1
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Cuevas-Zuviría B, Garcia AK, Rivier AJ, Rucker HR, Carruthers BM, Kaçar B. Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation. Mol Biol Evol 2024; 41:msae067. [PMID: 38526235 PMCID: PMC11018506 DOI: 10.1093/molbev/msae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.
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Affiliation(s)
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Holly R Rucker
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Kulkarni A, Ewen-Campen B, Terao K, Matsumoto Y, Li Y, Watanabe T, Kao JA, Parhad SS, Ylla G, Mizunami M, Extavour CG. oskar acts with the transcription factor Creb to regulate long-term memory in crickets. Proc Natl Acad Sci U S A 2023; 120:e2218506120. [PMID: 37192168 PMCID: PMC10214185 DOI: 10.1073/pnas.2218506120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 03/28/2023] [Indexed: 05/18/2023] Open
Abstract
Novel genes have the potential to drive the evolution of new biological mechanisms, or to integrate into preexisting regulatory circuits and contribute to the regulation of older, conserved biological functions. One such gene, the novel insect-specific gene oskar, was first identified based on its role in establishing the Drosophila melanogaster germ line. We previously showed that this gene likely arose through an unusual domain transfer event involving bacterial endosymbionts and played a somatic role before evolving its well-known germ line function. Here, we provide empirical support for this hypothesis in the form of evidence for a neural role for oskar. We show that oskar is expressed in the adult neural stem cells of a hemimetabolous insect, the cricket Gryllus bimaculatus. In these stem cells, called neuroblasts, oskar is required together with the ancient animal transcription factor Creb to regulate long-term (but not short-term) olfactory memory. We provide evidence that oskar positively regulates Creb, which plays a conserved role in long-term memory across animals, and that oskar in turn may be a direct target of Creb. Together with previous reports of a role for oskar in nervous system development and function in crickets and flies, our results are consistent with the hypothesis that oskar's original somatic role may have been in the insect nervous system. Moreover, its colocalization and functional cooperation with the conserved pluripotency gene piwi in the nervous system may have facilitated oskar's later co-option to the germ line in holometabolous insects.
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Affiliation(s)
- Arpita Kulkarni
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Ben Ewen-Campen
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Kanta Terao
- Graduate School of Life Science, Hokkaido University, Sapporo060-0810, Japan
| | | | - Yaolong Li
- Graduate School of Life Science, Hokkaido University, Sapporo060-0810, Japan
| | - Takayuki Watanabe
- Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
- Research Center for Integrative Evolutionary Science, School of Advanced Sciences, Sokendai-Hayama, Kanagawa240-0193, Japan
| | - Jonchee A. Kao
- Department of Molecular and Cellular Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Swapnil S. Parhad
- University of Massachusetts Chan Medical School, Program in Molecular Medicine, Worcester, MA01655
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
| | - Makoto Mizunami
- Faculty of Science, Hokkaido University, Sapporo060-0810, Japan
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- HHMI, Chevy Chase, MD20815
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3
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Karlowski WM, Varshney D, Zielezinski A. Taxonomically Restricted Genes in Bacillus may Form Clusters of Homologs and Can be Traced to a Large Reservoir of Noncoding Sequences. Genome Biol Evol 2023; 15:7039703. [PMID: 36790099 PMCID: PMC10003748 DOI: 10.1093/gbe/evad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Taxonomically restricted genes (TRGs) are unique for a defined group of organisms and may act as potential genetic determinants of lineage-specific, biological properties. Here, we explore the TRGs of highly diverse and economically important Bacillus bacteria by examining commonly used TRG identification parameters and data sources. We show the significant effects of sequence similarity thresholds, composition, and the size of the reference database in the identification process. Subsequently, we applied stringent TRG search parameters and expanded the identification procedure by incorporating an analysis of noncoding and non-syntenic regions of non-Bacillus genomes. A multiplex annotation procedure minimized the number of false-positive TRG predictions and showed nearly one-third of the alleged TRGs could be mapped to genes missed in genome annotations. We traced the putative origin of TRGs by identifying homologous, noncoding genomic regions in non-Bacillus species and detected sequence changes that could transform these regions into protein-coding genes. In addition, our analysis indicated that Bacillus TRGs represent a specific group of genes mostly showing intermediate sequence properties between genes that are conserved across multiple taxa and nonannotated peptides encoded by open reading frames.
