Molecular evolution of the Est-6 gene in Drosophila melanogaster: contrasting patterns of DNA variability in adjacent functional regions

Balakirev, Evgeniy S.; Balakirev, Elena I.; Ayala, Francisco J.

doi:10.1016/s0378-1119(02)00477-8

Cited by 21 publications

(19 citation statements)

References 34 publications

(30 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Saad et al (1994) also identified associations between Esterase-6 activity level and variation in male reproductive performance among isofemale lines. In addition to the functional characterization, several studies have identified nonneutral patterns of genetic variation in both the coding (Oakeshott et al 2001) and the 59-regulatory regions of Esterase-6 (Balakirev et al 2002;Odgers et al 2002). We have identified associations affecting male fitness that map to both the coding region and the 59-regulatory region of Esterase-6.…”

Section: Discussionmentioning

confidence: 99%

Associations Between Sperm Competition and Natural Variation in Male Reproductive Genes on the Third Chromosome of Drosophila melanogaster

Dumont²,

2007

View full text Add to dashboard Cite

We applied association analysis to elucidate the genetic basis for variation in phenotypes affecting postcopulatory sexual selection in a natural population of Drosophila melanogaster. We scored 96 third chromosome substitution lines for nine phenotypes affecting sperm competitive ability and genotyped them at 72 polymorphisms in 13 male reproductive genes. Significant heterogeneity among lines (P , 0.01) was detected for all phenotypes except male-induced refractoriness (P ¼ 0.053). We identified 24 associations (8 single-marker associations, 12 three-marker haplotype associations, and 4 cases of epistasis revealed by single-marker interactions). Fewer than 9 of these associations are likely to be false positives. Several associations were consistent with previous findings ½Acp70A with the male's influence on the female's refractoriness to remating (refractory), Esterase-6 with a male's remating probability (remating) and a measure of female offspring production ( fecundity), but many are novel associations with uncharacterized seminal fluid proteins. Four genes showed evidence for pleiotropic effects ½CG6168 with a measure of sperm competition (P29) and refractory, CG14560 with a defensive measure of sperm competition (P19) and a measure of female fecundity, Acp62F with P29 and a measure of female fecundity, and Esterase-6 with remating and a measure of female fecundity. Our findings provide evidence that pleiotropy and epistasis are important factors in the genetic architecture of male reproductive success and show that haplotype analyses can identify associations missed in the single-marker approach.

show abstract

Section: Discussionmentioning

confidence: 99%

Associations Between Sperm Competition and Natural Variation in Male Reproductive Genes on the Third Chromosome of Drosophila melanogaster

Dumont²,

2007

View full text Add to dashboard Cite

show abstract

“…The tests are not significant for the tin gene (as to the values observed for the most polymorphic Droin the Hudson et al 1994and McDonald 1996, 1998 sophila genes, such as Est-6 and Est-6 (Balakirev and tests). The tests are significant for the bap gene when Ayala 1996Ayala , 2003aAyala ,b, 2004Balakirev et al 1999Balakirev et al , 2002, applied to the homogeneous and heterogeneous sets 2003; Ayala et al 2002). The pattern of nucleotide of sequences separately (the haplotype groups are the variability in tin and bap is not compatible with an equilibrium model of selective neutrality.…”

mentioning

confidence: 99%

“…The silent variability of bap exon the presence of two sets of haplotypes for the ␤-esterase observed for the bap gene (Figures 1 and 3). There is a set of 13 sequences, 12 of them identical to each gene cluster of D. melanogaster, localized on the left arm of the third chromosome (Balakirev et al 1999 other plus one (no. 10) that differs by a nonsynonymous substitution, and a second set of fairly heterogeneous 2003).…”

mentioning

confidence: 99%

“…A similar relationship was observed between genes of the Ras-mediated signal transter together with negative (purifying) selection may be the main factors shaping the observed patterns of nucleduction pathway of Drosophila (Riley et al 2003 account for the excess of nearly identical sequences. Positive selection in the bap gene is supported by significant HKA (Hudson et al 1987), McDonald (1996, 1998, and haplotype (Hudson et al 1994 coding region is shaped by the influence of both direc- Positive selection drives the evolution of the Acp tional and balancing selection (Balakirev et al 1999, 29AB accessory gland protein in Drosophila. Genetics 152: 543-…”

mentioning

confidence: 99%

See 1 more Smart Citation

Nucleotide Variation in the tinman and bagpipe Homeobox Genes of Drosophila melanogaster

