1
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Di Stefano N, Ansani A, Schiavio A, Spence C. Prokofiev was (almost) right: A cross-cultural investigation of auditory-conceptual associations in Peter and the Wolf. Psychon Bull Rev 2024:10.3758/s13423-023-02435-7. [PMID: 38267741 DOI: 10.3758/s13423-023-02435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2023] [Indexed: 01/26/2024]
Abstract
Over recent decades, studies investigating cross-modal correspondences have documented the existence of a wide range of consistent cross-modal associations between simple auditory and visual stimuli or dimensions (e.g., pitch-lightness). Far fewer studies have investigated the association between complex and realistic auditory stimuli and visually presented concepts (e.g., musical excerpts-animals). Surprisingly, however, there is little evidence concerning the extent to which these associations are shared across cultures. To address this gap in the literature, two experiments using a set of stimuli based on Prokofiev's symphonic fairy tale Peter and the Wolf are reported. In Experiment 1, 293 participants from several countries and with very different language backgrounds rated the association between the musical excerpts, images and words representing the story's characters (namely, bird, duck, wolf, cat, and grandfather). The results revealed that participants tended to consistently associate the wolf and the bird with the corresponding musical excerpt, while the stimuli of other characters were not consistently matched across participants. Remarkably, neither the participants' cultural background, nor their musical expertise affected the ratings. In Experiment 2, 104 participants were invited to rate each stimulus on eight emotional features. The results revealed that the emotional profiles associated with the music and with the concept of the wolf and the bird were perceived as more consistent between observers than the emotional profiles associated with the music and the concept of the duck, the cat, and the grandpa. Taken together, these findings therefore suggest that certain auditory-conceptual associations are perceived consistently across cultures and may be mediated by emotional associations.
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Affiliation(s)
- Nicola Di Stefano
- National Research Council, Institute of Cognitive Sciences and Technologies, Rome, Italy.
| | - Alessandro Ansani
- Centre of Excellence in Music, Mind, Body and Brain, Department of Music, Art and Culture Studies, Jyväskylä, Finland
| | - Andrea Schiavio
- University of York, School of Arts and Creative Technologies, York, UK
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2
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McKinley GL, Peterson DJ. Using objective measures to examine the effect of suspect-filler similarity on eyewitness identification performance. Cogn Res Princ Implic 2023; 8:68. [PMID: 37930437 PMCID: PMC10628061 DOI: 10.1186/s41235-023-00522-w] [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: 03/19/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023] Open
Abstract
When selecting fillers to include in a police lineup, one must consider the level of similarity between the suspect and potential fillers. In order to reduce misidentifications, an innocent suspect should not stand out. Therefore, it is important that the fillers share some degree of similarity. Importantly, increasing suspect-filler similarity too much will render the task too difficult reducing correct identifications of a guilty suspect. Determining how much similarity yields optimal identification performance is the focus of the proposed study. Extant research on lineup construction has provided somewhat mixed results. In part, this is likely due to the subjective nature of similarity, which forces researchers to define similarity in relative terms. In the current study, we manipulate suspect-filler similarity via a multidimensional scaling model constructed using objective facial measurements. In doing so, we test the "propitious heterogeneity" and the diagnostic-feature-detection hypotheses which predict an advantage of lineups with low-similarity fillers in terms of discriminability. We found that filler similarity did not affect discriminability. We discuss limitations and future directions.
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3
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How does searching for faces among similar-looking distractors affect distractor memory? Mem Cognit 2023:10.3758/s13421-023-01405-7. [PMID: 36849759 DOI: 10.3758/s13421-023-01405-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 03/01/2023]
Abstract
Prior research has shown that searching for multiple targets in a visual search task enhances distractor memory in a subsequent recognition test. Three non-mutually exclusive accounts have been offered to explain this phenomenon. The mental comparison hypothesis states that searching for multiple targets requires participants to make more mental comparisons between the targets and the distractors, which enhances distractor memory. The attention allocation hypothesis states that participants allocate more attention to distractors because a multiple-target search cue leads them to expect a more difficult search. Finally, the partial match hypothesis states that searching for multiple targets increases the amount of featural overlap between targets and distractors, which necessitates greater attention in order to reject each distractor. In two experiments, we examined these hypotheses by manipulating visual working memory (VWM) load and target-distractor similarity of AI-generated faces in a visual search (i.e., RSVP) task. Distractor similarity was manipulated using a multidimensional scaling model constructed from facial landmarks and other metadata of each face. In both experiments, distractors from multiple-target searches were recognized better than distractors from single-target searches. Experiment 2 additionally revealed that increased target-distractor similarity during search improved distractor recognition memory, consistent with the partial match hypothesis.
