Here, we provide revised gene models for D. ananassae, D. yakuba, and D. simulans, which include untranslated regions and empirically verified intron-exon boundaries, as well as ortholog groups identified using a fuzzy reciprocal-best-hit blast comparison. Using these revised annotations, we perform differential expression testing using the cufflinks suite to provide a broad overview of differential expression between reproductive tissues and the carcass. We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans. We identify several cases of putative polycistronic transcripts, pointing to a combination of transcriptional read-through in the genome as well as putative gene fusion and fission events across taxa. We furthermore identify hundreds of lineage specific genes in each species with no blast hits among transcripts of any other Drosophila species, which are candidates for neofunctionalized proteins and a potential source of genetic novelty.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267930 | PMC |
| http://dx.doi.org/10.1534/g3.114.013532 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The protein encoded by the gene ( ) plays an essential role in early gametogenesis by complexing with the gene product of ( ) to promote germline stem cell daughter differentiation in males and females. Here, we compared the AlphaFold2 and AlphaFold Multimer predicted structures of Bam protein and the Bam:Bgcn protein complex between , where is necessary in gametogenesis to that in , where it is not. Despite significant sequence divergence, we find very little evidence of significant structural differences in high confidence regions of the structures across the four species.
View Article and Find Full Text PDFThe evolution and mutational robustness of chromatin accessibility in Drosophila.
Genome Biol
October 2023
Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, 10065, USA.
Background: The evolution of genomic regulatory regions plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems complicates the understanding of the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different species and tissues of Drosophila.
View Article and Find Full Text PDFThe evolution and mutational robustness of chromatin accessibility in .
bioRxiv
June 2023
Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA.
The evolution of regulatory regions in the genome plays a critical role in shaping the diversity of life. While this process is primarily sequence-dependent, the enormous complexity of biological systems has made it difficult to understand the factors underlying regulation and its evolution. Here, we apply deep neural networks as a tool to investigate the sequence determinants underlying chromatin accessibility in different tissues of .
View Article and Find Full Text PDF[The Involvement of the Gagr Gene, a Domesticated gag Retrovirus Gene, in the Stress-Response Pathway in Different Drosophila Species].
Mol Biol (Mosk)
June 2023
Department of Biology, Moscow State University, Moscow, 119234 Russia.
The Gagr gene is a domesticated gag retroelement gene in Drosophila melanogaster, whose function is associated with the stress response. The protein products of the Gagr gene and its homologues in different Drosophila species have a highly conserved structure; however, they demonstrate variability in the promoter region of the gene, which is apparently associated with the gradual acquisition of a new function and involvement in new signaling pathways. In this work, we studied the effect of oxidative stress induced by ammonium persulfate on the survival of various species of the genus Drosophila (D.
View Article and Find Full Text PDFIdentifying candidate de novo genes expressed in the somatic female reproductive tract of Drosophila melanogaster.
G3 (Bethesda)
August 2023
Department of Evolution and Ecology, University of California Davis, Davis, CA 95616, USA.
Most eukaryotic genes have been vertically transmitted to the present from distant ancestors. However, variable gene number across species indicates that gene gain and loss also occurs. While new genes typically originate as products of duplications and rearrangements of preexisting genes, putative de novo genes-genes born out of ancestrally nongenic sequence-have been identified.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!