Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome
Affiliation(s)
Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi-110 077, India. Present address: World Health Organization, Southeast Asian Regional Office, New Delhi, India.
Evolutionary Genomics and Bioinformatics Laboratory, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi-110 077, India. Present address: World Health Organization, Southeast Asian Regional Office, New Delhi, India.
ABSTRACT
Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome se-quence for detail characterization and obtain evolutionary status of different genes. The te-locentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majori-ties of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns; about half of the total known genes have only one or two in-trons. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gam-biae. We compared each individual gene of An. gambiae with 33 other taxa having whole ge-nome sequence information. In general, the mosquito Aedes aegypti was found to be ge-netically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in dif-ferent taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were in-ferred which corroborate the previous and pre-sent findings on genetic relationships across various taxa.
Understanding the genetic architecture of indi-vidual taxa of medical importance is the first step for designing disease preventive strategies. To understand the genetic details and evolu-tionary perspective of the model malaria vector, Anopheles gambiae and to use the information in other species of local importance, we scanned the published X-chromosome se-quence for detail characterization and obtain evolutionary status of different genes. The te-locentric X-chromosome contains 106 genes of known functions and 982 novel genes. Majori-ties of both the known and novel genes are with introns. The known genes are strictly biased towards less number of introns; about half of the total known genes have only one or two in-trons. The extreme sized (either long or short) genes were found to be most prevalent (58% short and 23% large). Statistically significant positive correlations between gene length and intron length as well as with intron number and intron length were obtained signifying the role of introns in contributing to the overall size of the known genes of X-chromosome in An. gam-biae. We compared each individual gene of An. gambiae with 33 other taxa having whole ge-nome sequence information. In general, the mosquito Aedes aegypti was found to be ge-netically closest and the yeast Saccharomyces cerevisiae as most distant taxa to An. gambiae. Further, only about a quarter of the known genes of X-chromosome were unique to An. gambiae and majorities have orthologs in dif-ferent taxa. A phylogenetic tree was constructed based on a single gene found to be highly orthologous across all the 34 taxa. Evolutionary relationships among 13 different taxa were in-ferred which corroborate the previous and pre-sent findings on genetic relationships across various taxa.
KEYWORDS
Anopheles gambiae; Comparative Genomics; Evolution; Malaria; Orthologous Genes; X-chromosome
Anopheles gambiae; Comparative Genomics; Evolution; Malaria; Orthologous Genes; X-chromosome
Cite this paper
nullSrivastava, H. , Dixit, J. , P. Dash, A. and Das, A. (2009) Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome. Journal of Biomedical Science and Engineering, 2, 304-311. doi: 10.4236/jbise.2009.25045.
nullSrivastava, H. , Dixit, J. , P. Dash, A. and Das, A. (2009) Fine-scale evolutionary genetic insights into Anopheles gambiae X-chromosome. Journal of Biomedical Science and Engineering, 2, 304-311. doi: 10.4236/jbise.2009.25045.
References
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W., and Varki, A., (2005) Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human genetic loss of N-glycolylneuraminic acid, Proceedings of National Academy of Sciences, 102, 12819– 12824.
[1] Hahn, M. W., Han, M. V., and Han, S. G., (2007) Gene family evolution across 12 Drosophila genome, Public Library of Science Genetics, 3, 1–12. [2] Matthee, C. A., Eick, G., Willows, M. S., Montgelard, C., Pardini, A. T., and Robinson, T. J., (2007) Indel evolution of mammalian introns and the utility of non coding nuclear mark-ers in eutherian phylogenetics, Molecular Phylogenetics and Evolution, 42, 827–837. [3] Cardazzo, B., Bargelloni, L., Toffolatti, L., and Patarnello, T., (2003) Intervening sequences in paralogous genes: A compara-tive genomic approach to study the evolution of X chromo-some introns, Molecular Biology and Evolution, 20, 2034–2041. [4] Gazave, E., Bonet, T. M., Fernando, O., Charlesworth, B., and Navarro, A., (2007) Patterns and rates of intron divergence between