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Ku C, Martin WF. A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. BMC Biol 2016; 14:89. [PMID: 27751184 PMCID: PMC5067920 DOI: 10.1186/s12915-016-0315-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/28/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do. RESULTS Here we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80-100 % amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share ≥70 % amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies. CONCLUSIONS Our analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70 % rule: Coding sequences in eukaryotic genomes that share more than 70 % amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.
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Affiliation(s)
- Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany.
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Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein. Nat Commun 2016; 7:12808. [PMID: 27649274 PMCID: PMC5034306 DOI: 10.1038/ncomms12808] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 08/03/2016] [Indexed: 12/17/2022] Open
Abstract
Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by ∼40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms. Tardigrades are resistant to extreme environmental conditions including dehydration, radiation and the vacuum of space. Here the authors present a high-quality genome which displays minimal horizontal gene transfer, and identify the unique tardigrade protein Dsup which suppresses DNA damage.
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Faddeeva-Vakhrusheva A, Derks MFL, Anvar SY, Agamennone V, Suring W, Smit S, van Straalen NM, Roelofs D. Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta. Genome Biol Evol 2016; 8:2106-17. [PMID: 27289101 PMCID: PMC4987106 DOI: 10.1093/gbe/evw134] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/16/2022] Open
Abstract
Collembola (springtails) are detritivorous hexapods that inhabit the soil and its litter layer. The ecology of the springtail Orchesella cincta is extensively studied in the context of adaptation to anthropogenically disturbed areas. Here, we present a draft genome of an O. cincta reference strain with an estimated size of 286.8 Mbp, containing 20,249 genes. In total, 446 gene families are expanded and 1,169 gene families evolved specific to this lineage. Besides these gene families involved in general biological processes, we observe gene clusters participating in xenobiotic biotransformation. Furthermore, we identified 253 cases of horizontal gene transfer (HGT). Although the largest percentage of them originated from bacteria (37.5%), we observe an unusually high percentage (30.4%) of such genes of fungal origin. The majority of foreign genes are involved in carbohydrate metabolism and cellulose degradation. Moreover, some foreign genes (e.g., bacillopeptidases) expanded after HGT. We hypothesize that horizontally transferred genes could be advantageous for food processing in a soil environment that is full of decaying organic material. Finally, we identified several lineage-specific genes, expanded gene families, and horizontally transferred genes, associated with altered gene expression as a consequence of genetic adaptation to metal stress. This suggests that these genome features may be preadaptations allowing natural selection to act on. In conclusion, this genome study provides a solid foundation for further analysis of evolutionary mechanisms of adaptation to environmental stressors.
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Affiliation(s)
| | - Martijn F L Derks
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Seyed Yahya Anvar
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Valeria Agamennone
- Department of Ecological Science, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Wouter Suring
- Department of Ecological Science, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Nico M van Straalen
- Department of Ecological Science, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Dick Roelofs
- Department of Ecological Science, Vrije University Amsterdam, Amsterdam, The Netherlands
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A functional difference between native and horizontally acquired genes in bdelloid rotifers. Gene 2016; 590:186-91. [PMID: 27312952 DOI: 10.1016/j.gene.2016.06.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 02/06/2023]
Abstract
The form of RNA processing known as SL trans-splicing involves the transfer of a short conserved sequence, the spliced leader (SL), from a noncoding SL RNA to the 5' ends of mRNA molecules. SL trans-splicing occurs in several animal taxa, including bdelloid rotifers (Rotifera, Bdelloidea). One striking feature of these aquatic microinvertebrates is the large proportion of foreign genes, i.e. those acquired by horizontal gene transfer from other organisms, in their genomes. However, whether such foreign genes behave similarly to native genes has not been tested in bdelloids or any other animal. We therefore used a combination of experimental and computational methods to examine whether transcripts of foreign genes in bdelloids were SL trans-spliced, like their native counterparts. We found that many foreign transcripts contain SLs, use similar splice acceptor sequences to native genes, and are able to undergo alternative trans-splicing. However, a significantly lower proportion of foreign mRNAs contains SL sequences than native transcripts. This demonstrates a novel functional difference between foreign and native genes in bdelloids and suggests that SL trans-splicing is not essential for the expression of foreign genes, but is acquired during their domestication.