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4
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McKinley GL, Peterson DJ. Using objective measures to examine the effect of suspect-filler similarity on eyewitness identification performance. Cogn Res Princ Implic 2022; 7:95. [PMID: 36271974 PMCID: PMC9588117 DOI: 10.1186/s41235-022-00442-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
When selecting fillers to include in a police lineup, one must consider the level of similarity between the suspect and potential fillers. In order to reduce misidentifications, an innocent suspect should not stand out. Therefore, it is important that the fillers share some degree of similarity. Importantly, increasing suspect-filler similarity too much will render the task too difficult reducing correct identifications of a guilty suspect. Determining how much similarity yields optimal identification performance is the focus of the proposed study. Extant research on lineup construction has provided somewhat mixed results. In part, this is likely because similarity is often defined in relative terms due to the subjective nature of similarity. In the current study, we propose an experiment in which we manipulate suspect-filler similarity via a multidimensional scaling model constructed using objective facial measurements. In doing so, we test the "propitious heterogeneity" and the diagnostic-feature-detection hypotheses which predict an advantage of lineups with low similarity fillers in terms of discriminability.
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Affiliation(s)
- Geoffrey L McKinley
- Department of Psychology, Skidmore College, 815 N. Broadway, Saratoga Springs, NY, 12866, USA.
| | - Daniel J Peterson
- Department of Psychology, Skidmore College, 815 N. Broadway, Saratoga Springs, NY, 12866, USA
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5
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Tanaka T, Maeda Y, Suhaimi N, Tsuneoka C, Nonoyama T, Yoshino T, Kato N, Lauersen KJ. Intron-mediated enhancement of transgene expression in the oleaginous diatom Fistulifera solaris towards bisabolene production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Lau JSH, Pashler H, Brady TF. Target templates in low target-distractor discriminability visual search have higher resolution, but the advantage they provide is short-lived. Atten Percept Psychophys 2021; 83:1435-1454. [PMID: 33409902 PMCID: PMC7787128 DOI: 10.3758/s13414-020-02213-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
When you search repeatedly for a set of items among very similar distractors, does that make you more efficient in locating the targets? To address this, we had observers search for two categories of targets among the same set of distractors across trials. Visual and conceptual similarity of the stimuli were validated with a multidimensional scaling analysis, and separately using a deep neural network model. After a few blocks of visual search trials, the distractor set was replaced. In three experiments, we manipulated the level of discriminability between the targets and distractors before and after the distractors were replaced. Our results suggest that in the presence of repeated distractors, observers generally become more efficient. However, the difficulty of the search task does impact how efficient people are when the distractor set is replaced. Specifically, when the training is easy, people are more impaired in a difficult transfer test. We attribute this effect to the precision of the target template generated during training. In particular, a coarse target template is created when the target and distractors are easy to discriminate. These coarse target templates do not transfer well in a context with new distractors. This suggests that learning with more distinct targets and distractors can result in lower performance when context changes, but observers recover from this effect quickly (within a block of search trials).
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Affiliation(s)
- Jonas Sin-Heng Lau
- Department of Psychology, University of California, San Diego, California 92093-0109, USA
| | - Hal Pashler
- Department of Psychology, University of California, San Diego, California 92093-0109, USA
| | - Timothy F Brady
- Department of Psychology, University of California, San Diego, California 92093-0109, USA.
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7
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Knopp M, Stockhorst S, van der Giezen M, Garg SG, Gould SB. The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3. Genome Biol Evol 2021; 13:6248096. [PMID: 33892498 PMCID: PMC8220308 DOI: 10.1093/gbe/evab085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2021] [Indexed: 12/22/2022] Open
Abstract
The identification of the asgard archaea has fueled speculations regarding the nature of the archaeal host in eukaryogenesis and its level of complexity prior to endosymbiosis. Here, we analyzed the coding capacity of 150 eukaryotes, 1,000 bacteria, and 226 archaea, including the only cultured member of the asgard archaea. Clustering methods that consistently recover endosymbiotic contributions to eukaryotic genomes recover an asgard archaeal-unique contribution of a mere 0.3% to protein families present in the last eukaryotic common ancestor, while simultaneously suggesting that this group's diversity rivals that of all other archaea combined. The number of homologs shared exclusively between asgard archaea and eukaryotes is only 27 on average. This tiny asgard archaeal-unique contribution to the root of eukaryotic protein families questions claims that archaea evolved complexity prior to eukaryogenesis. Genomic and cellular complexity remains a eukaryote-specific feature and is best understood as the archaeal host's solution to housing an endosymbiont.