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Affiliation(s)
- Wojciech M Karlowski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Deepti Varshney
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
| | - Andrzej Zielezinski
- Department of Computational Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, Poznan, Poland
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4
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Kimmel J, Schmitt M, Sinner A, Jansen PWTC, Mainye S, Ramón-Zamorano G, Toenhake CG, Wichers-Misterek JS, Cronshagen J, Sabitzki R, Mesén-Ramírez P, Behrens HM, Bártfai R, Spielmann T. Gene-by-gene screen of the unknown proteins encoded on Plasmodium falciparum chromosome 3. Cell Syst 2023; 14:9-23.e7. [PMID: 36657393 DOI: 10.1016/j.cels.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/07/2022] [Accepted: 12/08/2022] [Indexed: 01/19/2023]
Abstract
Taxon-specific proteins are key determinants defining the biology of all organisms and represent prime drug targets in pathogens. However, lacking comparability with proteins in other lineages makes them particularly difficult to study. In malaria parasites, this is exacerbated by technical limitations. Here, we analyzed the cellular location, essentiality, function, and, in selected cases, interactome of all unknown non-secretory proteins encoded on an entire P. falciparum chromosome. The nucleus was the most common localization, indicating that it is a hotspot of parasite-specific biology. More in-depth functional studies with four proteins revealed essential roles in DNA replication and mitosis. The mitosis proteins defined a possible orphan complex and a highly diverged complex needed for spindle-kinetochore connection. Structure-function comparisons indicated that the taxon-specific proteins evolved by different mechanisms. This work demonstrates the feasibility of gene-by-gene screens to elucidate the biology of malaria parasites and reveal critical parasite-specific processes of interest as drug targets.
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Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Marius Schmitt
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Alexej Sinner
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | | | - Sheila Mainye
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Gala Ramón-Zamorano
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Christa Geeke Toenhake
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, the Netherlands
| | | | - Jakob Cronshagen
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Ricarda Sabitzki
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Paolo Mesén-Ramírez
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Hannah Michaela Behrens
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
| | - Richárd Bártfai
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
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5
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Wang Z, Jin Q, Li Q, Ou X, Li S, Liu Z, Huang J. Multiplex PCR Identification of Aspergillus cristatus and Aspergillus chevalieri in Liupao Tea Based on Orphan Genes. Foods 2022; 11:2217. [PMID: 35892804 DOI: 10.3390/foods11152217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/21/2022] Open
Abstract
“Golden flower” fungi in dark tea are beneficial to human health. The rapid identification method of “golden flower” fungi can verify the quality of dark tea products and ensure food safety. In this study, 6 strains were isolated from Liupao tea. They were respectively identified as A. cristatus, A. chevalieri, and A. pseudoglaucus. A. pseudoglaucus was reported as Liupao tea “golden flower” fungus for the first time. It was found that the ITS and BenA sequences of A. cristatus and A. chevalieri were highly conserved. It is difficult to clearly distinguish these closely related species by ITS sequencing. To rapidly identify species, multiplex PCR species-specific primers were designed based on orphan genes screened by comparative genomics analysis. Multiplex PCR results showed that orphan genes were specific and effective for the identification of A. cristatus and A. chevalieri isolated from Liupao tea and Fu brick tea. We confirmed that orphan genes can be used for identification of closely related Aspergillus species. Validation showed that the method is convenient, rapid, robust, sequencing-free, and economical. This promising method will be greatly beneficial to the dark tea processing industry and consumers.
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6
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Jiang M, Li X, Dong X, Zu Y, Zhan Z, Piao Z, Lang H. Research Advances and Prospects of Orphan Genes in Plants. Front Plant Sci 2022; 13:947129. [PMID: 35874010 PMCID: PMC9305701 DOI: 10.3389/fpls.2022.947129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.
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Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Ye Zu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
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7
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Cardoso-Silva CB, Aono AH, Mancini MC, Sforça DA, da Silva CC, Pinto LR, Adams KL, de Souza AP. Taxonomically Restricted Genes Are Associated With Responses to Biotic and Abiotic Stresses in Sugarcane ( Saccharum spp.). Front Plant Sci 2022; 13:923069. [PMID: 35845637 PMCID: PMC9280035 DOI: 10.3389/fpls.2022.923069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological functions difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements and whole-genome duplication occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis revealed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs are involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.
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Affiliation(s)
- Cláudio Benício Cardoso-Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Alexandre Hild Aono
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Melina Cristina Mancini
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Carla Cristina da Silva
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Agronomy Department, Federal University of Viçosa (UFV), Viçosa, Brazil
| | - Luciana Rossini Pinto
- Sugarcane Research Advanced Centre, Agronomic Institute of Campinas (IAC/APTA), Ribeirão Preto, Brazil
| | - Keith L. Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Anete Pereira de Souza
- Center of Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
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8
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Weisman CM, Murray AW, Eddy SR. Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes. Curr Biol 2022; 32:2632-2639.e2. [PMID: 35588743 DOI: 10.1016/j.cub.2022.04.085] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage specific as a result. To evaluate the impact of such "annotation heterogeneity," we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.
