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Research: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
- Ge Gao,
- Maria D. Vibranovski,
- Li Zhang,
- Zheng Li,
- Ming Liu,
- Yong E. Zhang,
- Xinmin Li,
- Wenxia Zhang,
- Qichang Fan,
- Nicholas W. VanKuren,
- Manyuan Long,
- and Liping Wei
Genome Res. April 2014 24: 629-638; Published in Advance January 9, 2014, doi:10.1101/gr.165837.113
...key roles of noncoding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these noncoding RNAs. Profiling the transcriptome of Drosophila melanogaster with whole- tiling arrays found that 15% of male-biased transcribed fragments are intergenic noncoding RNAs (inc...
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Research: Evidence for the fixation of gene duplications by positive selection in Drosophila
- Margarida Cardoso-Moreira,
- J. Roman Arguello,
- Srikanth Gottipati,
- L.G. Harshman,
- Jennifer K. Grenier,
- and Andrew G. Clark
Genome Res. June 2016 26: 787-798; Published in Advance April 12, 2016, doi:10.1101/gr.199323.115
...of the polymorphic phase of the evolution of new genes in Drosophila melanogaster. Utilizing five distinct globally dispersed populations, we combine whole- sequencing data with gene expression profiles to (1) describe the diversity and abundance of new genes segregating in these five populations, (2) understand...
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Research: Age-dependent chromosomal distribution of male-biased genes in Drosophila
- Yong E. Zhang,
- Maria D. Vibranovski,
- Benjamin H. Krinsky,
- and Manyuan Long
Genome Res. November 2010 20: 1526-1533; Published in Advance August 26, 2010, doi:10.1101/gr.107334.110
...(DNA-level) or by de novo origination in Drosophila . Our genome-wide analysis revealed an excess of young X-linked male-biased genes. The proportion of X-linked male-biased genes then diminishes through time, leading to an autosomal excess of male-biased genes. The switch between X...
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LETTER: On the origin of new genes in Drosophila
- Qi Zhou,
- Guojie Zhang,
- Yue Zhang,
- Shiyu Xu,
- Ruoping Zhao,
- Zubing Zhan,
- Xin Li,
- Yun Ding,
- Shuang Yang,
- and Wen Wang
Genome Res. September 2008 18: 1446-1455; Published in Advance June 11, 2008, doi:10.1101/gr.076588.108
...case studies, the general principles governing this fundamental process are still unclear at the whole-genome level. Here, we unveil genome-wide patterns for the mutational mechanisms leading to new genes and their subsequent lineage-specific evolution at different time nodes in the Drosophila...
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Research: LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans
- Shengjun Tan,
- Margarida Cardoso-Moreira,
- Wenwen Shi,
- Dan Zhang,
- Jiawei Huang,
- Yanan Mao,
- Hangxing Jia,
- Yaqiong Zhang,
- Chunyan Chen,
- Yi Shao,
- Liang Leng,
- Zhonghua Liu,
- Xun Huang,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. December 2016 26: 1663-1675; Published in Advance October 20, 2016, doi:10.1101/gr.204925.116
.... In Drosophila melanogaster , we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...; Van Oss and Carvunis 2019; Betrán and Long 2022; Zhang et al. 2022). New genes can be integrated into essential bioprocesses, such as transcriptional regulation, RNA synthesis, and DNA repair (Ciccarelli et al. 2005; Ding et al. 2021). In Drosophila species, lineage-specific genes may control the key...
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Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
- Eugenio López-Cortegano,
- Jobran Chebib,
- Anika Jonas,
- Anastasia Vock,
- Sven Künzel,
- Peter D. Keightley,
- and Diethard Tautz
Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
...of Drosophila melanogaster (Muller 1928; Bateman 1959; Mukai 1964) and in humans by pedigree analysis (for review, see Nachman 2004). In recent decades, DNA sequencing techniques have greatly enhanced the ability to detect new mutations, allowing the estimation of mutation rates at the molecular level (Halligan...
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Resource: GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes
- Yi Shao,
- Chunyan Chen,
- Hao Shen,
- Bin Z. He,
- Daqi Yu,
- Shuai Jiang,
- Shilei Zhao,
- Zhiqiang Gao,
- Zhenglin Zhu,
- Xi Chen,
- Yan Fu,
- Hua Chen,
- Ge Gao,
- Manyuan Long,
- and Yong E. Zhang
Genome Res. April 2019 29: 682-696; Published in Advance March 12, 2019, doi:10.1101/gr.238733.118
...challenges in the study of new genes are the inference of gene ages and annotation of their protein-coding potential. To tackle these challenges, we created GenTree, an integrated online database that compiles age inferences from three major methods together with functional genomic data for new genes. Genome-wide...
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Research: Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
- Alexej Abyzov,
- Rebecca Iskow,
- Omer Gokcumen,
- David W. Radke,
- Suganthi Balasubramanian,
- Baikang Pei,
- Lukas Habegger,
- The 1000 Genomes Project Consortium,
- Charles Lee,
- and Mark Gerstein
Genome Res. December 2013 23: 2042-2052; Published in Advance September 11, 2013, doi:10.1101/gr.154625.113
...(RDV; presence/absence of retroduplications in individual s) within human populations is important for understanding human evolution and phenotypic variation. However, only a handful of studies of RDVs in humans and Drosophila have been conducted (Conrad et al. 2009; Karakoc et al. 2011; Schrider et al...
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