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Affiliation(s)
- Michael Knopp
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | - Simon Stockhorst
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | | | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Germany
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8
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Lim CS, Weinstein BN, Roy SW, Brown CM. Analysis of fungal genomes reveals commonalities of intron gain or loss and functions in intron-poor species. Mol Biol Evol 2021; 38:4166-4186. [PMID: 33772558 PMCID: PMC8476143 DOI: 10.1093/molbev/msab094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Brooke N Weinstein
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Scott W Roy
- Quantitative & Systems Biology, School of Natural Sciences, University of California-Merced, Merced, CA, USA.,Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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9
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Dommel M, Oh J, Huguet-Tapia JC, Guy E, Boulain H, Sugio A, Murugan M, Legeai F, Heck M, Smith CM, White FF. Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons. FRONTIERS IN PLANT SCIENCE 2020; 11:1230. [PMID: 33013944 PMCID: PMC7495047 DOI: 10.3389/fpls.2020.01230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/27/2020] [Indexed: 05/25/2023]
Abstract
Aphids secrete proteins from their stylets that evidence indicates function similar to pathogen effectors for virulence. Here, we describe two small candidate effector gene families of the pea aphid, Acyrthosiphon pisum, that share highly conserved secretory signal peptide coding regions and divergent non-secretory coding sequences derived from miniature exons. The KQY candidate effector family contains eleven members with additional isoforms, generated by alternative splicing. Pairwise comparisons indicate possible four unique KQY families based on coding regions without the secretory signal region. KQY1a, a representative of the family, is encoded by a 968 bp mRNA and a gene that spans 45.7 kbp of the genome. The locus consists of 37 exons, 33 of which are 15 bp or smaller. Additional KQY members, as well as members of the KHI family, share similar features. Differential expression analyses indicate that the genes are expressed preferentially in salivary glands. Proteomic analysis on salivary glands and saliva revealed 11 KQY members in salivary proteins, and KQY1a was detected in an artificial diet solution after aphid feeding. A single KQY locus and two KHI loci were identified in Myzus persicae, the peach aphid. Of the genes that can be anchored to chromosomes, loci are mostly scattered throughout the genome, except a two-gene region (KQY4/KQY6). We propose that the KQY family expanded in A. pisum through combinatorial assemblies of a common secretory signal cassette and novel coding regions, followed by classical gene duplication and divergence.
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Affiliation(s)
- Matthew Dommel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Endrick Guy
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Hélène Boulain
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Marimuthu Murugan
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Fabrice Legeai
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Michelle Heck
- USDA-ARS, Cornell University, Ithaca, NY, United States
| | - C. Michael Smith
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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10
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Sulakhe D, D'Souza M, Wang S, Balasubramanian S, Athri P, Xie B, Canzar S, Agam G, Gilliam TC, Maltsev N. Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. Brief Bioinform 2020; 20:1754-1768. [PMID: 29931155 DOI: 10.1093/bib/bby047] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
In recent years, the emphasis of scientific inquiry has shifted from whole-genome analyses to an understanding of cellular responses specific to tissue, developmental stage or environmental conditions. One of the central mechanisms underlying the diversity and adaptability of the contextual responses is alternative splicing (AS). It enables a single gene to encode multiple isoforms with distinct biological functions. However, to date, the functions of the vast majority of differentially spliced protein isoforms are not known. Integration of genomic, proteomic, functional, phenotypic and contextual information is essential for supporting isoform-based modeling and analysis. Such integrative proteogenomics approaches promise to provide insights into the functions of the alternatively spliced protein isoforms and provide high-confidence hypotheses to be validated experimentally. This manuscript provides a survey of the public databases supporting isoform-based biology. It also presents an overview of the potential global impact of AS on the human canonical gene functions, molecular interactions and cellular pathways.
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Affiliation(s)
- Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA
| | - Sandhya Balasubramanian
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Genentech, Inc. 1 DNA Way, Mail Stop: 35-6J, South San Francisco, CA, USA
| | - Prashanth Athri
- Department of Computer Science and Engineering, Amrita School of Engineering, Bengaluru, Amrita Vishwa Vidyapeetham, Kasavanahalli, Carmelaram P.O., Bengaluru, Karnataka, India
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - Stefan Canzar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, USA.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gady Agam
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, USA.,Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, USA
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11
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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12
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The spatial arrangement method of measuring similarity can capture high-dimensional semantic structures. Behav Res Methods 2020; 52:1906-1928. [DOI: 10.3758/s13428-020-01362-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 PMCID: PMC6944119 DOI: 10.7717/peerj.8344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 01/15/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium.,Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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14
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 DOI: 10.7287/peerj.preprints.27806v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 05/23/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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15
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Luo F, Yin M, Mo X, Sun C, Wu Q, Zhu B, Xiang M, Wang J, Wang Y, Li J, Zhang T, Xu B, Zheng H, Feng Z, Hu W. An improved genome assembly of the fluke Schistosoma japonicum. PLoS Negl Trop Dis 2019; 13:e0007612. [PMID: 31390359 PMCID: PMC6685614 DOI: 10.1371/journal.pntd.0007612] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/08/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis, which is a significant cause of morbidity in China and the Philippines. A single draft genome was available for S. japonicum, yet this assembly is very fragmented and only covers 90% of the genome, which make it difficult to be applied as a reference in functional genome analysis and genes discovery. FINDINGS In this study, we present a high-quality assembly of the fluke S. japonicum genome by combining 20 G (~53X) long single molecule real time sequencing reads with 80 G (~ 213X) Illumina paired-end reads. This improved genome assembly is approximately 370.5 Mb, with contig and scaffold N50 length of 871.9 kb and 1.09 Mb, representing 142.4-fold and 6.2-fold improvement over the released WGS-based assembly, respectively. Additionally, our assembly captured 85.2% complete and 4.6% partial eukaryotic Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 46.80% of the genome, and 10,089 of the protein-coding genes were predicted from the improved genome, of which 96.5% have been functionally annotated. Lastly, using the improved assembly, we identified 20 significantly expanded gene families in S. japonicum, and those genes were primarily enriched in functions of proteolysis and protein glycosylation. CONCLUSIONS Using the combination of PacBio and Illumina Sequencing technologies, we provided an improved high-quality genome of S. japonicum. This improved genome assembly, as well as the annotation, will be useful for the comparative genomics of the flukes and more importantly facilitate the molecular studies of this important parasite in the future.