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Affiliation(s)
- Caroline M Weisman
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton University, South Drive, Princeton, NJ 08540, USA.
| | - Andrew W Murray
- Department of Molecular & Cellular Biology, Harvard University, Divinity Avenue, Cambridge, MA 02138, USA
| | - Sean R Eddy
- Department of Molecular & Cellular Biology, Harvard University, Divinity Avenue, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Jones Bridge Road, Chevy Chase, MD 20815, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Oxford Street, Cambridge, MA 02138, USA
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9
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Ma D, Lai Z, Ding Q, Zhang K, Chang K, Li S, Zhao Z, Zhong F. Identification, Characterization and Function of Orphan Genes Among the Current Cucurbitaceae Genomes. Front Plant Sci 2022; 13:872137. [PMID: 35599909 PMCID: PMC9114813 DOI: 10.3389/fpls.2022.872137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) that are missing identifiable homologs in other lineages may potentially make contributions to a variety of biological functions. The Cucurbitaceae family consists of a wide range of fruit crops of worldwide or local economic significance. To date, very few functional mechanisms of OGs in Cucurbitaceae are known. In this study, we systematically identified the OGs of eight Cucurbitaceae species using a comparative genomics approach. The content of OGs varied widely among the eight Cucurbitaceae species, ranging from 1.63% in chayote to 16.55% in wax gourd. Genetic structure analysis showed that OGs have significantly shorter protein lengths and fewer exons in Cucurbitaceae. The subcellular localizations of OGs were basically the same, with only subtle differences. Except for aggregation in some chromosomal regions, the distribution density of OGs was higher near the telomeres and relatively evenly distributed on the chromosomes. Gene expression analysis revealed that OGs had less abundantly and highly tissue-specific expression. Interestingly, the largest proportion of these OGs was significantly more tissue-specific expressed in the flower than in other tissues, and more detectable expression was found in the male flower. Functional prediction of OGs showed that (1) 18 OGs associated with male sterility in watermelon; (2) 182 OGs associated with flower development in cucumber; (3) 51 OGs associated with environmental adaptation in watermelon; (4) 520 OGs may help with the large fruit size in wax gourd. Our results provide the molecular basis and research direction for some important mechanisms in Cucurbitaceae species and domesticated crops.
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Affiliation(s)
- Dongna Ma
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Zhengfeng Lai
- Subtropical Agricultural Research Institute, Fujian Academy of Agriculture Sciences, Fujian, China
| | - Qiansu Ding
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Kun Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Kaizhen Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Shuhao Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
| | - Zhizhu Zhao
- College of the Environment and Ecology, Xiamen University, Fujian, China
| | - Fenglin Zhong
- College of Horticulture, Fujian Agriculture and Forestry University, Fujian, China
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10
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Abstract
As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.
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Affiliation(s)
- Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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11
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Yates TB, Feng K, Zhang J, Singan V, Jawdy SS, Ranjan P, Abraham PE, Barry K, Lipzen A, Pan C, Schmutz J, Chen JG, Tuskan GA, Muchero W. The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa. Genome Biol Evol 2021; 13:evab198. [PMID: 34469536 PMCID: PMC8445398 DOI: 10.1093/gbe/evab198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/13/2022] Open
Abstract
Orphan genes are characteristic genomic features that have no detectable homology to genes in any other species and represent an important attribute of genome evolution as sources of novel genetic functions. Here, we identified 445 genes specific to Populus trichocarpa. Of these, we performed deeper reconstruction of 13 orphan genes to provide evidence of de novo gene evolution. Populus and its sister genera Salix are particularly well suited for the study of orphan gene evolution because of the Salicoid whole-genome duplication event which resulted in highly syntenic sister chromosomal segments across the Salicaceae. We leveraged this genomic feature to reconstruct de novo gene evolution from intergenera, interspecies, and intragenomic perspectives by comparing the syntenic regions within the P. trichocarpa reference, then P. deltoides, and finally Salix purpurea. Furthermore, we demonstrated that 86.5% of the putative orphan genes had evidence of transcription. Additionally, we also utilized the Populus genome-wide association mapping panel, a collection of 1,084 undomesticated P. trichocarpa genotypes to further determine putative regulatory networks of orphan genes using expression quantitative trait loci (eQTL) mapping. Functional enrichment of these eQTL subnetworks identified common biological themes associated with orphan genes such as response to stress and defense response. We also identify a putative cis-element for a de novo gene and leverage conserved synteny to describe evolution of a putative transcription factor binding site. Overall, 45% of orphan genes were captured in trans-eQTL networks.
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Affiliation(s)
- Timothy B Yates
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Chongle Pan
- School of Computer Science and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jin-Gui Chen
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
| | - Wellington Muchero
- Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Center for Bioenergy Innovation, Oak Ridge, Tennessee, USA
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12
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Rödelsperger C, Ebbing A, Sharma DR, Okumura M, Sommer RJ, Korswagen HC. Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution. Mol Biol Evol 2021; 38:229-243. [PMID: 32785688 PMCID: PMC8480184 DOI: 10.1093/molbev/msaa207] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence of gene function and expression during development can give rise to phenotypic differences at the level of cells, tissues, organs, and ultimately whole organisms. To gain insights into the evolution of gene expression and novel genes at spatial resolution, we compared the spatially resolved transcriptomes of two distantly related nematodes, Caenorhabditis elegans and Pristionchus pacificus, that diverged 60–90 Ma. The spatial transcriptomes of adult worms show little evidence for strong conservation at the level of single genes. Instead, regional expression is largely driven by recent duplication and emergence of novel genes. Estimation of gene ages across anatomical structures revealed an enrichment of novel genes in sperm-related regions. This provides first evidence in nematodes for the “out of testis” hypothesis that has been previously postulated based on studies in Drosophila and mammals. “Out of testis” genes represent a mix of products of pervasive transcription as well as fast evolving members of ancient gene families. Strikingly, numerous novel genes have known functions during meiosis in Caenorhabditis elegans indicating that even universal processes such as meiosis may be targets of rapid evolution. Our study highlights the importance of novel genes in generating phenotypic diversity and explicitly characterizes gene origination in sperm-related regions. Furthermore, it proposes new functions for previously uncharacterized genes and establishes the spatial transcriptome of Pristionchus pacificus as a catalog for future studies on the evolution of gene expression and function.
