Natural variation of gene models in Drosophila melanogaster

Yerbol Z. Kurmangaliyev, Alexander Favorov, Noha M. Osman, Kjong Van Lehmann, Daniel Campo, Matthew P. Salomon, John Tower, Mikhail S. Gelfand, Sergey V. Nuzhdin

Research output: Contribution to journalArticle

Abstract

Background: Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. Results: Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments. Conclusions: Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila.

Original languageEnglish (US)
Article number198
JournalBMC Genomics
Volume16
Issue number1
DOIs
StatePublished - Mar 17 2015

Fingerprint

Drosophila melanogaster
Quantitative Trait Loci
Genes
Alleles
Genotype
Allelic Imbalance
Proteins
Transcriptome
Introns
Open Reading Frames
Drosophila
Exons
Protein Isoforms
Mutation
Population

Keywords

  • Drosophila
  • Natural variation
  • Quantitative trait loci
  • Splicing

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Kurmangaliyev, Y. Z., Favorov, A., Osman, N. M., Lehmann, K. V., Campo, D., Salomon, M. P., ... Nuzhdin, S. V. (2015). Natural variation of gene models in Drosophila melanogaster. BMC Genomics, 16(1), [198]. https://doi.org/10.1186/s12864-015-1415-6

Natural variation of gene models in Drosophila melanogaster. / Kurmangaliyev, Yerbol Z.; Favorov, Alexander; Osman, Noha M.; Lehmann, Kjong Van; Campo, Daniel; Salomon, Matthew P.; Tower, John; Gelfand, Mikhail S.; Nuzhdin, Sergey V.

In: BMC Genomics, Vol. 16, No. 1, 198, 17.03.2015.

Research output: Contribution to journalArticle

Kurmangaliyev, YZ, Favorov, A, Osman, NM, Lehmann, KV, Campo, D, Salomon, MP, Tower, J, Gelfand, MS & Nuzhdin, SV 2015, 'Natural variation of gene models in Drosophila melanogaster', BMC Genomics, vol. 16, no. 1, 198. https://doi.org/10.1186/s12864-015-1415-6
Kurmangaliyev YZ, Favorov A, Osman NM, Lehmann KV, Campo D, Salomon MP et al. Natural variation of gene models in Drosophila melanogaster. BMC Genomics. 2015 Mar 17;16(1). 198. https://doi.org/10.1186/s12864-015-1415-6
Kurmangaliyev, Yerbol Z. ; Favorov, Alexander ; Osman, Noha M. ; Lehmann, Kjong Van ; Campo, Daniel ; Salomon, Matthew P. ; Tower, John ; Gelfand, Mikhail S. ; Nuzhdin, Sergey V. / Natural variation of gene models in Drosophila melanogaster. In: BMC Genomics. 2015 ; Vol. 16, No. 1.
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