Clines and adaptive evolution in the methuselah gene region in Drosophila melanogaster

2003 ◽  
Vol 12 (5) ◽  
pp. 1277-1285 ◽  
Author(s):  
David D. Duvernell ◽  
Paul S. Schmidt ◽  
Walter F. Eanes
Keyword(s):  
Drosophila Melanogaster ◽  
Adaptive Evolution ◽  
Gene Region

scholarly journals Reciprocal recombination and the evolution of the ribosomal gene family of Drosophila melanogaster.

Genetics ◽  
1989 ◽  
Vol 122 (3) ◽  
pp. 617-624 ◽  
Author(s):  
S M Williams ◽  
J A Kennison ◽  
L G Robbins ◽  
C Strobeck
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Ribosomal Rna ◽  
Natural Populations ◽  
Ribosomal Gene ◽  
Gene Region ◽  
Ribosomal Rna Gene ◽  
Reciprocal Recombination ◽  
Y Chromosomes ◽  
Length Polymorphisms

Abstract The role of reciprocal recombination in the coevolution of the ribosomal RNA gene family on the X and Y chromosomes of Drosophila melanogaster was assessed by determining the frequency and nature of such exchange. In order to detect exchange events within the ribosomal RNA gene family, both flanking markers and restriction fragment length polymorphisms within the tandemly repeated gene family were used. The vast majority of crossovers between flanking markers were within the ribosomal RNA gene region, indicating that this region is a hotspot for heterochromatic recombination. The frequency of crossovers within the ribosomal RNA gene region was approximately 10(-4) in both X/X and X/Y individuals. In conjunction with published X chromosome-specific and Y chromosome-specific sequences and restriction patterns, the data indicate that reciprocal recombination alone cannot be responsible for the observed variation in natural populations.

scholarly journals Patterns of Sequence Variability and Divergence at the diminutive Gene Region of Drosophila melanogaster: Complex Patterns Suggest an Ancestral Selective Sweep

Genetics ◽  
2007 ◽  
Vol 177 (2) ◽  
pp. 1071-1085 ◽  
Author(s):  
Jeffrey D. Jensen ◽  
Vanessa L. Bauer DuMont ◽  
Adeline B. Ashmore ◽  
Angela Gutierrez ◽  
Charles F. Aquadro
Keyword(s):  
Drosophila Melanogaster ◽  
Selective Sweep ◽  
Gene Region ◽  
Sequence Variability ◽  
Complex Patterns

Multiple products from the shavenbaby-ovo gene region of Drosophila melanogaster: relationship to genetic complexity

1994 ◽  
Vol 14 (10) ◽  
pp. 6809-6818
Author(s):  
M D Garfinkel ◽  
J Wang ◽  
Y Liang ◽  
A P Mahowald
Keyword(s):  
Drosophila Melanogaster ◽  
Germ Line ◽  
Gene Region ◽  
Multiple Products ◽  
Zinc Finger Motifs ◽  
Genetic Complexity ◽  
Complex Locus ◽  
Female Germ Line ◽  
Sensory Structures ◽  
Pole Cells

The Drosophila melanogaster shavenbaby (svb)-ovo gene region is a complex locus, containing two distinct but comutable genetic functions. ovo is required for survival and differentiation of female germ line cells and plays a role in germ line sex determination. In contrast, svb is required in both male and female embryos for the production of epidermal locomotor and sensory structures. Sequences required for the two genetic functions are partially overlapping. ovo corresponds to a previously described germ line-dependent 5.0-kb poly(A)+ mRNA that first appears in the germarium and accumulates in nurse cells during oogenesis. The 5.0-kb mRNA is stored in the egg, but it is rapidly lost in the embryos except for its continued presence in the germ line precursor pole cells. The ovo mRNA predicts a 1,028-amino-acid 110.6-kDa protein homologous with transcription factors. We have identified an embryonic mRNA, 7.1 kb in length, that contains exons partially overlapping those of the 5.0-kb poly(A)+ mRNA. The spatial distribution of this newly discovered transcript during midembryogenesis suggests that it corresponds to the svb function. The arrangement of exons common to the 5.0- and 7.1-kb mRNAs suggests that the Ovo and Svb proteins share DNA-binding specificity conferred by four Cys2-His2 zinc finger motifs but differ functionally in their capacity to interact with other components of the transcription machinery.

scholarly journals GCAT dotplots characterize precisely and imprecisely defined topological features of DNA

2021 ◽  
Author(s):  
Janet I Collett ◽  
Stephen R Pearce
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Element ◽  
Reference Genome ◽  
Gene Region ◽  
Two Dimensional ◽  
Stop Codons ◽  
Topological Features ◽  
Large Intron ◽  
Sequence Elements

Two dimensional graphical dotplotting is adopted to identify sequence elements and their variants in lengths of DNA of up to 10 kb. Named GCAT for identification of precisely defined short sequences and their variants, its use complements the precise matching of many computational programs, including BLAST. Short reiterated search sequences are entered in the Y axis of the dotplot program to be matched at their identical and near identical sites in a sequence of interest entered in the X axis. The result is a barcode like representation of the identified sequence elements along the X axis of the dotplot. Alignments of searches and sequence landmarks provide visualization of composition and juxtapositions. The method is described here by example of characterizations of three distinctive sequences available in the annotated Drosophila melanogaster reference genome (www.flybase.org): the Jonah 99C gene region, the transcript of Dipeptidase B and the transposable element roo. Surprising observations emerging from these explorations include in frame STOP codons in the large exonic intron of Dip-B, high A content of the replicative strand of roo as TE example and similarities of its ORF and the large intron of Dip B.