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Affiliation(s)
- Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annabel Ebbing
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Devansh Raj Sharma
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands.,Developmental Biology, Department of Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht, The Netherlands
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13
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Abstract
In addition to known genes, much of the human genome is transcribed into RNA. Chance formation of novel open reading frames (ORFs) can lead to the translation of myriad new proteins. Some of these ORFs may yield advantageous adaptive de novo proteins. However, widespread translation of noncoding DNA can also produce hazardous protein molecules, which can misfold and/or form toxic aggregates. The dynamics of how de novo proteins emerge from potentially toxic raw materials and what influences their long-term survival are unknown. Here, using transcriptomic data from human and five other primates, we generate a set of transcribed human ORFs at six conservation levels to investigate which properties influence the early emergence and long-term retention of these expressed ORFs. As these taxa diverged from each other relatively recently, we present a fine scale view of the evolution of novel sequences over recent evolutionary time. We find that novel human-restricted ORFs are preferentially located on GC-rich gene-dense chromosomes, suggesting their retention is linked to pre-existing genes. Sequence properties such as intrinsic structural disorder and aggregation propensity-which have been proposed to play a role in survival of de novo genes-remain unchanged over time. Even very young sequences code for proteins with low aggregation propensities, suggesting that genomic regions with many novel transcribed ORFs are concomitantly less likely to produce ORFs which code for harmful toxic proteins. Our data indicate that the survival of these novel ORFs is largely stochastic rather than shaped by selection.
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Affiliation(s)
- Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Jonathan F Schmitz
- Institute for Evolution and Biodiversity, University of Münster, Germany
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14
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Gao Q, Jin X, Xia E, Wu X, Gu L, Yan H, Xia Y, Li S. Identification of Orphan Genes in Unbalanced Datasets Based on Ensemble Learning. Front Genet 2020; 11:820. [PMID: 33133122 PMCID: PMC7567012 DOI: 10.3389/fgene.2020.00820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/08/2020] [Indexed: 11/13/2022] Open
Abstract
Orphan genes are associated with regulatory patterns, but experimental methods for identifying orphan genes are both time-consuming and expensive. Designing an accurate and robust classification model to detect orphan and non-orphan genes in unbalanced distribution datasets poses a particularly huge challenge. Synthetic minority over-sampling algorithms (SMOTE) are selected in a preliminary step to deal with unbalanced gene datasets. To identify orphan genes in balanced and unbalanced Arabidopsis thaliana gene datasets, SMOTE algorithms were then combined with traditional and advanced ensemble classified algorithms respectively, using Support Vector Machine, Random Forest (RF), AdaBoost (adaptive boosting), GBDT (gradient boosting decision tree), and XGBoost (extreme gradient boosting). After comparing the performance of these ensemble models, SMOTE algorithms with XGBoost achieved an F1 score of 0.94 with the balanced A. thaliana gene datasets, but a lower score with the unbalanced datasets. The proposed ensemble method combines different balanced data algorithms including Borderline SMOTE (BSMOTE), Adaptive Synthetic Sampling (ADSYN), SMOTE-Tomek, and SMOTE-ENN with the XGBoost model separately. The performances of the SMOTE-ENN-XGBoost model, which combined over-sampling and under-sampling algorithms with XGBoost, achieved higher predictive accuracy than the other balanced algorithms with XGBoost models. Thus, SMOTE-ENN-XGBoost provides a theoretical basis for developing evaluation criteria for identifying orphan genes in unbalanced and biological datasets.
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Affiliation(s)
- Qijuan Gao
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
| | - Xiu Jin
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiangwei Wu
- School of Resources and Environment, Anhui Agricultural University, Hefei, China
| | - Lichuan Gu
- School of Information and Computer Science, Anhui Agricultural University, Hefei, China
| | - Hanwei Yan
- Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, China
| | - Yingchun Xia
- School of Information and Computer Science, Anhui Agricultural University, Hefei, China
| | - Shaowen Li
- Anhui Province Key Laboratory of Smart Agricultural Technology and Equipment, Anhui Agriculture University, Hefei, China
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15
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Abstract
Analysis of yeast, fly and human genomes suggests that sequence divergence is not the main source of orphan genes.