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Affiliation(s)
- Fang Luo
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Mingbo Yin
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Xiaojin Mo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Chengsong Sun
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qunfeng Wu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Bingkuan Zhu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Manyu Xiang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jipeng Wang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yi Wang
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jian Li
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zheng Feng
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
| | - Wei Hu
- Department of infectious diseases, Huashan Hospital, State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory of Parasite and Vector Biology of China Ministry of Health, WHO Collaborating Centre for Tropical Diseases, Joint Research Laboratory of Genetics and Ecology on Parasite-host Interaction, Chinese Center for Disease Control and Prevention & Fudan University, Shanghai, China
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16
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Spitzer L, Binkofski F, Willmes K, Bruehl S. Executive functions in aphasia: A novel aphasia screening for cognitive flexibility in everyday communication. Neuropsychol Rehabil 2019; 30:1701-1719. [DOI: 10.1080/09602011.2019.1601572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- L. Spitzer
- Clinical and Cognitive Neurosciences, Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - F. Binkofski
- Clinical and Cognitive Neurosciences, Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - K. Willmes
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - S. Bruehl
- Neuroscience and Aphasia Research Unit, Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
- Clinical and Cognitive Neurosciences, Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
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17
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Egg-laying decisions based on olfactory cues enhance offspring fitness in Stomoxys calcitrans L. (Diptera: Muscidae). Sci Rep 2019; 9:3850. [PMID: 30846772 PMCID: PMC6405918 DOI: 10.1038/s41598-019-40479-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/11/2019] [Indexed: 11/08/2022] Open
Abstract
Selection of oviposition substrate is critical in holometabolous insects. Female stable flies, Stomoxys calcitrans, locate and select vertebrate herbivore dung in which they lay their eggs. However, the preference for vertebrate herbivore dung by S. calcitrans females, its fitness consequences for offspring, and the semiochemicals used to locate and select oviposition substrates remain unclear. Using oviposition choice tests and life table bioassays we found that gravid female S. calcitrans prefer to oviposit on donkey and sheep dung, which also improves the performance of their offspring. GC-MS analysis followed by random forest classification identified β-citronellene and carvone as the most important predictive volatile organic compounds of donkey and sheep dung, respectively. In multiple choice oviposition bioassays, S. calcitrans laid more eggs in wet sand containing β-citronellene and carvone than in other treatments. The attractiveness of these compounds was confirmed in a field trial, with traps baited with β-citronellene and carvone catching more S. calcitrans. We conclude that gravid female S. calcitrans use semiochemical cues to choose oviposition substrates that maximise offspring fitness.
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18
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Wang SE, Amir AS, Nguyen T, Poole AM, Simoes-Barbosa A. Spliceosomal introns in Trichomonas vaginalis revisited. Parasit Vectors 2018; 11:607. [PMID: 30482228 PMCID: PMC6260720 DOI: 10.1186/s13071-018-3196-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The human protozoan parasite Trichomonas vaginalis is an organism of interest for understanding eukaryotic evolution. Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: only 62 putative introns have been annotated in this genome, and little or no experimental evidence exists to back up these predictions. Results This study revisited the 62 annotated introns of T. vaginalis derived from the genome sequencing plus previous publications. After experimental validation and a new genome-wide search, we confirmed the presence of introns in 32 genes and 18 others were concluded to be intronless. Sequence analyses classified the validated introns into two types, based on distinctive features such as length and conservation of splice site motifs. Conclusions Our study provides an updated list of intron-containing genes in the genome of T. vaginalis. Our findings suggests the existence of two intron ‘families’ spread among T. vaginalis protein-coding genes. Additional studies are needed to understand the functional separation of these two classes of introns and to assess the existence of further introns in the T. vaginalis genome. Electronic supplementary material The online version of this article (10.1186/s13071-018-3196-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Abdul S Amir
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tai Nguyen
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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19
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Saysani A, Corballis MC, Corballis PM. The colour of words: how dichromats construct a colour space. VISUAL COGNITION 2018. [DOI: 10.1080/13506285.2018.1524804] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Armin Saysani
- School of Psychology and Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Michael C. Corballis
- School of Psychology and Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Paul M. Corballis
- School of Psychology and Centre for Brain Research, The University of Auckland, Auckland, New Zealand
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20
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Grau-Bové X, Ruiz-Trillo I, Irimia M. Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Genome Biol 2018; 19:135. [PMID: 30223879 PMCID: PMC6142364 DOI: 10.1186/s13059-018-1499-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022] Open
Abstract
