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Wang J, Tao F, Marowsky NC, Fan C. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes. PLANT PHYSIOLOGY 2016; 172:427-40. [PMID: 27485883 PMCID: PMC5074645 DOI: 10.1104/pp.16.01177] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 08/01/2016] [Indexed: 05/02/2023]
Abstract
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Nicholas C Marowsky
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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Wang J, Tao F, Marowsky NC, Fan C. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes. PLANT PHYSIOLOGY 2016. [PMID: 27485883 DOI: 10.1104/pp.l6.01177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Nicholas C Marowsky
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
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Milligan MJ, Harvey E, Yu A, Morgan AL, Smith DL, Zhang E, Berengut J, Sivananthan J, Subramaniam R, Skoric A, Collins S, Damski C, Morris KV, Lipovich L. Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome. Front Genet 2016; 7:26. [PMID: 27047535 PMCID: PMC4805607 DOI: 10.3389/fgene.2016.00026] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/08/2016] [Indexed: 12/19/2022] Open
Abstract
Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseudo60 (processed and unprocessed, Ensembl 60); two public lncRNA catalogs: Broad Institute, GENCODE v17; NCBI annotated piRNAs; and NHGRI clinical variants. The data sets were retrieved from the UCSC Genome Database using the UCSC Table Browser. We identified 2277 loci containing exon-to-exon overlaps between pseudogenes, both processed and unprocessed, and long non-coding RNA genes. Of these loci we identified 1167 with Genbank EST and full-length cDNA support providing direct evidence of transcription on one or both strands with exon-to-exon overlaps. The analysis converged on 313 pseudogene-lncRNA exon-to-exon overlaps that were bidirectionally supported by both full-length cDNAs and ESTs. In the process of identifying transcribed pseudogenes, we generated a comprehensive, positionally non-redundant encyclopedia of human pseudogenes, drawing upon multiple, and formerly disparate public pseudogene repositories. Collectively, these observations suggest that pseudogenes are pervasively transcribed on both strands and are common drivers of gene regulation.
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Affiliation(s)
- Michael J Milligan
- Center for Molecular Medicine and Genetics, Wayne State University Detroit, MI, USA
| | - Erin Harvey
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Albert Yu
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Ashleigh L Morgan
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Daniela L Smith
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Eden Zhang
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Jonathan Berengut
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Jothini Sivananthan
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Radhini Subramaniam
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Aleksandra Skoric
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Scott Collins
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Caio Damski
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Kevin V Morris
- Department of Biotechnology and Biomedical Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University Detroit, MI, USA
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Abstract
A report on the Wellcome Trust retreat on devising a consensus framework for the validation of novel human protein coding loci, held in Hinxton, U.K., May 11-13, 2015.
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Affiliation(s)
- Elspeth A. Bruford
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and University of Geneva, Faculty of Medicine, CMU, Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Abstract
By definition, pseudogenes are relics of former genes that no longer possess biological functions. Operationally, they are identified based on disruptions of open reading frames (ORFs) or presumed losses of promoter activities. Intriguingly, a recent human proteomic study reported peptides encoded by 107 pseudogenes. These peptides may play currently unrecognized physiological roles. Alternatively, they may have resulted from accidental translations of pseudogene transcripts and possess no function. Comparing between human and macaque orthologs, we show that the nonsynonymous to synonymous substitution rate ratio (ω) is significantly smaller for translated pseudogenes than other pseudogenes. In particular, five of 34 translated pseudogenes amenable to evolutionary analysis have ω values significantly lower than 1, indicative of the action of purifying selection. This and other findings demonstrate that some but not all translated pseudogenes have selected functions at the protein level. Hence, neither ORF disruption nor presence of protein product disproves or proves gene functionality at the protein level.
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Affiliation(s)
- Jinrui Xu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
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Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. G3-GENES GENOMES GENETICS 2015; 5:1721-36. [PMID: 26109357 PMCID: PMC4528329 DOI: 10.1534/g3.115.018929] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase (http://flybase.org). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3′ UTRs (up to 15–18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.
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