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Affiliation(s)
- Urminder Singh
- Department of Genetics, Developmental and Cell Biology, Iowa State UniversityAmesUnited States
| | - Eve Syrkin Wurtele
- Department of Genetics, Developmental and Cell Biology, Iowa State UniversityAmesUnited States
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16
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Vakirlis N, Carvunis AR, McLysaght A. Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. eLife 2020; 9:e53500. [PMID: 32066524 PMCID: PMC7028367 DOI: 10.7554/elife.53500] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
The origin of 'orphan' genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do not exist. The relative contribution of the two processes remains unknown. Here, we harness the special circumstance of conserved synteny to estimate the contribution of complete divergence to the pool of orphan genes. By separately comparing yeast, fly and human genes to related taxa using conservative criteria, we find that complete divergence accounts, on average, for at most a third of eukaryotic orphan and taxonomically restricted genes. We observe that complete divergence occurs at a stable rate within a phylum but at different rates between phyla, and is frequently associated with gene shortening akin to pseudogenization.
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Affiliation(s)
- Nikolaos Vakirlis
- Smurfit Institute of GeneticsTrinity College Dublin, University of DublinDublinIreland
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of MedicineUniversity of PittsburghPittsburghUnited States
| | - Aoife McLysaght
- Smurfit Institute of GeneticsTrinity College Dublin, University of DublinDublinIreland
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17
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Drukewitz SH, Bokelmann L, Undheim EAB, von Reumont BM. Toxins from scratch? Diverse, multimodal gene origins in the predatory robber fly Dasypogon diadema indicate a dynamic venom evolution in dipteran insects. Gigascience 2019; 8:giz081. [PMID: 31289835 PMCID: PMC6615979 DOI: 10.1093/gigascience/giz081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/07/2019] [Accepted: 06/14/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Venoms and the toxins they contain represent molecular adaptations that have evolved on numerous occasions throughout the animal kingdom. However, the processes that shape venom protein evolution are poorly understood because of the scarcity of whole-genome data available for comparative analyses of venomous species. RESULTS We performed a broad comparative toxicogenomic analysis to gain insight into the genomic mechanisms of venom evolution in robber flies (Asilidae). We first sequenced a high-quality draft genome of the hymenopteran hunting robber fly Dasypogon diadema, analysed its venom by a combined proteotranscriptomic approach, and compared our results with recently described robber fly venoms to assess the general composition and major components of asilid venom. We then applied a comparative genomics approach, based on 1 additional asilid genome, 10 high-quality dipteran genomes, and 2 lepidopteran outgroup genomes, to reveal the evolutionary mechanisms and origins of identified venom proteins in robber flies. CONCLUSIONS While homologues were identified for 15 of 30 predominant venom protein in the non-asilid genomes, the remaining 15 highly expressed venom proteins appear to be unique to robber flies. Our results reveal that the venom of D. diadema likely evolves in a multimodal fashion comprising (i) neofunctionalization after gene duplication, (ii) expression-dependent co-option of proteins, and (iii) asilid lineage-specific orphan genes with enigmatic origin. The role of such orphan genes is currently being disputed in evolutionary genomics but has not been discussed in the context of toxin evolution. Our results display an unexpected dynamic venom evolution in asilid insects, which contrasts the findings of the only other insect toxicogenomic evolutionary analysis, in parasitoid wasps (Hymenoptera), where toxin evolution is dominated by single gene co-option. These findings underpin the significance of further genomic studies to cover more neglected lineages of venomous taxa and to understand the importance of orphan genes as possible drivers for venom evolution.
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Affiliation(s)
- Stephan Holger Drukewitz
- Institute for Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
- Project group Bioresources, Animal Venomics, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstrasse 2, 35392 Gießen, Germany
| | - Lukas Bokelmann
- Evolutionary Genetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, St. Lucia, QLD 4072, Australia
- Centre for Ecology and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Björn M von Reumont
- Project group Bioresources, Animal Venomics, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstrasse 2, 35392 Gießen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
- Institute for Insect Biotechnology, Justus Liebig University, Heinrich Buff Ring 58, 35394 Gießen, Germany
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18
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Choi J, Lee JJ, Jeon J. Genomic Insights into the Rice Blast Fungus through Estimation of Gene Emergence Time in Phylogenetic Context. Mycobiology 2018; 46:361-369. [PMID: 30637144 PMCID: PMC6319468 DOI: 10.1080/12298093.2018.1542970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 06/09/2023]
Abstract
The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.