Background Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode across non-animal eukaryotes, animals have unusually high rates of exon skipping. However, when and how this high prevalence of exon skipping evolved is unknown. Since exon skipping can greatly expand proteomes, answering these questions sheds light on the evolution of higher organismal complexity in metazoans. Results We used RNA-seq data to quantify exon skipping and intron retention frequencies across 65 eukaryotic species, with particular focus on early branching animals and unicellular holozoans. We found that only bilaterians have significantly increased their exon skipping frequencies compared to all other eukaryotic groups. Unlike in other eukaryotes, however, exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving sequences, suggesting that exon skipping involvement in proteome expansion predated the increase in frequency. We also identified architectural features consistently associated with higher exon skipping rates within all studied eukaryotic genomes. Remarkably, these architectures became more prevalent during animal evolution, indicating co-evolution between genome architectures and exon skipping frequencies. Conclusion We suggest that the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes. Electronic supplementary material The online version of this article (10.1186/s13059-018-1499-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. .,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain. .,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
| | - Manuel Irimia
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10-12, 08002, Barcelona, Catalonia, Spain.
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21
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Schaefke B, Sun W, Li YS, Fang L, Chen W. The evolution of posttranscriptional regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1485. [PMID: 29851258 DOI: 10.1002/wrna.1485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Abstract
"DNA makes RNA makes protein." After transcription, mRNAs undergo a series of intertwining processes to be finally translated into functional proteins. The "posttranscriptional" regulation (PTR) provides cells an extended option to fine-tune their proteomes. To meet the demands of complex organism development and the appropriate response to environmental stimuli, every step in these processes needs to be finely regulated. Moreover, changes in these regulatory processes are important driving forces underlying the evolution of phenotypic differences across different species. The major PTR mechanisms discussed in this review include the regulation of splicing, polyadenylation, decay, and translation. For alternative splicing and polyadenylation, we mainly discuss their evolutionary dynamics and the genetic changes underlying the regulatory differences in cis-elements versus trans-factors. For mRNA decay and translation, which, together with transcription, determine the cellular RNA or protein abundance, we focus our discussion on how their divergence coordinates with transcriptional changes to shape the evolution of gene expression. Then to highlight the importance of PTR in the evolution of higher complexity, we focus on their roles in two major phenomena during eukaryotic evolution: the evolution of multicellularity and the division of labor between different cell types and tissues; and the emergence of diverse, often highly specialized individual phenotypes, especially those concerning behavior in eusocial insects. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution Translation > Translation Regulation RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California San Francisco, San Francisco
| | - Yi-Sheng Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China.,Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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22
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Lim CS, T. Wardell SJ, Kleffmann T, Brown CM. The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res 2018; 46:4575-4591. [PMID: 29684192 PMCID: PMC5961209 DOI: 10.1093/nar/gky282] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/28/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Introns in mRNA leaders are common in complex eukaryotes, but often overlooked. These introns are spliced out before translation, leaving exon-exon junctions in the mRNA leaders (leader EEJs). Our multi-omic approach shows that the number of leader EEJs inversely correlates with the main protein translation, as does the number of upstream open reading frames (uORFs). Across the five species studied, the lowest levels of translation were observed for mRNAs with both leader EEJs and uORFs (29%). This class of mRNAs also have ribosome footprints on uORFs, with strong triplet periodicity indicating uORF translation. Furthermore, the positions of both leader EEJ and uORF are conserved between human and mouse. Thus, the uORF, in combination with leader EEJ predicts lower expression for nearly one-third of eukaryotic proteins.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Samuel J T. Wardell
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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23
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Intersectionality of Ethnicity/Race and Gender in the Phenomenology of African American College Students’ Presenting Problems: a Profile Analysis Using Nonmetric Multidimensional Scaling. INTERNATIONAL JOURNAL FOR THE ADVANCEMENT OF COUNSELLING 2018. [DOI: 10.1007/s10447-018-9326-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Vosseberg J, Snel B. Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery. Biol Direct 2017; 12:30. [PMID: 29191215 PMCID: PMC5709842 DOI: 10.1186/s13062-017-0201-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/20/2017] [Indexed: 12/31/2022] Open
Abstract
ᅟ The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Although not fully resolved, recent findings have started to shed some light on how and why the spliceosome originated. In this paper we review how the spliceosome has evolved and discuss its origin and subsequent evolution in light of different general hypotheses on the evolution of complexity. Comparative analyses have established that the catalytic core of this ribonucleoprotein (RNP) complex, as well as the spliceosomal introns, evolved from self-splicing group II introns. Most snRNAs evolved from intron fragments and the essential Prp8 protein originated from the protein that is encoded by group II introns. Proteins that functioned in other RNA processes were added to this core and extensive duplications of these proteins substantially increased the complexity of the spliceosome prior to the eukaryotic diversification. The splicing machinery became even more complex in animals and plants, yet was simplified in eukaryotes with streamlined genomes. Apparently, the spliceosome did not evolve its complexity gradually, but in rapid bursts, followed by stagnation or even simplification. We argue that although both adaptive and neutral evolution have been involved in the evolution of the spliceosome, especially the latter was responsible for the emergence of an enormously complex eukaryotic splicing machinery from simple self-splicing sequences. Reviewers This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Vivek Anantharaman.
