Assignment 1

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Image 1. Anopheles mosquito image.

1) What was the research project?

This project was looking at the genus Anopheles, which is the only genus of mosquitos that can transmit malaria, and trying to map the genomic material of each species within the genus to find which variations within the genome allow for conditions suited for malaria transmission and which variations do not so that future experiments can dive further into this to try to combat malaria and other diseases.

2) Were they testing a hypothesis or doing discovery science?

The project was discovery science. They had sequenced the genomes for 16 different species of mosquito taken from areas of the world where malaria is prevalent. In addition to sequencing the genomes they also used RNA sequencing transcriptomes in order to find out which genes were actually being expressed. This project was simply trying to provide 16 reference genomes for future experiments to gain further insight on a very surface level understanding into what allows for a mosquito species to be more fit to transmit malaria over others.

Figure 1. (A) Map of where the various species of Anopheles are found. (B/C) Dendrogram of the species of Anopheles and Drospohila. (D) Genome mapped showing where Anopheles gambiae is similar to no other species (red) and where there are no similarities to other Anopheles (yellow).

3) What genomic technology was used in the project?

The project began with sequencing “genomic DNA and whole-body RNA” (Neafsey, et al, 2015) that were obtained from both “laboratory colonies and wild-caught specimens” (Neafsey, et al, 2015) using Illumina sequencing. They then used genome annotation and RNA sequencing of transcriptomes to get a complete picture of protein-encoding genes for each species of mosquito. The Anopheles genus has a closest relative with the genus Drosphila so they first looked at the chromosomes and where on the chromosomes is there frequent recombination within each species and then used this information to determine which sequences were ancestral and which were species specific. They found that the X chromosome had the highest rates of rearrangement. After obtaining this information they looked at which genes and chromosomes encode which traits that are seen to be important for a mosquito’s ability to transmit malaria through the use of both genomic analysis and RNA sequencing of transcriptomes.

Figure 2. (A) Chromosomal mapping of genes within species to show rearrangement throughout evolution. (C) Levels of rearrangement for each species at given elements. (D) Diagram of gene movement in a chromosome. Band size is proportional to the number of genes imported/exported from that area.

4) What was the take home message?

The take home message of this project is to recognize that there are distinct genomic differences between the species that are capable of transmitting malaria and those that are not within in the Anopheles genus. Being able to map the evolution of various Anopheles species will not only help with identifying which species can carry malaria and in what regions but could allow for genetic manipulation of mosquito populations in order to prevent malaria in high-risk areas. Being able to map where on the genome and which species a gene that is necessary for malaria transmission will likely be very important as we continue to combat the issue of malaria throughout the world. The experiment was just trying to provide reference information so that future experiments can look further into how the genome and other factors might affect the vectorial capacity of a mosquito to carry malaria and further experimentation on how we can prevent this on a large scale.

Figure 3. Evolutionary rate was determined based on amino acid divergence of genes encoding each trait. dn/ds is showing selection pressures by using an algorithm relating copy number with number of orthologs for each trait. And number of genes and species that show each trait.

5) What is your evaluation of the project?

The project as a whole I think will be very useful for future genomic analysis of Anopheles and how it might affect future prevention of malaria within high-risk countries.

One issue I had with the paper was with Figure 3. There were assumptions made on which traits contribute to vectorial capacity of a species but there was not a lot of discussion on how they chose which traits to focus on. Neafsey et al explained in a lot of detail a good number of the traits that are used to determine vectorial capacity and does an excellent job throughout the discussion on explaining the reasoning behind looking at each trait. I do, however, think that it would have been helpful if there was some explanation on why certain traits were not selected as criteria or if maybe some traits did not show any correlation to vectorial capacity that were not included in this paper.

REFERENCES:

Anopheles. Digital image. Scientists Against Malaria. Web.

Daniel E. Neafsey1,*,†, Robert M. Waterhouse2,3,4,5,*, Mohammad R. Abai6, Sergey S. Aganezov7, Max A. Alekseyev7, James E. Allen8, James Amon9, Bruno Arcà10, Peter Arensburger11, Gleb Artemov12, Lauren A. Assour13, Hamidreza Basseri6, Aaron Berlin1, Bruce, Daniel E. Neafsey, Robert M. Waterhouse, Mohammad R. Abai, Sergey S. Aganezov, Max A. Alekseyev, James E. Allen, James Amon, Bruno Arcà, Peter Arensburger, Gleb Artemov, Lauren A. Assour, Hamidreza Basseri, Aaron Berlin, Bruce W. Birren, Stephanie A. Blan, and Science02 Jan 2015. "Highly Evolvable Malaria Vectors: The Genomes of 16 Anopheles Mosquitoes." Highly Evolvable Malaria Vectors: The Genomes of 16 Anopheles Mosquitoes | Science. Web. 06 Feb. 2017.

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