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Affiliation(s)
- Jaeyoung Choi
- Convergence Research Center for Smart Farm Solution, Korea Institute of Science and Technology, Gangneung25451, Korea
| | - Jong-Joon Lee
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk38541, Korea
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk38541, Korea
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19
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Hu Y, Schmitt-Engel C, Schwirz J, Stroehlein N, Richter T, Majumdar U, Bucher G. A morphological novelty evolved by co-option of a reduced gene regulatory network and gene recruitment in a beetle. Proc Biol Sci 2018; 285:rspb.2018.1373. [PMID: 30135167 DOI: 10.1098/rspb.2018.1373] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/25/2018] [Indexed: 12/18/2022] Open
Abstract
The mechanisms underlying the evolution of morphological novelties have remained enigmatic but co-option of existing gene regulatory networks (GRNs), recruitment of genes and the evolution of orphan genes have all been suggested to contribute. Here, we study a morphological novelty of beetle pupae called gin-trap. By combining the classical candidate gene approach with unbiased screening in the beetle Tribolium castaneum, we find that 70% of the tested components of the wing network were required for gin-trap development. However, many downstream and even upstream components were not included in the co-opted network. Only one gene was recruited from another biological context, but it was essential for the anteroposterior symmetry of the gin-traps, which represents a gin-trap-unique morphological innovation. Our data highlight the importance of co-option and modification of GRNs. The recruitment of single genes may not be frequent in the evolution of morphological novelties, but may be essential for subsequent diversification of the novelties. Finally, after having screened about 28% of annotated genes in the Tribolium genome to identify the genes required for gin-trap development, we found none of them are orphan genes, suggesting that orphan genes may have played only a minor, if any, role in the evolution of gin-traps.
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Affiliation(s)
- Yonggang Hu
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Christian Schmitt-Engel
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Jonas Schwirz
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Nadi Stroehlein
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Tobias Richter
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Upalparna Majumdar
- Department of Biology, Division of Developmental Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, GZMB, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
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20
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Benevenuto J, Teixeira-Silva NS, Kuramae EE, Croll D, Monteiro-Vitorello CB. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. Front Microbiol 2018; 9:660. [PMID: 29681893 PMCID: PMC5897528 DOI: 10.3389/fmicb.2018.00660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.
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Affiliation(s)
- Juliana Benevenuto
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Natalia S. Teixeira-Silva
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel (UNINE), Neuchâtel, Switzerland
| | - Claudia B. Monteiro-Vitorello
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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21
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Baalsrud HT, Tørresen OK, Solbakken MH, Salzburger W, Hanel R, Jakobsen KS, Jentoft S. De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Mol Biol Evol 2018; 35:593-606. [PMID: 29216381 PMCID: PMC5850335 DOI: 10.1093/molbev/msx311] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
New genes can arise through duplication of a pre-existing gene or de novo from non-coding DNA, providing raw material for evolution of new functions in response to a changing environment. A prime example is the independent evolution of antifreeze glycoprotein genes (afgps) in the Arctic codfishes and Antarctic notothenioids to prevent freezing. However, the highly repetitive nature of these genes complicates studies of their organization. In notothenioids, afgps evolved from an extant gene, yet the evolutionary origin of afgps in codfishes is unknown. Here, we demonstrate that afgps in codfishes have evolved de novo from non-coding DNA 13-18 Ma, coinciding with the cooling of the Northern Hemisphere. Using whole-genome sequence data from several codfishes and notothenioids, we find higher copy number of afgp in species exposed to more severe freezing suggesting a gene dosage effect. Notably, antifreeze function is lost in one lineage of codfishes analogous to the afgp losses in non-Antarctic notothenioids. This indicates that selection can eliminate the antifreeze function when freezing is no longer imminent. In addition, we show that evolution of afgp-assisting antifreeze potentiating protein genes (afpps) in notothenioids coincides with origin and lineage-specific losses of afgp. The origin of afgps in codfishes is one of the first examples of an essential gene born from non-coding DNA in a non-model species. Our study underlines the power of comparative genomics to uncover past molecular signatures of genome evolution, and further highlights the impact of de novo gene origin in response to a changing selection regime.
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Affiliation(s)
- Helle Tessand Baalsrud
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Ole Kristian Tørresen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Monica Hongrø Solbakken
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Walter Salzburger
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Reinhold Hanel
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
| | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
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22
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Abstract
Orphan genes refer to a group of protein-coding genes lacking recognizable homologs in the other organisms. Extensive studies have demonstrated that numerous newly sequenced genomes contain a significant number of orphan genes, which have important roles in plant's responses to the environment. Due to a lack of phylogenetic conservation, the origin of orphan genes and their functions are currently not well defined. In the present study, a Poaceae orphan genes database (POGD; http://bioinfo.ahau.edu.cn/pogd) was established to serve as a user-friendly web interface for entry browsing, searching and downloading orphan genes from various plants. Four Poaceae species, including Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, are included in the current version of POGD. The database provides gene descriptions (chromosome strands, physical location), gene product records (protein length, isoelectric point, molecular weight as well as gene and protein sequences) and functional annotations (cellular role, gene ontology category, subcellular localization prediction). Basic Local Alignment Search Tool and comparative analyses were also provided on the website. POGD will serve as a comprehensive and reliable repository, which will help uncover regulatory mechanisms of orphan genes and may assist in the development of comparative genomics in plant biology.
