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Wang S, Shen Y, Lin Z, Miao Y, Wang C, Zhang W, Zhang Y. New genes driven by segmental duplications share a testis-specific expression pattern in the chromosome-level genome assembly of tree sparrow. Integr Zool 2024; 19:1004-1008. [PMID: 38014459 DOI: 10.1111/1749-4877.12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Based on a chromosome-level genome assembly, a burst of new genes with different structures but a similar testis-specific expression pattern was detected in tree sparrow.
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Affiliation(s)
- Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yue Shen
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Zhaocun Lin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yuquan Miao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Chengqi Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
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2
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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024; 299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
Abstract
Despite being previously regarded as extremely unlikely, the idea that entirely novel protein-coding genes can emerge from non-coding sequences has gradually become accepted over the past two decades. Examples of "de novo origination", resulting in lineage-specific "orphan" genes, lacking coding orthologs, are now produced every year. However, many are likely cases of duplicates that are difficult to recognize. Here, I re-examine the claims and show that four very well-known examples of genes alleged to have emerged completely "from scratch"- FLJ33706 in humans, Goddard in fruit flies, BSC4 in baker's yeast and AFGP2 in codfish-may have plausible evolutionary ancestors in pre-existing genes. The first two are likely highly diverged retrogenes coding for regulatory proteins that have been misidentified as orphans. The antifreeze glycoprotein, moreover, may not have evolved from repetitive non-genic sequences but, as in several other related cases, from an apolipoprotein that could have become pseudogenized before later being reactivated. These findings detract from various claims made about de novo gene birth and show there has been a tendency not to invest the necessary effort in searching for homologs outside of a very limited syntenic or phylostratigraphic methodology. A robust approach is used for improving detection that draws upon similarities, not just in terms of statistical sequence analysis, but also relating to biochemistry and function, to obviate notable failures to identify homologs.
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Hu Qian S, Shi MW, Wang DY, Fear JM, Chen L, Tu YX, Liu HS, Zhang Y, Zhang SJ, Yu SS, Oliver B, Chen ZX. Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster. Brief Bioinform 2023; 24:bbad177. [PMID: 37232385 PMCID: PMC10505420 DOI: 10.1093/bib/bbad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
The volume of ribonucleic acid (RNA)-seq data has increased exponentially, providing numerous new insights into various biological processes. However, due to significant practical challenges, such as data heterogeneity, it is still difficult to ensure the quality of these data when integrated. Although some quality control methods have been developed, sample consistency is rarely considered and these methods are susceptible to artificial factors. Here, we developed MassiveQC, an unsupervised machine learning-based approach, to automatically download and filter large-scale high-throughput data. In addition to the read quality used in other tools, MassiveQC also uses the alignment and expression quality as model features. Meanwhile, it is user-friendly since the cutoff is generated from self-reporting and is applicable to multimodal data. To explore its value, we applied MassiveQC to Drosophila RNA-seq data and generated a comprehensive transcriptome atlas across 28 tissues from embryogenesis to adulthood. We systematically characterized fly gene expression dynamics and found that genes with high expression dynamics were likely to be evolutionarily young and expressed at late developmental stages, exhibiting high nonsynonymous substitution rates and low phenotypic severity, and they were involved in simple regulatory programs. We also discovered that human and Drosophila had strong positive correlations in gene expression in orthologous organs, revealing the great potential of the Drosophila system for studying human development and disease.
