The Aedes aegypti genome: a comparative perspective
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector
Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M, Ren Q, Zdobnov EM, Lobo NF, Campbell KS, Brown SE, Bonaldo MF, Zhu J, Sinkins SP, Hogenkamp DG, Amedo P, Arsenburger P, Atkinson PW, Bidwell S, Biedler J, Birney E, Bruggner RV, Costas J, Coy MR, Crabtree J, Crawford M, Debruyn B, Decaprio D, Eiglmeier K, Eisenstadt E, El-Dorry H, Gelbart WM, Gomes SL, Hammond M, Hannick LI, Hogan JR, Holmes MH, Jaffe D, Johnston SJ, Kennedy RC, Koo H, Kravitz S, Kriventseva EV, Kulp D, Labutti K, Lee E, Li S, Lovin DD, Mao C, Mauceli E, Menck CF, Miller JR, Montgomery P, Mori A, Nascimento AL, Naveira HF, Nusbaum C, O'leary SB, Orvis J, Pertea M, Quesneville H, Reidenbach KR, Rogers YH, Roth CW, Schneider JR, Schatz M, Shumway M, Stanke M, Stinson EO, Tubio JM, Vanzee JP, Verjovski-Almeida S, Werner D, White O, Wyder S, Zeng Q, Zhao Q, Zhao Y, Hill CA, Raikhel AS, Soares MB, Knudson DL, Lee NH, Galagan J, Salzberg SL, Paulsen IT, Dimopoulos G, Collins FH, Bruce B, Fraser-Liggett CM, Severson DW.
Science. 2007 Jun 22;316(5832):1718-23. Epub 2007 May 17.
- As expected, Aedes and Anopheles mosquitoes exhibit much higher conservation of ortholog identity and gene synteny than mosquito and fly or mosquito and hymenoptera comparisons:
11_orthologs <protein_identity> orth_in_synteny Aaeg_Agam 6790 71.93% 77.54% Aaeg_Flyb 6144 55.43% 31.41% Agam_Flyb 6583 57.59% 34.95% Aaeg_Amel 5648 52.70% 15.79% Agam_Amel 6083 54.21% 18.58% Amel_Flyb 6324 50.70% 13.43%
- The estimation of number of synteny breaks in Aedes and Anophles lineages (as supported by the retained synteny to fly and honey bee) suggests about 2 times higher rate of genome shuffling in Aedes lineage. This observation might be explained by a higher transposon activity in Aedes known to facilitate inversions.
- Comparison of gene family size dynamics showed most prominent expansions of Cytochrome P450, A10/OS-D pheromone-binding, insect cuticle, allergen related, HMG-I and HMG-Y gene families in Aedes as compared to only Cadherin in Anopheles. This analysis has also revealed some genes of Rhabdovirus origin. The expansions of various Zinc finger domains gene families is also may be of transposon/viral origin.
Data (A.aeg, A.gam, D.mel, A.mel):
- All_vs_all Smith-Waterman homology comparison (!!! 331Mb zipped)
- Orthologous groups (distribution of orthologs)
- Gene-based synteny on pair-wise 1:1 orthologs
- Gene-based synteny of A.aeg-A.gam-D.mel 1:1:1 orthologs (requiring at least two orthologues to be next to each other in all tree genomes with no more than one intervening gene)
- InterPro protein domains/families (raw data: A.aeg, A.gam, D.mel!!! X Mb):