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Keshavarz M, Savriama Y, Refki P, Reeves RG, Tautz D. Natural copy number variation of tandemly repeated regulatory SNORD RNAs leads to individual phenotypic differences in mice. Mol Ecol 2021; 30:4708-4722. [PMID: 34252239 DOI: 10.1111/mec.16076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/05/2021] [Indexed: 12/01/2022]
Abstract
Genic copy number differences can have phenotypic consequences, but so far this has not been studied in detail in natural populations. Here, we analysed the natural variation of two families of tandemly repeated regulatory small nucleolar RNAs (SNORD115 and SNORD116) in the house mouse (Mus musculus). They are encoded within the Prader-Willi Syndrome gene region, known to be involved in behavioural, metabolic, and osteogenic functions in mammals. We determined that the copy numbers of these SNORD RNAs show substantial natural variation, both in wild-derived mice as well as in an inbred mouse strain (C57BL/6J). We show that copy number differences are subject to change across generations, making them highly variable and resulting in individual differences. In transcriptome data from brain samples, we found SNORD copy-number correlated regulation of possible target genes, including Htr2c, a predicted target gene of SNORD115, as well as Ankrd11, a predicted target gene of SNORD116. Ankrd11 is a chromatin regulator, which has previously been implicated in regulating the development of the skull. Based on morphometric shape analysis of the skulls of individual mice of the inbred strain, we show that shape measures correlate with SNORD116 copy numbers in the respective individuals. Our results suggest that the variable dosage of regulatory RNAs can lead to phenotypic variation between individuals that would typically have been ascribed to environmentally induced variation, while it is actually encoded in individual differences of copy numbers of regulatory molecules.
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Affiliation(s)
| | - Yoland Savriama
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Peter Refki
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - R Guy Reeves
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
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2
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Karn RC, Yazdanifar G, Pezer Ž, Boursot P, Laukaitis CM. Androgen-Binding Protein (Abp) Evolutionary History: Has Positive Selection Caused Fixation of Different Paralogs in Different Taxa of the Genus Mus? Genome Biol Evol 2021; 13:6377336. [PMID: 34581786 PMCID: PMC8525912 DOI: 10.1093/gbe/evab220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 11/14/2022] Open
Abstract
Comparison of the androgen-binding protein (Abp) gene regions of six Mus genomes provides insights into the evolutionary history of this large murid rodent gene family. We identified 206 unique Abp sequences and mapped their physical relationships. At least 48 are duplicated and thus present in more than two identical copies. All six taxa have substantially elevated LINE1 densities in Abp regions compared with flanking regions, similar to levels in mouse and rat genomes, although nonallelic homologous recombination seems to have only occurred in Mus musculus domesticus. Phylogenetic and structural relationships support the hypothesis that the extensive Abp expansion began in an ancestor of the genus Mus. We also found duplicated Abpa27's in two taxa, suggesting that previously reported selection on a27 alleles may have actually detected selection on haplotypes wherein different paralogs were lost in each. Other studies reported that a27 gene and species trees were incongruent, likely because of homoplasy. However, L1MC3 phylogenies, supposed to be homoplasy-free compared with coding regions, support our paralog hypothesis because the L1MC3 phylogeny was congruent with the a27 topology. This paralog hypothesis provides an alternative explanation for the origin of the a27 gene that is suggested to be fixed in the three different subspecies of Mus musculus and to mediate sexual selection and incipient reinforcement between at least two of them. Finally, we ask why there are so many Abp genes, especially given the high frequency of pseudogenes and suggest that relaxed selection operates over a large part of the gene clusters.
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Affiliation(s)
- Robert C Karn
- Gene Networks in Neural and Developmental Plasticity, Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | | | - Željka Pezer
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Pierre Boursot
- Institut des Sciences de l'Evolution Montpellier, Université de Montpellier, CNRS, IRD, France
| | - Christina M Laukaitis
- Carle Health and Carle Illinois College of Medicine, University of Illinois, Urbana-Champaign, USA
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3
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Clifton BD, Jimenez J, Kimura A, Chahine Z, Librado P, Sánchez-Gracia A, Abbassi M, Carranza F, Chan C, Marchetti M, Zhang W, Shi M, Vu C, Yeh S, Fanti L, Xia XQ, Rozas J, Ranz JM. Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study. Mol Biol Evol 2021; 37:2584-2600. [PMID: 32359138 PMCID: PMC7475035 DOI: 10.1093/molbev/msaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Jamie Jimenez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Zeinab Chahine
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Pablo Librado
- Laboratoire AMIS CNRS UMR 5288, Faculté de Médicine de Purpan, Université Paul Sabatier, Toulouse, France
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Mashya Abbassi
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Francisco Carranza
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Carolus Chan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Marcella Marchetti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Christine Vu
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Shudan Yeh
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA.,Department of Life Sciences, National Central University, Taoyuan City, Zhongli District, Taiwan
| | - Laura Fanti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
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Xu Z, Wang X, Zhang Z, An Q, Wen Y, Wang D, Liu X, Li Z, Lyu S, Li L, Wang E, Ru B, Xu Z, Huang Y. Copy number variation of CADM2 gene revealed its association with growth traits across Chinese Capra hircus (goat) populations. Gene 2020; 741:144519. [PMID: 32126252 DOI: 10.1016/j.gene.2020.144519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/15/2022]
Abstract
Copy number variations (CNVs) are the wide structural variations ranging from 50 bp to several Mb at genome which can affect gene expression and further impacting growth and development traits of livestock. Comparing with single nucleotide polymorphisms (SNPs), CNVs can better explain the genetic and phenotypic diversity, are increasingly important in biological research. As a member of immunoglobulin super-family, cell adhesion molecule 2 (CADM2) plays a vital role in cancer development and metabolic regulation. Here, we tested the CNV of CADM2 gene in 443 goats across five breeds (Guizhou white goat, GZW; Guizhou black goat, GZB; Africa Nubian goat, AN; Boer goat × Huai goat, BH; Boer goat, BG) and detected its association with phenotypic traits. Subsequently, we analyzed the CADM2 gene expression level in different tissues of NB goats (n = 3, Nubian × Black) and the transcriptional expression in lung is much higher than others. The results showed that the CNV of CADM2 has a significant association with withers height and body length in GZB goat (P < 0.01), in which individuals with type of deletion were superior to those with duplication or normal type in term of body hight and body length (P < 0.01). In summary, this study confirmed the association between CNV of CADM2 gene and growth traits, and our research data indicated the CADM2-CNV may considered as a prospective candidate for the molecular marker-assisted selection breeding of goat growth traits, which conducived to accelerating the genetic amelioration in Chinese goats.
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Affiliation(s)
- Zijie Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Shijie Lyu
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Lijuan Li
- Guizhou University of Engineering Science, Institute of Bijie Test Area, Bijie, Guizhou 551700, People's Republic of China
| | - Eryao Wang
- College of Agriculture and Forestry Engineering, Tongren University, Tongren, Guizhou 554300, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, People's Republic of China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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