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Affiliation(s)
- Sheng Hu Qian
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Meng-Wei Shi
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan-Yang Wang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Justin M Fear
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lu Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xuan Tu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong-Shan Liu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan Zhang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuai-Jie Zhang
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Shan-Shan Yu
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian Oliver
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhen-Xia Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
- Section of Developmental Genomics, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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5
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Fraimovitch E, Hagai T. Promoter evolution of mammalian gene duplicates. BMC Biol 2023; 21:80. [PMID: 37055747 PMCID: PMC10100218 DOI: 10.1186/s12915-023-01590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/06/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Gene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following duplication as well paralog gene divergence in sequence, expression and function have been extensively studied. However, relatively little is known about the evolution of promoter regions of gene duplicates and how they influence gene duplicate divergence. Here, we focus on promoters of paralog genes, comparing their similarity in sequence, in the sets of transcription factors (TFs) that bind them, and in their overall promoter architecture. RESULTS We observe that promoters of recent duplications display higher sequence similarity between them and that sequence similarity rapidly declines between promoters of more ancient paralogs. In contrast, similarity in cis-regulation, as measured by the set of TFs that bind promoters of both paralogs, does not simply decrease with time from duplication and is instead related to promoter architecture-paralogs with CpG Islands (CGIs) in their promoters share a greater fraction of TFs, while CGI-less paralogs are more divergent in their TF binding set. Focusing on recent duplication events and partitioning them by their duplication mechanism enables us to uncover promoter properties associated with gene retention, as well as to characterize the evolution of promoters of newly born genes: In recent retrotransposition-mediated duplications, we observe asymmetry in cis-regulation of paralog pairs: Retrocopy genes are lowly expressed and their promoters are bound by fewer TFs and are depleted of CGIs, in comparison with the original gene copy. Furthermore, looking at recent segmental duplication regions in primates enable us to compare successful retentions versus loss of duplicates, showing that duplicate retention is associated with fewer TFs and with CGI-less promoter architecture. CONCLUSIONS In this work, we profiled promoters of gene duplicates and their inter-paralog divergence. We also studied how their characteristics are associated with duplication time and duplication mechanism, as well as with the fate of these duplicates. These results underline the importance of cis-regulatory mechanisms in shaping the evolution of new genes and their fate following duplication.
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Affiliation(s)
- Evgeny Fraimovitch
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.
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6
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Rabbani M, Zheng X, Manske GL, Vargo A, Shami AN, Li JZ, Hammoud SS. Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses. Annu Rev Genet 2022; 56:339-368. [PMID: 36070560 PMCID: PMC10722372 DOI: 10.1146/annurev-genet-080320-040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a complex differentiation process coordinated spatiotemporally across and along seminiferous tubules. Cellular heterogeneity has made it challenging to obtain stage-specific molecular profiles of germ and somatic cells using bulk transcriptomic analyses. This has limited our ability to understand regulation of spermatogenesis and to integrate knowledge from model organisms to humans. The recent advancement of single-cell RNA-sequencing (scRNA-seq) technologies provides insights into the cell type diversity and molecular signatures in the testis. Fine-grained cell atlases of the testis contain both known and novel cell types and define the functional states along the germ cell developmental trajectory in many species. These atlases provide a reference system for integrated interspecies comparisons to discover mechanistic parallels and to enable future studies. Despite recent advances, we currently lack high-resolution data to probe germ cell-somatic cell interactions in the tissue environment, but the use of highly multiplexed spatial analysis technologies has begun to resolve this problem. Taken together, recent single-cell studies provide an improvedunderstanding of gametogenesis to examine underlying causes of infertility and enable the development of new therapeutic interventions.
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Affiliation(s)
- Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Xianing Zheng
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Gabe L Manske
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander Vargo
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Adrienne N Shami
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA;
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Urology, University of Michigan, Ann Arbor, Michigan, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
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Huang Y, Shang R, Lu GA, Zeng W, Huang C, Zou C, Tang T. Spatiotemporal Regulation of a Single Adaptively Evolving Trans-Regulatory Element Contributes to Spermatogenetic Expression Divergence in Drosophila. Mol Biol Evol 2022; 39:6605656. [PMID: 35687719 PMCID: PMC9254010 DOI: 10.1093/molbev/msac127] [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] [Indexed: 11/25/2022] Open
Abstract
Due to extensive pleiotropy, trans-acting elements are often thought to be evolutionarily constrained. While the impact of trans-acting elements on gene expression evolution has been extensively studied, relatively little is understood about the contribution of a single trans regulator to interspecific expression and phenotypic divergence. Here, we disentangle the effects of genomic context and miR-983, an adaptively evolving young microRNA, on expression divergence between Drosophila melanogaster and D. simulans. We show miR-983 effects promote interspecific expression divergence in testis despite its antagonism with the often-predominant context effects. Single-cyst RNA-seq reveals that distinct sets of genes gain and lose miR-983 influence under disruptive or diversifying selection at different stages of spermatogenesis, potentially helping minimize antagonistic pleiotropy. At the round spermatid stage, the effects of miR-983 are weak and distributed, coincident with the transcriptome undergoing drastic expression changes. Knocking out miR-983 causes reduced sperm length with increased within-individual variation in D. melanogaster but not in D. simulans, and the D. melanogaster knockout also exhibits compromised sperm defense ability. Our results provide empirical evidence for the resolution of antagonistic pleiotropy and also have broad implications for the function and evolution of new trans regulators.
