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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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Intracellular common gardens reveal niche differentiation in transposable element community during bacterial adaptive evolution. THE ISME JOURNAL 2023; 17:297-308. [PMID: 36434281 PMCID: PMC9860058 DOI: 10.1038/s41396-022-01344-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
The distribution and abundance of transposable elements across the tree of life have significantly shaped the evolution of cellular organisms, but the underlying mechanisms shaping these ecological patterns remain elusive. Here we establish a "common garden" approach to study causal ecological interactions between a xenogeneic conditional lethal sacB gene and the community of transposable insertion sequences (ISs) in a multipartite prokaryote genome. Xenogeneic sacB of low, medium, or high GC content was individually inserted into three replicons of a model bacterium Sinorhizobium fredii, and exhibited replicon- and GC-dependent variation in genetic stability. This variation was largely attributable to multidimensional niche differentiation for IS community members. The transposition efficiency of major active ISs depended on the nucleoid-associated xenogeneic silencer MucR. Experimentally eliminating insertion activity of specific ISs by deleting MucR strongly demonstrated a dominant role of niche differentiation among ISs. This intracellular common garden approach in the experimental evolution context allows not only for evaluating genetic stability of natural and synthetic xenogeneic genes of different sequence signatures in host cells but also for tracking and testing causal relationships in unifying ecological principles in genome ecology.
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Kudraszow NL, Fasano MV. Robust approaches to redundancy analysis. COMMUN STAT-THEOR M 2022. [DOI: 10.1080/03610926.2022.2087882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nadia L. Kudraszow
- Centro de Matemática de La Plata (CMaLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- CONICET, La Plata, Argentina
| | - M. Victoria Fasano
- Centro de Matemática de La Plata (CMaLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Stitzer MC, Anderson SN, Springer NM, Ross-Ibarra J. The genomic ecosystem of transposable elements in maize. PLoS Genet 2021; 17:e1009768. [PMID: 34648488 PMCID: PMC8547701 DOI: 10.1371/journal.pgen.1009768] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/26/2021] [Accepted: 08/10/2021] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.
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Affiliation(s)
- Michelle C. Stitzer
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
| | - Sarah N. Anderson
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jeffrey Ross-Ibarra
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California, United States of America
- Genome Center, University of California, Davis, California, United States of America
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Kremer SC, Linquist S, Saylor B, Elliott TA, Gregory TR, Cottenie K. Transposable element persistence via potential genome-level ecosystem engineering. BMC Genomics 2020; 21:367. [PMID: 32429843 PMCID: PMC7236351 DOI: 10.1186/s12864-020-6763-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The nuclear genomes of eukaryotes vary enormously in size, with much of this variability attributable to differential accumulation of transposable elements (TEs). To date, the precise evolutionary and ecological conditions influencing TE accumulation remain poorly understood. Most previous attempts to identify these conditions have focused on evolutionary processes occurring at the host organism level, whereas we explore a TE ecology explanation. RESULTS As an alternative (or additional) hypothesis, we propose that ecological mechanisms occurring within the host cell may contribute to patterns of TE accumulation. To test this idea, we conducted a series of experiments using a simulated asexual TE/host system. Each experiment tracked the accumulation rate for a given type of TE within a particular host genome. TEs in this system had a net deleterious effect on host fitness, which did not change over the course of experiments. As one might expect, in the majority of experiments TEs were either purged from the genome or drove the host population to extinction. However, in an intriguing handful of cases, TEs co-existed with hosts and accumulated to very large numbers. This tended to occur when TEs achieved a stable density relative to non-TE sequences in the genome (as opposed to reaching any particular absolute number). In our model, the only way to maintain a stable density was for TEs to generate new, inactive copies at a rate that balanced with the production of active (replicating) copies. CONCLUSIONS From a TE ecology perspective, we suggest this could be interpreted as a case of ecosystem engineering within the genome, where TEs persist by creating their own "habitat".
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Affiliation(s)
- Stefan C Kremer
- School of Computer Science, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Stefan Linquist
- Department of Philosophy, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brent Saylor
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - T Ryan Gregory
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Karl Cottenie
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Danielopol DL, Cristescu ME. The contribution of Nicolae Botnariuc to evolutionary biology using systems theory. Genome 2015; 58:iii-vi. [PMID: 26523951 DOI: 10.1139/gen-2015-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Dan L Danielopol
- a Institute of Earth Sciences (Geology and Paleontology), Karl-Franzens-University Graz, Heinrichstrasse 26, A-8010 Graz, Austria
| | - Melania E Cristescu
- b Department of Biology, McGill University, 1205 Docteur Penfield, Stewart Biology Building N6/1, Montreal, QC H3A 1B1, Canada
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Linquist S, Cottenie K, Elliott TA, Saylor B, Kremer SC, Gregory TR. Applying ecological models to communities of genetic elements: the case of neutral theory. Mol Ecol 2015; 24:3232-42. [DOI: 10.1111/mec.13219] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Stefan Linquist
- Department of Philosophy; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - Karl Cottenie
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - Tyler A. Elliott
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - Brent Saylor
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - Stefan C. Kremer
- School of Computer Science; University of Guelph; Guelph Ontario Canada N1G 2W1
| | - T. Ryan Gregory
- Department of Integrative Biology; University of Guelph; Guelph Ontario Canada N1G 2W1
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