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Affiliation(s)
- Julian Vosseberg
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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25
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Koonin EV. Viruses and mobile elements as drivers of evolutionary transitions. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0442. [PMID: 27431520 PMCID: PMC4958936 DOI: 10.1098/rstb.2015.0442] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 12/22/2022] Open
Abstract
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of ‘public goods’. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host–parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions. This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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26
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Grau-Bové X, Torruella G, Donachie S, Suga H, Leonard G, Richards TA, Ruiz-Trillo I. Dynamics of genomic innovation in the unicellular ancestry of animals. eLife 2017; 6:26036. [PMID: 28726632 PMCID: PMC5560861 DOI: 10.7554/elife.26036] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/11/2017] [Indexed: 12/29/2022] Open
Abstract
Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here, we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions. Thus, the foundations of animal genome architecture were laid before the origin of complex multicellularity – highlighting the necessity of a unicellular perspective to understand early animal evolution. DOI:http://dx.doi.org/10.7554/eLife.26036.001 Hundreds of millions of years ago, some single-celled organisms gained the ability to work together and form multicellular organisms. This transition was a major step in evolution and took place at separate times in several parts of the tree of life, including in animals, plants, fungi and algae. Animals are some of the most complex organisms on Earth. Their single-celled ancestors were also quite genetically complex themselves and their genomes (the complete set of the organism’s DNA) already contained many genes that now coordinate the activity of the cells in a multicellular organism. The genome of an animal typically has certain features: it is large, diverse and contains many segments (called introns) that are not genes. By seeing if the single-celled relatives of animals share these traits, it is possible to learn more about when specific genetic features first evolved, and whether they are linked to the origin of animals. Now, Grau-Bové et al. have studied the genomes of several of the animal kingdom’s closest single-celled relatives using a technique called whole genome sequencing. This revealed that there was a period of rapid genetic change in the single-celled ancestors of animals during which their genes became much more diverse. Another ‘explosion’ of diversity happened after animals had evolved. Furthermore, the overall amount of the genomic content inside cells and the number of introns found in the genome rapidly increased in separate, independent events in both animals and their single-celled ancestors. Future research is needed to investigate whether other multicellular life forms – such as plants, fungi and algae – originated in the same way as animal life. Understanding how the genetic material of animals evolved also helps us to understand the genetic structures that affect our health. For example, genes that coordinate the behavior of cells (and so are important for multicellular organisms) also play a role in cancer, where cells break free of this regulation to divide uncontrollably. DOI:http://dx.doi.org/10.7554/eLife.26036.002
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Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Barcelona, Catalonia, Spain
| | - Guifré Torruella
- Unité d'Ecologie, Systématique et Evolution, Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Stuart Donachie
- Department of Microbiology, University of Hawai'i at Mānoa, Honolulu, United States.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawai'i at Mānoa, Honolulu, United States
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Guy Leonard
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Thomas A Richards
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Barcelona, Catalonia, Spain.,ICREA, Passeig Lluís Companys, Barcelona, Catalonia, Spain
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Kruppa J, Jung K. Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. BMC Bioinformatics 2017; 18:232. [PMID: 28464790 PMCID: PMC5414140 DOI: 10.1186/s12859-017-1645-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Analyses of molecular high-throughput data often lack in robustness, i.e. results are very sensitive to the addition or removal of a single observation. Therefore, the identification of extreme observations is an important step of quality control before doing further data analysis. Standard outlier detection methods for univariate data are however not applicable, since the considered data are high-dimensional, i.e. multiple hundreds or thousands of features are observed in small samples. Usually, outliers in high-dimensional data are solely detected by visual inspection of a graphical representation of the data by the analyst. Typical graphical representation for high-dimensional data are hierarchical cluster tree or principal component plots. Pure visual approaches depend, however, on the individual judgement of the analyst and are hard to automate. Existing methods for automated outlier detection are only dedicated to data of a single experimental groups. Results In this work we propose to use bagplots, the 2-dimensional extension of the boxplot, to automatically identify outliers in the subspace of the first two principal components of the data. Furthermore, we present for the first time the gemplot, the 3-dimensional extension of boxplot and bagplot, which can be used in the subspace of the first three principal components. Bagplot and gemplot surround the regular observations with convex hulls and observations outside these hulls are regarded as outliers. The convex hulls are determined separately for the observations of each experimental group while the observations of all groups can be displayed in the same subspace of principal components. We demonstrate the usefulness of this approach on multiple sets of artificial data as well as one set of gene expression data from a next-generation sequencing experiment, and compare the new method to other common approaches. Furthermore, we provide an implementation of the gemplot in the package ‘gemPlot’ for the R programming environment. Conclusions Bagplots and gemplots in subspaces of principal components are useful for automated and objective outlier identification in high-dimensional data from molecular high-throughput experiments. A clear advantage over other methods is that multiple experimental groups can be displayed in the same figure although outlier detection is performed for each individual group. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1645-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jochen Kruppa
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, Hannover, D-30559, Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, Hannover, D-30559, Germany.