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Affiliation(s)
- Yumei Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Rui Shang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Guang-An Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Weishun Zeng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Chenglong Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Chuangchao Zou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong Province, China
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Raxwal VK, Singh S, Agarwal M, Riha K. Transcriptional and post-transcriptional regulation of young genes in plants. BMC Biol 2022; 20:134. [PMID: 35676681 PMCID: PMC9178820 DOI: 10.1186/s12915-022-01339-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background New genes continuously emerge from non-coding DNA or by diverging from existing genes, but most of them are rapidly lost and only a few become fixed within the population. We hypothesized that young genes are subject to transcriptional and post-transcriptional regulation to limit their expression and minimize their exposure to purifying selection. Results We performed a protein-based homology search across the tree of life to determine the evolutionary age of protein-coding genes present in the rice genome. We found that young genes in rice have relatively low expression levels, which can be attributed to distal enhancers, and closed chromatin conformation at their transcription start sites (TSS). The chromatin in TSS regions can be re-modeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis tend to be targeted by nonsense-mediated RNA decay, presenting another layer of regulation limiting their expression. Conclusions These data suggest that transcriptional and post-transcriptional mechanisms contribute to the conditional expression of young genes, which may alleviate purging selection while providing an opportunity for phenotypic exposure and functionalization. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01339-7.
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Affiliation(s)
- Vivek Kumar Raxwal
- Department of Botany, University of Delhi, Delhi, 110007, India. .,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
| | - Somya Singh
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Manu Agarwal
- Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Karel Riha
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
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Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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10
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Cherezov RO, Vorontsova JE, Simonova OB. The Phenomenon of Evolutionary “De Novo Generation” of Genes. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Su Q, He H, Zhou Q. On the Origin and Evolution of Drosophila New Genes during Spermatogenesis. Genes (Basel) 2021; 12:1796. [PMID: 34828402 PMCID: PMC8621406 DOI: 10.3390/genes12111796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
The origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testes and avoid the X chromosome, presumably because of meiotic sex chromosome inactivation (MSCI). Here, we analyze the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared with their parental copies, probably due to the more intensive sperm competition or sexual conflict. Our results dissect the complex factors including age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testes, and identify new gene cases that show divergent cell-level expression patterns from their progenitors for future functional studies.
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Affiliation(s)
- Qianwei Su
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (Q.S.); (H.H.)
| | - Huangyi He
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (Q.S.); (H.H.)
| | - Qi Zhou
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; (Q.S.); (H.H.)
- Department of Neuroscience and Developmental Biology, University of Vienna, 1030 Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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Witt E, Svetec N, Benjamin S, Zhao L. Transcription Factors Drive Opposite Relationships between Gene Age and Tissue Specificity in Male and Female Drosophila Gonads. Mol Biol Evol 2021; 38:2104-2115. [PMID: 33481021 PMCID: PMC8097261 DOI: 10.1093/molbev/msab011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolutionarily young genes are usually preferentially expressed in the testis across species. Although it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using Drosophila gene expression data, we confirmed previous findings that younger genes are disproportionately testis biased and older genes are disproportionately ovary biased. We found that the relationship between gene age and expression is stronger in the ovary than any other tissue and weakest in testis. We performed ATAC-seq on Drosophila testis and found that although genes of all ages are more likely to have open promoter chromatin in testis than in ovary, promoter chromatin alone does not explain the ovary bias of older genes. Instead, we found that upstream transcription factor (TF) expression is highly predictive of gene expression in ovary but not in testis. In the ovary, TF expression is more predictive of gene expression than open promoter chromatin, whereas testis gene expression is similarly influenced by both TF expression and open promoter chromatin. We propose that the testis is uniquely able to express younger genes controlled by relatively few TFs, whereas older genes with more TF partners are broadly expressed with peak expression most likely in the ovary. The testis allows widespread baseline expression that is relatively unresponsive to regulatory changes, whereas the ovary transcriptome is more responsive to trans-regulation and has a higher ceiling for gene expression.
