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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
..., the X Chromosome has an excess of ancient genes (25.42%) but a deficiency of young genes (57.16%) (Fig. 4A). Conversely, among male-specific reproductive disease genes, younger genes exhibited a higher excess rate than ancient ones (193.96% vs. 80.09%) (Fig. 4A). These patterns suggest an age-dependent...
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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
...cells (Vibranovski et al. 2009a). In D. melanogaster and in Caenorhabditis elegans gonads, male-biased coding genes are found to be underrepresented on the X chromosome (Betrán et al. 2002; Parisi et al. 2003; Ranz et al. 2003; Reinke et al. 2004). In Drosophila this underrepresentation is observed only...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...). This is consistent with previous findings of an enrichment of novel genes on the X Chromosome of Drosophila (Betrán et al. 2002; Levine et al. 2006). Thus, de novo candidates are not uniformly distributed across chromosomes and are particularly enriched on P. pacificus Chromosome X.View larger version...
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Research: Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
- Daniel R. Schrider,
- Kristian Stevens,
- Charis M. Cardeño,
- Charles H. Langley,
- and Matthew W. Hahn
Genome Res. December 2011 21: 2087-2095; doi:10.1101/gr.116434.110
...chromosome in Drosophila . Further efforts to identify retrogene and intron presence/absence polymorphisms will undoubtedly improve our understanding of the evolution of gene copy number and gene structure. Footnotes ↵ 5 Corresponding author. E-mail dschride...
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Research: Haploid selection drives new gene male germline expression
- Julia B. Raices,
- Paulo A. Otto,
- and Maria D. Vibranovski
Genome Res. July 2019 29: 1115-1122; Published in Advance June 20, 2019, doi:10.1101/gr.238824.118
...Y, Lu S, Zhao S, Zheng X, Long M, Wei L. 2009. Positive selection for the male functionality of a co-retroposed gene in the hominoids. BMC Evol Biol 9: 252. doi:10.1186/1471-2148-9-252 ↵Zhang YE, Vibranovski MD, Krinsky BH, Long M. 2010. Age-dependent chromosomal distribution of male-biased genes...
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Research: Disentangling the relationship between sex-biased gene expression and X-linkage
- Richard P. Meisel,
- John H. Malone,
- and Andrew G. Clark
Genome Res. July 2012 22: 1255-1265; Published in Advance April 12, 2012, doi:10.1101/gr.132100.111
.....org Genome Research 1255 www..org of X-linked genes with male-biased expression is an emergent property of the Drosophila X chromosome and not intrinsic to the proto-X. Three hypotheses have been put forth to explain the deficiency of genes with male-biased expression on the Drosophila X chromosome. First...
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Research: Slightly deleterious genomic variants and transcriptome perturbations in Down syndrome embryonic selection
- Konstantin Popadin,
- Stephan Peischl,
- Marco Garieri,
- M. Reza Sailani,
- Audrey Letourneau,
- Federico Santoni,
- Samuel W. Lukowski,
- Georgii A. Bazykin,
- Sergey Nikolaev,
- Diogo Meyer,
- Laurent Excoffier,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. January 2018 28: 1-10; Published in Advance December 13, 2017, doi:10.1101/gr.228411.117
...samples and 16 fibroblast transcriptomes) and observed a deficit of slightly deleterious variants on Chromosome 21 and decreased transcriptome-wide variation in the expression level of highly constrained genes. We interpret these results as signatures of embryonic selection, and propose a genetic handicap...
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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
.... 2000) or InterPro family annotation (Hunter et al. 2009). In both cases, we calculated the gene age distribution for each GO or InterPro family category, divided by chromosomes. For example, the Krueppel-associated box C2H2 zinc-finger protein family (KZNF) was known to have expanded especially...
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