humans and chimpanzees, Genome Biology, 8, 1–13. [5] Huynen, M. A. and Bork, P., (1998) Measuring genome evolu-tion, Proceedings of National Academy of Sciences USA, 95, 5849–5856. [6] Clark, A. G., Eisen, B. M., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., et al., (2007) Evolution of genes and genomes on the Drosophila phylogeny, Nature, 450, 203–218. [7] WHO. (2005) World malaria report. http://www.rbm.who.int/wmr. [8] Zakeri, S., Afsharpad, M., Raeisi, A., and Djadid, N. D., (2007) Prevalence of mutations associated with antimalarial drugs in Plasmodium falciparum isolates prior to the introduction of sulphadoxine-pyrimethamine as first- line treatment in Iran, Malaria Journal, 6, 1–2. [9] Holt, R. A., Subramanian, G. M., Helpern, A., Sutton, G. G., Charlab, R., Nusskern, D. R., et al., (2002) The genome se-quence of the malaria mosquito Anopheles gambiae, Science, 298, 129–149. [10] Stephen, S. F., (2004) The X chromosome in population ge-netics, Nature Reviews Genetics, 5, 43–51. [11] Vogl, C., Das, A., Beaumont, M., Mohanty, S., and Stephan, W., (2003) Population subdivision and molecular sequence variation: Theory and and analysis of Drosophila ananassae data, Genetics, 165, 1385–1395. [12] Bains, J. F., Das, A., Mousset, S., and Stephan, W., (2004) The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae, Genetics, 168, 1987–1998. [13] Das, A., Mohanty, S., and Stephan, W., (2004) Inferring the population structure and demography of Drosophila ananassae from multilocus data, Genetics, 168, 1975– 1985. [14] Castillo-Davis, C. I., Mekhedov, S. L., Hartl, D. L., Koonin, E. V., and Kondrashov, F. A., (2002) Selection for short introns in highly expressed genes, Nature Genetics, 31, 414–418. [15] Vinogrado, A. E. (2004) Compactness of human housekeeping genes: Selection for economy or genomic design, Trends in Genetics, 20, 248–253. [16] Jain, M., Tyagi, A. K., and Khurana, J. P., (2006) Genome wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa), Genomics, 88, 360–371. [17] Jain, M., Khurana, P., Tyagi, A. K., and Khurana, J., (2007) Genome-wide analysis of intronless genes in rice and Arabi-dopsis, Functional & Integrative Genomics, In Press. [18] Simpson, A. G. B., Macquarrie, E. K., Roger, A. J., (2002) Eukaryotic evolution: Early origin of canonical introns, Nature, 419, 270. [19] Jones, A. K., Grauso, M., and Sattelle, B. D., (2004) The nico-tinic acetylcholine receptor gene family of the malaria mos-quito, Anopheles gambiae, Genomics, 85, 176– 187. [20] Matsuda, K., Buchigham, S. D., Kleier, D., Rauh, J. J., Grauso, M., and Sattelle, D. B., (2001) Neonicotinoids: Insecticides acting on insect nicotinic acetylcholine receptors, Trends in Pharmacological Sciences, 22, 573–580. [21] Bond, G. J., Marina, C. F., and Williams, T., (2004) The natu-rally derived insecticide spinosad is highly toxic to Aedes and Anopheles mosquito larvae, Medical and Veterinary Entomol-ogy, 18, 50–56. [22] Manuel, I., David, P., and Scott, W. R., (2007) Coevolution of genomic intron number and splice sites, Trends in Genetics, 23, 321–325. [23] Jordan, I. K., Marino-Ramirez, L., Wolf, Y. I., and Koonin, E. V., (2004) Conservation and co-evolution in the scale-free human gene co-expression network, Mole- culer Biologyand Evolution, 21, 2058–2070. [24] Carmel L., Rogozin I. B., Wolf, Y. I., and Koonin, E. V., (2007) Evolutionarily conserved genes preferentially accumulate in-trons, Genome Research, 17, 1045–1050. [25] Castillo-Davis, C. I., Bedford, T. B. C., and Hartl, D. L., (2004) Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and mouse malaria parasite, Mo-lecular Biology and Evolution, 21, 1422– 1427. [26] Stirling, B., Yang, Z. K., Gunter, L. E., Tuskan, G. A., and Bradshaw, H. D., (2003) Comparative sequence analysis be-tween orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity, Canadian Journal of Forest Research, 33, 2245–2255. [27] Bohbot, J., Pitts, R. J., Kwon, H. W., Rutzler, M., Robertson, H. M., and Zwiebel, L. J. (2007) Molecular characterization of Aedes aegypti odorant receptor gene family, Insect Molecular Biology, 16, 525–537. [28] Uddin, M., Wildman, D. E., Liu, G., Xu, W., Johnson, R. M., Hof, P. R., et al., (2004) Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression analysis, Proceedings of National Acad-emy of Sciences, 101, 2957– 2962. [29] Gilad, Y., Man, O., and Glusman, G., (2005) A comparison of the human and chimpanzee olfactory receptor gene repertoires, Genome Research, 15, 224–230. [30] Martin, M. J., Rayner, J. C., Gagneux, P, Barnwell, J. W., and Varki, A., (2005) Evolution of human-chimpanzee differences in malaria susceptibility: Relationship to human genetic loss of N-glycolylneuraminic acid, Proceedings of National Academy of Sciences, 102, 12819– 12824.