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Lang D, Wang X, Liu C, Geng W, Irwin DM, Chen S, Li C, Yu L, Xiao H. Birth-and-death evolution of ribonuclease 9 genes in Cetartiodactyla. SCIENCE CHINA LIFE SCIENCES 2022; 66:1170-1182. [PMID: 36443512 DOI: 10.1007/s11427-022-2195-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022]
Abstract
RNase9 plays a reproductive function and has been recognized as an important member of the ribonuclease (RNase) A superfamily, a gene family that is widely used as a model for molecular evolutionary studies. Here, we identified 178 RNase9 genes from 95 Cetartiodactyla species that represent all four lineages and 21 families of this clade. Unexpectedly, RNase9 experienced an evolutionary scenario of "birth and death" in Ruminantia, and expression analyses showed that duplicated RNase9A and RNase9B genes are expressed in reproductive tissues (epididymis, vas deferens or prostate). This expression pattern combined with the estimate that these genes duplicated during the middle Eocene, a time when Ruminantia become a successful lineage, suggests that the RNase9 gene duplication might have been advantageous for promoting sperm motility and male fertility as an adaptation to climate seasonality changes of this period. In contrast, all RNase9 genes were lost in the Cetacean lineage, which might be associated with their high levels of prostatic lesions and lower reproductive rates as adaptations to a fully aquatic environment and a balance to the demands of ocean resources. This study reveals a complex and intriguing evolutionary history and functional divergence for RNase9 in Cetartiodactyla, providing new insights into the evolution of the RNaseA superfamily and molecular mechanisms for organismal adaptations to the environment.
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Affiliation(s)
- Datian Lang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- Biodiversity Research Center of Wumeng Mountain, Department of Agronomy and Life Science, Zhaotong University, Zhaotong, 657000, China
| | - Xiaoping Wang
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Chunbing Liu
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Weihang Geng
- School of Life Sciences, Yunnan University, Kunming, 650500, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Li Yu
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
| | - Heng Xiao
- School of Life Sciences, Yunnan University, Kunming, 650500, China.
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
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Troskie RL, Faulkner GJ, Cheetham SW. Processed pseudogenes: A substrate for evolutionary innovation: Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. Bioessays 2021; 43:e2100186. [PMID: 34569081 DOI: 10.1002/bies.202100186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element-1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non-functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide-ranging biological and pathological processes. Also see the video abstract here: https://youtu.be/iUY_mteVoPI.
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Affiliation(s)
- Robin-Lee Troskie
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
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Venera-Pontón DE, Driskell AC, De Grave S, Felder DL, Scioli JA, Collin R. Documenting decapod biodiversity in the Caribbean from DNA barcodes generated during field training in taxonomy. Biodivers Data J 2020; 8:e47333. [PMID: 31966024 PMCID: PMC6960234 DOI: 10.3897/bdj.8.e47333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/28/2019] [Indexed: 11/15/2022] Open
Abstract
DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.
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Affiliation(s)
- Dagoberto E. Venera-Pontón
- Smithsonian Tropical Research Institute, Balboa, PanamaSmithsonian Tropical Research InstituteBalboaPanama
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Amy C. Driskell
- Laboratories of Analytical Biology, Department of Invertebrate Zoology, Smithsonian Institution, Washington, D.C., United States of AmericaLaboratories of Analytical Biology, Department of Invertebrate Zoology, Smithsonian InstitutionWashington, D.C.United States of America
| | - Sammy De Grave
- Oxford University Museum of Natural History, Oxford, United KingdomOxford University Museum of Natural HistoryOxfordUnited Kingdom
| | - Darryl L. Felder
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Justin A. Scioli
- University of Louisiana at Lafayette, Lafayette, United States of AmericaUniversity of Louisiana at LafayetteLafayetteUnited States of America
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Balboa, PanamaSmithsonian Tropical Research InstituteBalboaPanama
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Liu G, Liu GJ, Tan JX, Lin H. DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions. Genomics 2018; 111:1167-1175. [PMID: 30055231 DOI: 10.1016/j.ygeno.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/07/2018] [Accepted: 07/15/2018] [Indexed: 12/15/2022]
Abstract
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.
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Affiliation(s)
- Guoqing Liu
- The School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China.
| | - Guo-Jun Liu
- School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia
| | - Jiu-Xin Tan
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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The implication of DNA bending energy for nucleosome positioning and sliding. Sci Rep 2018; 8:8853. [PMID: 29891930 PMCID: PMC5995830 DOI: 10.1038/s41598-018-27247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/24/2018] [Indexed: 11/24/2022] Open
Abstract
Nucleosome not only directly affects cellular processes, such as DNA replication, recombination, and transcription, but also severs as a fundamentally important target of epigenetic modifications. Our previous study indicated that the bending property of DNA is important in nucleosome formation, particularly in predicting the dyad positions of nucleosomes on a DNA segment. Here, we investigated the role of bending energy in nucleosome positioning and sliding in depth to decipher sequence-directed mechanism. The results show that bending energy is a good physical index to predict the free energy in the process of nucleosome reconstitution in vitro. Our data also imply that there are at least 20% of the nucleosomes in budding yeast do not adopt canonical positioning, in which underlying sequences wrapped around histones are structurally symmetric. We also revealed distinct patterns of bending energy profile for distinctly organized chromatin structures, such as well-positioned nucleosomes, fuzzy nucleosomes, and linker regions and discussed nucleosome sliding in terms of bending energy. We proposed that the stability of a nucleosome is positively correlated with the strength of the bending anisotropy of DNA segment, and both accessibility and directionality of nucleosome sliding is likely to be modulated by diverse patterns of DNA bending energy profile.
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