedes aegypti, the principal mosquito vector for many arboviruses that causes yellow fever, dengue, Zika, and chikungunya, increasingly infects millions of people every year. With an escalating burden of infections and the relative failure of traditional control methods, the development of innovative control measures has become of paramount importance. The use of gene drives has recently sparked significant enthusiasm for the genetic control of mosquito populations, however no such system has been developed in Ae. aegypti. To fill this void and demonstrate efficacy in Ae. aegypti, here we develop several CRISPR-based split-gene drives for use in this vector. With cleavage rates up to 100% and transmission rates as high as 94%, 2 mathematical models predict that these systems could spread anti-pathogen effector genes into wild Ae. aegypti populations in a safe, confinable and reversible manner appropriate for field trials and effective for controlling disease. These findings could expedite the development of effectorlinked gene drives that could safely control wild populations of Ae. aegypti to combat local pathogen transmission. Significance StatementAe. aegypti is a globally distributed arbovirus vector spreading deadly pathogens to millions of people annually. Current control methods are inadequate and therefore new technologies need to be innovated and implemented. With the aim of providing new tools for controlling this pest, here we engineered and tested several split gene drives in this species. These drives functioned at very high efficiency and may provide a tool to fill the void in controlling this vector. Taken together, our results provide compelling path forward for the feasibility of future effector-linked split-drive technologies that can contribute to the safe, sustained control and potentially the elimination of pathogens transmitted by this species.

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Section: Sex-biased Inheritance Of Gdementioning

confidence: 89%

“…Of note, the Ae. aegypti reference genome sequences were generated using this strain (54,73). Mosquitoes were raised in incubators at 28.0°C with 70-80% humidity and a 12hour light/dark cycle.…”

Section: Insect Rearingmentioning

confidence: 99%

Development of a Confinable Gene-Drive System in the Human Disease Vector,Aedes aegypti

Li¹,

Yang²,

Kandul³

et al. 2019

Preprint

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“…Chromosome‐level assembly can be obtained by using HiC scaffolding and BioNano. These two techniques were used together or solely on insect genomes recently, such as T. castaneum (red flour beetle; Shelton et al ., ), A. mellifera (western honey bee), Galleria mellonella (greater wax moth), A. aegypti (yellow fever mosquito; Matthews et al ., ; Whitfield et al ., ), Trichoplusia ni (cabbage looper; Fu et al ., ) and Cydia pomonella (codling moth). We can expect the coming of an era of high‐quality insect genomes. In‐depth analysis of insect genome data is a bottleneck at present.…”

Section: Perspectivesmentioning

confidence: 99%

“…Long-read assembly was also used to resolve large repetitive regions for a cell line (Whitfield et al, 2017), which were unable to be determined by previous methods. Recently, a better assembly of mosquito genomes was implemented by combining both the PacBio and Hi-C techniques (Matthews et al, 2018).…”

Section: Disease Vector Insectsmentioning

confidence: 99%

Insect genomes: progress and challenges

Zhao

et al. 2019

Insect Molecular Biology

138

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In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome‐sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein‐coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well‐studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data‐mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.

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“…Previously, a comprehensive developmental transcriptome study of Ae. aegypti analyzed and provided insight into the complexity of the basic biology of these mosquitoes (Akbari et al 2013a;Matthews et al 2018). This enormous dataset has provided the community with a foundation of data enabling the functional characterization of novel germline promoters (Akbari et al 2014b) which have subsequently been used to develop highly potent Cas9 endonuclease expressing strains Akbari et al 2014b) in addition to gene drives (Li et al 2019).…”

Section: Introductionmentioning

confidence: 99%

The Developmental Transcriptome ofAe. albopictus,a Major Worldwide Human Disease Vector

Gamez¹,

Antoshechkin

Méndez‐Sánchez

et al. 2019

Preprint

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Aedes albopictus mosquitoes are important vectors for a number of human pathogens including the Zika, dengue, and chikungunya viruses. Capable of displacing Aedes aegypti populations, it adapts to cooler environments which increases its geographical range and transmission potential. There are limited control strategies for Aedes albopictus mosquitoes which is likely attributed to the lack of comprehensive biological studies on this emerging vector. To fill this void, here using RNAseq we characterized Aedes albopictus mRNA expression profiles at 47 distinct time points throughout development providing the first high-resolution comprehensive view of the developmental transcriptome of this worldwide human disease vector. This enabled us to identify several patterns of shared gene expression among tissues as well as sex-specific expression patterns. Moreover, to illuminate the similarities and differences between Aedes aegypti, a related human disease vector, we performed a comparative analysis using the two developmental transcriptomes. We identify life stages were the two species exhibited significant differential expression among orthologs. These findings provide insights into the similarities and differences between Aedes albopictus and Aedes aegypti mosquito biology. In summary, the results generated from this study should form the basis for future investigations on the biology of Aedes albopictus mosquitoes and provide a goldmine resource for the development of transgene-based vector control strategies.

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Improved reference genome of Aedes aegypti informs arbovirus vector control

Cited by 495 publications

References 85 publications

Development of a Confinable Gene-Drive System in the Human Disease Vector,Aedes aegypti

Development of a Confinable Gene-Drive System in the Human Disease Vector,Aedes aegypti

Insect genomes: progress and challenges

The Developmental Transcriptome ofAe. albopictus,a Major Worldwide Human Disease Vector

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