Balakirev

Ayala

2004

Genetics

View full text Add to dashboard Cite

The tinman (tin) and bagpipe (bap) genes are members of the NK homeobox gene family of Drosophila, so that tin occupies a higher position than bap in the regulatory hierarchy. Little is known about the level and pattern of genetic polymorphism in homeobox genes. We have analyzed nucleotide polymorphism in 27 strains of Drosophila melanogaster and one each of D. simulans and D. sechellia, within two closely linked regions encompassing a partial sequence of tin and the complete sequence of bap. The two genes exhibit different levels and patterns of nucleotide diversity. Two sets of sharply divergent sequence types are detected for tin. The haplotype structure of bap is more complex: about half of the sequences are identical (or virtually so), while the rest are fairly heterogeneous. The level of silent nucleotide variability is 0.0063 for tin but significantly higher, 0.0141, for bap, a level of polymorphism comparable to the most polymorphic structural genes of D. melanogaster. Recombination rate and gene conversion are also higher for bap than for tin. There is strong linkage disequilibrium, with the highest values in the introns of both genes and exon II of bap. The patterns of polymorphism in tin and bap are not compatible with an equilibrium model of selective neutrality. We suggest that negative selection and demographic history are the major factors shaping the pattern of nucleotide polymorphism in the tin and bap genes; moreover, there are clear indications of positive selection in the bap gene.T HE population polymorphism of homeobox genes observed in the Arabidopsis thaliana CAULIFLOWER homeotic gene, which was in this case attributed to positive in Drosophila has received scant attention. Begun selection (Purugganan and Suddith 1998). Nucleoet al. (1994) investigated restriction-map polymorphism tide polymorphism has been investigated also for the in the cut locus region of D. melanogaster and D. simulans.even-skipped (Ludwig and Kreitman 1995), Ultrabithorax The amount of nucleotide variation was in both species (Gibson and Hogness 1996), and OdysseusH (Ting et about one-fourth of the average amount in comparable al. 1998) Drosophila homeobox genes. The data obrestriction-map studies of gene regions with normal retained for these genes, however, involved only interspecombination (Aquadro 1992), even though the gene cific comparisons or only very few sequences, so that is located in a genomic region with "normal" recombinaintraspecific variability could not be estimated. On the tion rate. Begun et al. (1994) suggested that selective average, Drosophila regulatory loci display reduced levsweeps associated with some closely linked gene(s) might els of diversity (less than half) compared to structural account for the decreased variability of cut. Baines et al. genes (Moriyama and Powell 1996). In contrast, the (2002) investigated nucleotide polymorphism in the D.level of polymorphism is about the same in some plant melanogaster bicoid region. The level of silent polymorregulatory genes as in str...

show abstract

“…Whereas DNA sequencing provides detailed information that is essential for understanding the function and evolution of genes and their flanking regions, whole-genome characterization provides the genetic context in which these functions and changes take place (13)(14)(15). Although much progress has been made in the assembly of large-genome regions from raw sequence data, the short scope of individual sequencing reactions (on the order of 1 kb) makes complete genome characterization by sequencing alone an extremely challenging task (16,17).…”

mentioning

confidence: 99%

Nanometer-localized multiple single-molecule fluorescence microscopy

Wu²,

Mets³

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

289

231

View full text Add to dashboard Cite

Fitting the image of a single molecule to the point spread function of an optical system greatly improves the precision with which single molecules can be located. Centroid localization with nanometer precision has been achieved when a sufficient number of photons are collected. However, if multiple single molecules reside within a diffraction-limited spot, this localization approach does not work. This paper demonstrates nanometer-localized multiple single-molecule (NALMS) fluorescence microscopy by using both centroid localization and photobleaching of the single fluorophores. Short duplex DNA strands are used as nanoscale ''rulers'' to validate the NALMS microscopy approach. Nanometer accuracy is demonstrated for two to five single molecules within a diffraction-limited area. NALMS microscopy will greatly facilitate singlemolecule study of biological systems because it covers the gap between fluorescence resonance energy transfer-based (<10 nm) and diffraction-limited microscopy (>100 nm) measurements of the distance between two fluorophores. Application of NALMS microscopy to DNA mapping with <10-nm (i.e., 30-base) resolution is demonstrated. It is well known that the spatial resolution of an optical system is limited by the Rayleigh criterion (1),where is the wavelength of the collected photons and N.A. is the numerical aperture of the system. Using visible light (i.e., Ϸ500 nm) and a high N.A. objective (i.e. Ͼ1) allows achieving Ϸ250-nm lateral resolution. However, most biological macromolecules (DNA, RNA, proteins, etc.) and molecular machines (e.g., ribosome and spliceosome) are much smaller in two or all three dimensions, with important features or subassemblies lying within 10 nm of each other (2). Fluorescence resonance energy transfer (FRET) is widely used for studying biological systems on the nanometer scale (i.e., Ͻ10 nm; ref. 3). FRET occurs over distances similar to the Förster radius, which is Ϸ5 nm for common fluorophores (4). However, FRET only gives the relative distance between two probes, whereas their absolute positions remain unknown. Centroid localization, which has been used for single-particle tracking, allows determination of the centroid position of the particle to a much better precision than the length scale defined by the Rayleigh criterion (5-7). Recently, this approach to localizing fluorophores has been applied to single dye molecules (Cy3 and Rhodamine dyes) bound to molecular motors, and 2-nm precision in localization has been achieved when an oxygen scavenging buffer was used to suppress photobleaching (8, 9). However, centroid localization can only be used for isolated single molecules and it does not improve the resolution of the imaging system. It has been shown that two probes with different fluorescent wavelengths can be resolved within 10 nm because they are spectrally distinguishable (10). This method does not help when two or more objects with the same emission spectrum are within a diffraction-limited spot. Imaging applications beyond even the capabilities of ''su...

show abstract

Molecular evolution of the Est-6 gene in Drosophila melanogaster: contrasting patterns of DNA variability in adjacent functional regions

Cited by 21 publications

References 34 publications

Associations Between Sperm Competition and Natural Variation in Male Reproductive Genes on the Third Chromosome of Drosophila melanogaster

Associations Between Sperm Competition and Natural Variation in Male Reproductive Genes on the Third Chromosome of Drosophila melanogaster

Nucleotide Variation in the tinman and bagpipe Homeobox Genes of Drosophila melanogaster

Nanometer-localized multiple single-molecule fluorescence microscopy

Contact Info

Product

Resources

About