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Affiliation(s)
- Chensong Yao
- Graduate School, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Hanwei Yan
- Laboratory of Modern Biotechnology, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Xiaodan Zhang
- School of Information and Computer Science, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
| | - Rongfu Wang
- Department of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230036, P.R. China
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23
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Bornberg-Bauer E, Schmitz J, Heberlein M. Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'. Biochem Soc Trans 2015; 43:867-73. [PMID: 26517896 DOI: 10.1042/BST20150089] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Proteins are the workhorses of the cell and, over billions of years, they have evolved an amazing plethora of extremely diverse and versatile structures with equally diverse functions. Evolutionary emergence of new proteins and transitions between existing ones are believed to be rare or even impossible. However, recent advances in comparative genomics have repeatedly called some 10%-30% of all genes without any detectable similarity to existing proteins. Even after careful scrutiny, some of those orphan genes contain protein coding reading frames with detectable transcription and translation. Thus some proteins seem to have emerged from previously non-coding 'dark genomic matter'. These 'de novo' proteins tend to be disordered, fast evolving, weakly expressed but also rapidly assuming novel and physiologically important functions. Here we review mechanisms by which 'de novo' proteins might be created, under which circumstances they may become fixed and why they are elusive. We propose a 'grow slow and moult' model in which first a reading frame is extended, coding for an initially disordered and non-globular appendage which, over time, becomes more structured and may also become associated with other proteins.
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24
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Bowling BV, Schultheis PJ, Strome ED. Implementation and assessment of a yeast orphan gene research project: involving undergraduates in authentic research experiences and progressing our understanding of uncharacterized open reading frames. Yeast 2015; 33:43-53. [PMID: 26460164 DOI: 10.1002/yea.3139] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/02/2015] [Accepted: 10/08/2015] [Indexed: 01/07/2023] Open
Abstract
Saccharomyces cerevisiae was the first eukaryotic organism to be sequenced; however, little progress has been made in recent years in furthering our understanding of all open reading frames (ORFs). From October 2012 to May 2015 the number of verified ORFs had only risen from 75.31% to 78%, while the number of uncharacterized ORFs had decreased from 12.8% to 11% (representing > 700 genes still left in this category; http://www.yeastgenome.org/genomesnapshot). Course-based research has been shown to increase student learning while providing experience with real scientific investigation; however, implementation in large, multi-section courses presents many challenges. This study sought to test the feasibility and effectiveness of incorporating authentic research into a core genetics course, with multiple instructors, to increase student learning and progress our understanding of uncharacterized ORFs. We generated a module-based annotation toolkit and utilized easily accessible bioinformatics tools to predict gene function for uncharacterized ORFs within the Saccharomyces Genome Database (SGD). Students were each assigned an uncharacterized ORF, which they annotated using contemporary comparative genomics methodologies, including multiple sequence alignment, conserved domain identification, signal peptide prediction and cellular localization algorithms. Student learning outcomes were measured by quizzes, project reports and presentations, as well as a post-project questionnaire. Our results indicate that the authentic research experience had positive impacts on students' perception of their learning and their confidence to conduct future research. Furthermore, we believe that creation of an online repository and adoption and/or adaptation of this project across multiple researchers and institutions could speed the process of gene function prediction.
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Affiliation(s)
- Bethany V Bowling
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
| | - Patrick J Schultheis
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
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Mayer MG, Sommer RJ. Nematode orphan genes are adopted by conserved regulatory networks and find a home in ecology. Worm 2015; 4:e1082029. [PMID: 27123366 PMCID: PMC4826153 DOI: 10.1080/21624054.2015.1082029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/06/2015] [Indexed: 11/26/2022]
Abstract
Nematode dauer formation represents an essential survival and dispersal strategy and is one of a few ecologically relevant traits that can be studied in laboratory approaches. Under harsh environmental conditions, the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus arrest their development and induce the formation of stress-resistant dauer larvae in response to dauer pheromones, representing a key example of phenotypic plasticity. Previous studies have indicated that in P. pacificus, many wild isolates show cross-preference of dauer pheromones and compete for access to a limited food source. When investigating the genetic mechanisms underlying this intraspecific competition, we recently discovered that the orphan gene dauerless (dau-1) controls dauer formation by copy number variation. Our results show that dau-1 acts in parallel to or downstream of steroid hormone signaling but upstream of the nuclear hormone receptor daf-12, suggesting that DAU-1 represents a novel inhibitor of DAF-12. Phylogenetic analysis reveals that the observed copy number variation is part of a complex series of gene duplication events that occurred over short evolutionary time scales. Here, we comment on the incorporation of novel or fast-evolving genes into conserved genetic networks as a common principle for the evolution of phenotypic plasticity and intraspecific competition. We discuss the possibility that orphan genes might often function in the regulation and execution of ecologically relevant traits. Given that only few ecological processes can be studied in model organisms, the function of such genes might often go unnoticed, explaining the large number of uncharacterized genes in model system genomes.