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28
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Abstract
Repeating sequences generated from RNA gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. A simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-Ψ-β-barrel (DPBB) type RNA polymerases (RNAPs), general transcription factors (GTFs), and promoters. A general rule that emerges is that biological complexity that arises through generation of repeats is often bounded by solubility and closure (i.e., to form a pseudo-dimer or a barrel). Because the first DNA genomes were replicated by DNA template-dependent RNA synthesis followed by RNA template-dependent DNA synthesis via reverse transcriptase, the first DNA replication origins were initially 2-DPBB type RNAP promoters. A simplifying model for evolution of promoters/replication origins via repetition of core promoter elements is proposed. The model can explain why Pribnow boxes in bacterial transcription (i.e., (-12)TATAATG(-6)) so closely resemble TATA boxes (i.e., (-31)TATAAAAG(-24)) in archaeal/eukaryotic transcription. The evolution of anchor DNA sequences in bacterial (i.e., (-35)TTGACA(-30)) and archaeal (BRE(up); BRE for TFB recognition element) promoters is potentially explained. The evolution of BRE(down) elements of archaeal promoters is potentially explained.
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Affiliation(s)
- Zachary F Burton
- a Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI , USA
| | - Kristopher Opron
- b Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - Guowei Wei
- b Department of Mathematics , Michigan State University , E. Lansing , MI , USA
| | - James H Geiger
- c Department of Chemistry , Michigan State University , E. Lansing , MI , USA
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29
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Biswas K, Chakraborty S, Podder S, Ghosh TC. Insights into the dN/dS ratio heterogeneity between brain specific genes and widely expressed genes in species of different complexity. Genomics 2016; 108:11-7. [DOI: 10.1016/j.ygeno.2016.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 01/07/2023]
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30
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Mühlhausen S, Hellkamp M, Kollmar M. GenePainter v. 2.0 resolves the taxonomic distribution of intron positions. ACTA ACUST UNITED AC 2014; 31:1302-4. [PMID: 25434742 DOI: 10.1093/bioinformatics/btu798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 11/25/2014] [Indexed: 11/12/2022]
Abstract
UNLABELLED Conserved intron positions in eukaryotic genes can be used to reconstruct phylogenetic trees, to resolve ambiguous subfamily relationships in protein families and to infer the history of gene families. This version of GenePainter facilitates working with large datasets through options to select specific subsets for analysis and visualization, and through providing exhaustive statistics. GenePainter's application in phylogenetic analyses is considerably extended by the newly implemented integration of the exon-intron pattern conservation with phylogenetic trees. AVAILABILITY AND IMPLEMENTATION The software along with detailed documentation is available at http://www.motorprotein.de/genepainter and as Supplementary Material. CONTACT mako@nmr.mpibpc.mpg.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marcel Hellkamp
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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31
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The relative ages of eukaryotes and akaryotes. J Mol Evol 2014; 79:228-39. [PMID: 25179144 DOI: 10.1007/s00239-014-9643-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022]
Abstract
The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.
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32
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Abstract
In this work we review the current knowledge on the prehistory, origins, and evolution of spliceosomal introns. First, we briefly outline the major features of the different types of introns, with particular emphasis on the nonspliceosomal self-splicing group II introns, which are widely thought to be the ancestors of spliceosomal introns. Next, we discuss the main scenarios proposed for the origin and proliferation of spliceosomal introns, an event intimately linked to eukaryogenesis. We then summarize the evidence that suggests that the last eukaryotic common ancestor (LECA) had remarkably high intron densities and many associated characteristics resembling modern intron-rich genomes. From this intron-rich LECA, the different eukaryotic lineages have taken very distinct evolutionary paths leading to profoundly diverged modern genome structures. Finally, we discuss the origins of alternative splicing and the qualitative differences in alternative splicing forms and functions across lineages.