scholarly journals A-to-I RNA Editing Uncovers Hidden Signals of Adaptive Genome Evolution in Animals

2020 ◽  
Vol 12 (4) ◽  
pp. 345-357 ◽  
Author(s):  
Niko Popitsch ◽  
Christian D Huber ◽  
Ilana Buchumenski ◽  
Eli Eisenberg ◽  
Michael Jantsch ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Single Nucleotide Polymorphisms ◽  
Genome Evolution ◽  
Rna Editing ◽  
Adaptive Evolution ◽  
Population Genomics ◽  
Common Type ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cellular Machinery

Abstract In animals, the most common type of RNA editing is the deamination of adenosines (A) into inosines (I). Because inosines basepair with cytosines (C), they are interpreted as guanosines (G) by the cellular machinery and genomically encoded G alleles at edited sites mimic the function of edited RNAs. The contribution of this hardwiring effect on genome evolution remains obscure. We looked for population genomics signatures of adaptive evolution associated with A-to-I RNA edited sites in humans and Drosophila melanogaster. We found that single nucleotide polymorphisms at edited sites occur 3 (humans) to 15 times (Drosophila) more often than at unedited sites, the nucleotide G is virtually the unique alternative allele at edited sites and G alleles segregate at higher frequency at edited sites than at unedited sites. Our study reveals that a significant fraction of coding synonymous and nonsynonymous as well as silent and intergenic A-to-I RNA editing sites are likely adaptive in the distantly related human and Drosophila lineages.

scholarly journals Centromere Targeting Element within the Histone Fold Domain of Cid

2002 ◽  
Vol 22 (21) ◽  
pp. 7553-7561 ◽  
Author(s):  
Danielle Vermaak ◽  
Hillary S. Hayden ◽  
Steven Henikoff
Keyword(s):  
Drosophila Melanogaster ◽  
Green Fluorescent Protein ◽  
Adaptive Evolution ◽  
Fluorescent Protein ◽  
Conserved Residues ◽  
Histone Fold ◽  
Histone Fold Domain ◽  
Dna Specificity ◽  
Green Fluorescent

ABSTRACT Centromeres require specialized nucleosomes; however, the mechanism of localization is unknown. Drosophila sp. centromeric nucleosomes contain the Cid H3-like protein. We have devised a strategy for identifying elements within Cid responsible for its localization to centromeres. By expressing Cid from divergent Drosophila species fused to green fluorescent protein in Drosophila melanogaster cells, we found that D. bipectinata Cid fails to localize to centromeres. Cid chimeras consisting of the D. bipectinata histone fold domain (HFD) replaced with segments from D. melanogaster identified loop I of the HFD as being critical for targeting to centromeres. Conversely, substitution of D. bipectinata loop I into D. melanogaster abolished centromeric targeting. In either case, loop I was the only segment capable of conferring targeting. Within loop I, we identified residues that are critical for targeting. Most mutations of conserved residues abolished targeting, and length reductions were deleterious. Taken together with the fact that H3 loop I makes numerous contacts with DNA and with the adaptive evolution of Cid, our results point to the importance of DNA specificity for targeting. We suggest that the process of deposition of (Cid.H4)2 tetramers allows for discriminating contacts to be made between loop I and DNA, providing the specificity needed for targeting.

scholarly journals Multiple products from the shavenbaby-ovo gene region of Drosophila melanogaster: relationship to genetic complexity.

1994 ◽  
Vol 14 (10) ◽  
pp. 6809-6818 ◽  
Author(s):  
M D Garfinkel ◽  
J Wang ◽  
Y Liang ◽  
A P Mahowald
Keyword(s):  
Drosophila Melanogaster ◽  
Germ Line ◽  
Gene Region ◽  
Multiple Products ◽  
Zinc Finger Motifs ◽  
Genetic Complexity ◽  
Complex Locus ◽  
Female Germ Line ◽  
Sensory Structures ◽  
Pole Cells

The Drosophila melanogaster shavenbaby (svb)-ovo gene region is a complex locus, containing two distinct but comutable genetic functions. ovo is required for survival and differentiation of female germ line cells and plays a role in germ line sex determination. In contrast, svb is required in both male and female embryos for the production of epidermal locomotor and sensory structures. Sequences required for the two genetic functions are partially overlapping. ovo corresponds to a previously described germ line-dependent 5.0-kb poly(A)+ mRNA that first appears in the germarium and accumulates in nurse cells during oogenesis. The 5.0-kb mRNA is stored in the egg, but it is rapidly lost in the embryos except for its continued presence in the germ line precursor pole cells. The ovo mRNA predicts a 1,028-amino-acid 110.6-kDa protein homologous with transcription factors. We have identified an embryonic mRNA, 7.1 kb in length, that contains exons partially overlapping those of the 5.0-kb poly(A)+ mRNA. The spatial distribution of this newly discovered transcript during midembryogenesis suggests that it corresponds to the svb function. The arrangement of exons common to the 5.0- and 7.1-kb mRNAs suggests that the Ovo and Svb proteins share DNA-binding specificity conferred by four Cys2-His2 zinc finger motifs but differ functionally in their capacity to interact with other components of the transcription machinery.

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