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Affiliation(s)
- Melanie G Mayer
- Max Planck Institute for Developmental Biology ; Tübingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology ; Tübingen, Germany
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Beike AK, Lang D, Zimmer AD, Wüst F, Trautmann D, Wiedemann G, Beyer P, Decker EL, Reski R. Insights from the cold transcriptome of Physcomitrella patens: global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation. New Phytol 2015; 205:869-81. [PMID: 25209349 PMCID: PMC4301180 DOI: 10.1111/nph.13004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/17/2014] [Indexed: 05/21/2023]
Abstract
The whole-genome transcriptomic cold stress response of the moss Physcomitrella patens was analyzed and correlated with phenotypic and metabolic changes. Based on time-series microarray experiments and quantitative real-time polymerase chain reaction, we characterized the transcriptomic changes related to early stress signaling and the initiation of cold acclimation. Transcription-associated protein (TAP)-encoding genes of P. patens and Arabidopsis thaliana were classified using generalized linear models. Physiological responses were monitored with pulse-amplitude-modulated fluorometry, high-performance liquid chromatography and targeted high-performance mass spectrometry. The transcript levels of 3220 genes were significantly affected by cold. Comparative classification revealed a global specialization of TAP families, a transcript accumulation of transcriptional regulators of the stimulus/stress response and a transcript decline of developmental regulators. Although transcripts of the intermediate to later response are from evolutionarily conserved genes, the early response is dominated by species-specific genes. These orphan genes may encode as yet unknown acclimation processes.
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Affiliation(s)
- Anna K Beike
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- Institut für Humangenetik, Universitätsklinikum FreiburgBreisacherstr. 33, D-79106, Freiburg, Germany
| | - Florian Wüst
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Danika Trautmann
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- Institut National de la Recherche Agronomique28 rue de Herrlisheim, F-68021, Colmar, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Peter Beyer
- Cell Biology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of FreiburgSchänzlestraße 1, D-79104, Freiburg, Germany
- FRISYS - Freiburg Initiative for Systems Biology79104, Freiburg, Germany
- BIOSS–Centre for Biological Signaling Studies79104, Freiburg, Germany
- FRIAS– Freiburg Institute for Advanced Studies79104, Freiburg, Germany
- TIP–Trinational Institute for Plant Research79104, Freiburg, Germany
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27
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Guillén Y, Rius N, Delprat A, Williford A, Muyas F, Puig M, Casillas S, Ràmia M, Egea R, Negre B, Mir G, Camps J, Moncunill V, Ruiz-Ruano FJ, Cabrero J, de Lima LG, Dias GB, Ruiz JC, Kapusta A, Garcia-Mas J, Gut M, Gut IG, Torrents D, Camacho JP, Kuhn GCS, Feschotte C, Clark AG, Betrán E, Barbadilla A, Ruiz A. Genomics of ecological adaptation in cactophilic Drosophila. Genome Biol Evol 2014; 7:349-66. [PMID: 25552534 PMCID: PMC4316639 DOI: 10.1093/gbe/evu291] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (>3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.
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Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Núria Rius
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Alejandra Delprat
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | | | - Francesc Muyas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Marta Puig
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Sònia Casillas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Miquel Ràmia
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Raquel Egea
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Barbara Negre
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gisela Mir
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jordi Camps
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - Valentí Moncunill
- Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Spain
| | - Leonardo G de Lima
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Guilherme B Dias
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jeronimo C Ruiz
- Informática de Biossistemas, Centro de Pesquisas René Rachou-Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Juan P Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Spain
| | - Gustavo C S Kuhn
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington
| | - Antonio Barbadilla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
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Abstract
In contrast to the tree of life (TOF) theory, species are mosaics of gene sequences with different origins. Observations of the extensive lateral sequence transfers in all organisms have demonstrated that the genomes of all life forms are collections of genes with different evolutionary histories that cannot be represented by a single TOF. Moreover, genes themselves commonly have several origins due to recombination. The human genome is not free from recombination events, so it is a mosaic like other organisms' genomes. Recent studies have demonstrated evidence for the integration of parasitic DNA into the human genome. Lateral transfer events have been accepted as major contributors of genome evolution in free-living bacteria. Furthermore, the accumulation of genomic sequence data provides evidence for extended genetic exchanges in intracellular bacteria and suggests that such events constitute an agent that promotes and maintains all bacterial species. Archaea and viruses also form chimeras containing primarily bacterial but also eukaryotic sequences. In addition to lateral transfers, orphan genes are indicative of the fact that gene creation is a permanent and unsettled phenomenon. Currently, a rhizome may more adequately represent the multiplicity and de novo creation of a genome. We wanted to confirm that the term “rhizome” in evolutionary biology applies to the entire cellular life history. This view of evolution should resemble a clump of roots representing the multiple origins of the repertoires of the genes of each species.
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Affiliation(s)
- Kalliopi Georgiades
- Faculté de Médecine La Timone, Unité de Recherche en Maladies Infectieuses Tropical Emergentes (URMITE), CNRS-IRD UMR 6236-198, Université de la Méditerranée Marseille, France
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29
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Abstract
Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin’s descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.
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Affiliation(s)
- Kalliopi Georgiades
- Unité de Recherche en Maladies Infectieuses Tropical Emergentes, CNRS-IRD UMR 6236-198, Université de la Méditerranée Marseille, France.
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