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Affiliation(s)
- Evan Witt
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Sigi Benjamin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
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Gui Q, Deng S, Zhou Z, Cao W, Zhang X, Shi W, Cai X, Jiang W, Cui Z, Hu Z, Chen X. Transcriptome Analysis in Yeast Reveals the Externality of Position Effects. Mol Biol Evol 2021; 38:3294-3307. [PMID: 33871622 PMCID: PMC8321525 DOI: 10.1093/molbev/msab104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activity of a gene newly integrated into a chromosome depends on the genomic context of the integration site. This “position effect” has been widely reported, although the other side of the coin, that is, how integration affects the local chromosomal environment, has remained largely unexplored, as have the mechanism and phenotypic consequences of this “externality” of the position effect. Here, we examined the transcriptome profiles of approximately 250 Saccharomyces cerevisiae strains, each with GFP integrated into a different locus of the wild-type strain. We found that in genomic regions enriched in essential genes, GFP expression tended to be lower, and the genes near the integration site tended to show greater expression reduction. Further joint analysis with public genome-wide histone modification profiles indicated that this effect was associated with H3K4me2. More importantly, we found that changes in the expression of neighboring genes, but not GFP expression, significantly altered the cellular growth rate. As a result, genomic loci that showed high GFP expression immediately after integration were associated with growth disadvantages caused by elevated expression of neighboring genes, ultimately leading to a low total yield of GFP in the long run. Our results were consistent with competition for transcriptional resources among neighboring genes and revealed a previously unappreciated facet of position effects. This study highlights the impact of position effects on the fate of exogenous gene integration and has significant implications for biological engineering and the pathology of viral integration into the host genome.
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Affiliation(s)
- Qian Gui
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shuyun Deng
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - ZhenZhen Zhou
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Waifang Cao
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xin Zhang
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenjun Shi
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiujuan Cai
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Wenbing Jiang
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, Precision Medicine Institute, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Precision Medicine Institute, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoshu Chen
- Department of Biology and Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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Zhang X, Pavlicev M, Jones HN, Muglia LJ. Eutherian-Specific Gene TRIML2 Attenuates Inflammation in the Evolution of Placentation. Mol Biol Evol 2020; 37:507-523. [PMID: 31633784 PMCID: PMC6993854 DOI: 10.1093/molbev/msz238] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Evolution of highly invasive placentation in the stem lineage of eutherians and subsequent extension of pregnancy set eutherians apart from other mammals, that is, marsupials with short-lived placentas, and oviparous monotremes. Recent studies suggest that eutherian implantation evolved from marsupial attachment reaction, an inflammatory process induced by the direct contact of fetal placenta with maternal endometrium after the breakdown of the shell coat, and shortly before the onset of parturition. Unique to eutherians, a dramatic downregulation of inflammation after implantation prevents the onset of premature parturition, and is critical for the maintenance of gestation. This downregulation likely involved evolutionary changes on maternal as well as fetal/placental side. Tripartite-motif family-like2 (TRIML2) only exists in eutherian genomes and shows preferential expression in preimplantation embryos, and trophoblast-derived structures, such as chorion and placental disc. Comparative genomic evidence supports that TRIML2 originated from a gene duplication event in the stem lineage of Eutheria that also gave rise to eutherian TRIML1. Compared with TRIML1, TRIML2 lost the catalytic RING domain of E3 ligase. However, only TRIML2 is induced in human choriocarcinoma cell line JEG3 with poly(I:C) treatment to simulate inflammation during viral infection. Its knockdown increases the production of proinflammatory cytokines and reduces trophoblast survival during poly(I:C) stimulation, while its overexpression reduces proinflammatory cytokine production, supporting TRIML2’s role as a regulatory inhibitor of the inflammatory pathways in trophoblasts. TRIML2’s potential virus-interacting PRY/SPRY domain shows significant signature of selection, suggesting its contribution to the evolution of eutherian-specific inflammation regulation during placentation.
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Affiliation(s)
- Xuzhe Zhang
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH
| | - Mihaela Pavlicev
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH
| | - Helen N Jones
- Division of Pediatric Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH
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Affiliation(s)
- Stephen Branden Van Oss
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
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