Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages
Abstract How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-05427-4 |
| _version_ | 1797557199898148864 |
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| author | Bryan D. Clifton Imtiyaz Hariyani Ashlyn Kimura Fangning Luo Alvin Nguyen José M. Ranz |
| author_facet | Bryan D. Clifton Imtiyaz Hariyani Ashlyn Kimura Fangning Luo Alvin Nguyen José M. Ranz |
| author_sort | Bryan D. Clifton |
| collection | DOAJ |
| description | Abstract How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family. |
| first_indexed | 2024-03-10T17:13:59Z |
| format | Article |
| id | doaj.art-4183d60dc9c841918025408c1a617506 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-10T17:13:59Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-4183d60dc9c841918025408c1a6175062023-11-20T10:33:52ZengNature PortfolioCommunications Biology2399-36422023-10-016111110.1038/s42003-023-05427-4Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stagesBryan D. Clifton0Imtiyaz Hariyani1Ashlyn Kimura2Fangning Luo3Alvin Nguyen4José M. Ranz5Department of Ecology and Evolutionary Biology, University of California IrvineDepartment of Ecology and Evolutionary Biology, University of California IrvineDepartment of Ecology and Evolutionary Biology, University of California IrvineDepartment of Ecology and Evolutionary Biology, University of California IrvineDepartment of Ecology and Evolutionary Biology, University of California IrvineDepartment of Ecology and Evolutionary Biology, University of California IrvineAbstract How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.https://doi.org/10.1038/s42003-023-05427-4 |
| spellingShingle | Bryan D. Clifton Imtiyaz Hariyani Ashlyn Kimura Fangning Luo Alvin Nguyen José M. Ranz Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages Communications Biology |
| title | Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages |
| title_full | Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages |
| title_fullStr | Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages |
| title_full_unstemmed | Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages |
| title_short | Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages |
| title_sort | paralog transcriptional differentiation in the d melanogaster specific gene family sdic across populations and spermatogenesis stages |
| url | https://doi.org/10.1038/s42003-023-05427-4 |
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