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Affiliation(s)
- Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S3E1, Canada
| | - Scott William Roy
- Department of Biology, San Francisco State University, San Francisco, California 94132
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33
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Gorlova O, Fedorov A, Logothetis C, Amos C, Gorlov I. Genes with a large intronic burden show greater evolutionary conservation on the protein level. BMC Evol Biol 2014; 14:50. [PMID: 24629165 PMCID: PMC3995522 DOI: 10.1186/1471-2148-14-50] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 03/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The existence of introns in eukaryotic genes is believed to provide an evolutionary advantage by increasing protein diversity through exon shuffling and alternative splicing. However, this eukaryotic feature is associated with the necessity of exclusion of intronic sequences, which requires considerable energy expenditure and can lead to splicing errors. The relationship between intronic burden and evolution is poorly understood. The goal of this study was to analyze the relationship between the intronic burden and the level of evolutionary conservation of the gene. RESULTS We found a positive correlation between the level of evolutionary conservation of a gene and its intronic burden. The level of evolutionary conservation was estimated using the conservation index (CI). The CI value was determined on the basis of the most distant ortholog of the human protein sequence and ranged from 0 (the gene was unique to the human genome) to 9 (an ortholog of the human gene was detected in plants). In multivariable model, both the number of introns and total intron size remained significant predictors of CI. We also found that the number of alternative splice variants was positively correlated with CI.The expression level of a gene was negatively correlated with the number of introns and total size of intronic region. Genes with a greater intronic burden had lower density of missense and nonsense mutations in the coding regions of the gene, which suggests that they are under a stronger pressure from purifying selection. CONCLUSIONS We identified a positive association between intronic burden and CI. One of the possible explanations of this is the idea of a cost-benefits balance. Evolutionarily conserved (functionally important) genes can "afford" the negative consequences of maintaining multiple introns because these consequences are outweighed by the benefit of maintaining the gene. Evolutionarily conserved and functionally important genes may use introns to create novel splice variants to tune the gene function to developmental stage and tissue type.
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Affiliation(s)
| | | | | | | | - Ivan Gorlov
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon 03766, NH, USA.
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34
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Koonin EV, Dolja VV. A virocentric perspective on the evolution of life. Curr Opin Virol 2013; 3:546-57. [PMID: 23850169 PMCID: PMC4326007 DOI: 10.1016/j.coviro.2013.06.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 06/12/2013] [Accepted: 06/13/2013] [Indexed: 01/12/2023]
Abstract
Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous and might substantially exceed the diversity of cellular organisms. Unlike cellular organisms with their uniform replication-expression scheme, viruses possess either RNA or DNA genomes and exploit all conceivable replication-expression strategies. Although viruses extensively exchange genes with their hosts, there exists a set of viral hallmark genes that are shared by extremely diverse groups of viruses to the exclusion of cellular life forms. Coevolution of viruses and host defense systems is a key aspect in the evolution of both viruses and cells, and viral genes are often recruited for cellular functions. Together with the fundamental inevitability of the emergence of genomic parasites in any evolving replicator system, these multiple lines of evidence reveal the central role of viruses in the entire evolution of life.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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35
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Wang L, Stein LD. Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process. BMC Evol Biol 2013; 13:57. [PMID: 23448166 PMCID: PMC3732091 DOI: 10.1186/1471-2148-13-57] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/22/2013] [Indexed: 12/02/2022] Open
Abstract
Background Most eukaryotic genes are interrupted by spliceosomal introns. The evolution of exon-intron structure remains mysterious despite rapid advance in genome sequencing technique. In this work, a novel approach is taken based on the assumptions that the evolution of exon-intron structure is a stochastic process, and that the characteristics of this process can be understood by examining its historical outcome, the present-day size distribution of internal translated exons (exon). Through the combination of simulation and modeling the size distribution of exons in different species, we propose a general random fragmentation process (GRFP) to characterize the evolution dynamics of exon-intron structure. This model accurately predicts the probability that an exon will be split by a new intron and the distribution of novel insertions along the length of the exon. Results As the first observation from this model, we show that the chance for an exon to obtain an intron is proportional to its size to the 3rd power. We also show that such size dependence is nearly constant across gene, with the exception of the exons adjacent to the 5′ UTR. As the second conclusion from the model, we show that intron insertion loci follow a normal distribution with a mean of 0.5 (center of the exon) and a standard deviation of 0.11. Finally, we show that intron insertions within a gene are independent of each other for vertebrates, but are more negatively correlated for non-vertebrate. We use simulation to demonstrate that the negative correlation might result from significant intron loss during evolution, which could be explained by selection against multi-intron genes in these organisms. Conclusions The GRFP model suggests that intron gain is dynamic with a higher chance for longer exons; introns are inserted into exons randomly with the highest probability at the center of the exon. GRFP estimates that there are 78 introns in every 10 kb coding sequences for vertebrate genomes, agreeing with empirical observations. GRFP also estimates that there are significant intron losses in the evolution of non-vertebrate genomes, with extreme cases of around 57% intron loss in Drosophila melanogaster, 28% in Caenorhabditis elegans, and 24% in Oryza sativa.
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Affiliation(s)
- Liya Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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