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55
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Jensen L, Grant JR, Laughinghouse HD, Katz LA. Assessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa. Evolution 2016; 70:1322-33. [DOI: 10.1111/evo.12935] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/04/2016] [Accepted: 04/19/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Lindy Jensen
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Current Address: Department of Molecular and Integrative Physiology; University of Michigan; Ann Arbor Michigan 48109
| | - Jessica R. Grant
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
| | | | - Laura A. Katz
- Department of Biological Sciences; Smith College; Northampton Massachusetts 01063
- Program in Organismic and Evolutionary Biology; University of Massachusetts; Amherst Massachusetts 01003
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Reply to Bemm et al. and Arakawa: Identifying foreign genes in independent Hypsibius dujardini genome assemblies. Proc Natl Acad Sci U S A 2016; 113:E3058-61. [PMID: 27173900 DOI: 10.1073/pnas.1601149113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A 2016; 113:5053-5058. [PMID: 27035985 DOI: 10.1101/033464] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
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Affiliation(s)
- Georgios Koutsovoulos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Lewis Stevens
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jennifer Daub
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Claire Conlon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Habib Maroon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Fran Thomas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Aziz A Aboobaker
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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58
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Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A 2016; 113:5053-8. [PMID: 27035985 PMCID: PMC4983863 DOI: 10.1073/pnas.1600338113] [Citation(s) in RCA: 167] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
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Affiliation(s)
- Georgios Koutsovoulos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Lewis Stevens
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jennifer Daub
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Claire Conlon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Habib Maroon
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Fran Thomas
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Aziz A Aboobaker
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
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59
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Shain DH, Halldórsdóttir K, Pálsson F, Aðalgeirsdóttir G, Gunnarsson A, Jónsson Þ, Lang SA, Pálsson HS, Steinþórssson S, Arnason E. Colonization of maritime glacier ice by bdelloid Rotifera. Mol Phylogenet Evol 2016; 98:280-7. [DOI: 10.1016/j.ympev.2016.02.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/22/2016] [Accepted: 02/22/2016] [Indexed: 11/26/2022]
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Havill NP, Shiyake S, Lamb Galloway A, Foottit RG, Yu G, Paradis A, Elkinton J, Montgomery ME, Sano M, Caccone A. Ancient and modern colonization of North America by hemlock woolly adelgid, Adelges tsugae (Hemiptera: Adelgidae), an invasive insect from East Asia. Mol Ecol 2016; 25:2065-80. [PMID: 26880353 DOI: 10.1111/mec.13589] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/05/2016] [Accepted: 02/09/2016] [Indexed: 01/15/2023]
Abstract
Hemlock woolly adelgid, Adelges tsugae, is an invasive pest of hemlock trees (Tsuga) in eastern North America. We used 14 microsatellites and mitochondrial COI sequences to assess its worldwide genetic structure and reconstruct its colonization history. The resulting information about its life cycle, biogeography and host specialization could help predict invasion by insect herbivores. We identified eight endemic lineages of hemlock adelgids in central China, western China, Ulleung Island (South Korea), western North America, and two each in Taiwan and Japan, with the Japanese lineages specializing on different Tsuga species. Adelgid life cycles varied at local and continental scales with different sexual, obligately asexual and facultatively asexual lineages. Adelgids in western North America exhibited very high microsatellite heterozygosity, which suggests ancient asexuality. The earliest lineages diverged in Asia during Pleistocene glacial periods, as estimated using approximate Bayesian computation. Colonization of western North America was estimated to have occurred prior to the last glacial period by adelgids directly ancestral to those in southern Japan, perhaps carried by birds. The modern invasion from southern Japan to eastern North America caused an extreme genetic bottleneck with just two closely related clones detected throughout the introduced range. Both colonization events to North America involved host shifts to unrelated hemlock species. These results suggest that genetic diversity, host specialization and host phylogeny are not predictive of adelgid invasion. Monitoring non-native sentinel host trees and focusing on invasion pathways might be more effective methods of preventing invasion than making predictions using species traits or evolutionary history.
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Affiliation(s)
- Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, Connecticut 06514, USA
| | | | - Ashley Lamb Galloway
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Robert G Foottit
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Guoyue Yu
- Institute of Plant & Environmental Protection, Beijing Academy of Agricultural & Forestry Science, Beijing 100097, China
| | - Annie Paradis
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - Joseph Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | - Masakazu Sano
- Systematic Entomology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Hokkaido, Japan
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
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62
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Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga. Genetics 2016; 203:255-68. [PMID: 27017627 DOI: 10.1534/genetics.116.186734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/21/2016] [Indexed: 12/12/2022] Open
Abstract
RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piwi-interacting RNAs (piRNAs) are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga, the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25-31 nucleotides in length and have a strong 5'-uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originate from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased toward 3'-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome.
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Debortoli N, Li X, Eyres I, Fontaneto D, Hespeels B, Tang CQ, Flot JF, Van Doninck K. Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex. Curr Biol 2016; 26:723-32. [PMID: 26948882 DOI: 10.1016/j.cub.2016.01.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/27/2015] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
Although strict asexuality is supposed to be an evolutionary dead end, morphological, cytogenetic, and genomic data suggest that bdelloid rotifers, a clade of microscopic animals, have persisted and diversified for more than 60 Myr in an ameiotic fashion. Moreover, the genome of bdelloids of the genus Adineta comprises 8%-10% of genes of putative non-metazoan origin, indicating that horizontal gene transfers are frequent within this group and suggesting that this mechanism may also promote genetic exchanges among bdelloids as well. To test this hypothesis, we used five independent sequence markers to study the genetic diversity of 576 Adineta vaga individuals from a park in Belgium. Haplowebs and GMYC analyses revealed the existence of six species among our sampled A. vaga individuals, with strong evidence of both intra- and interspecific recombination. Comparison of genomic regions of three allele-sharing individuals further revealed signatures of genetic exchanges scattered among regions evolving asexually. Our findings suggest that bdelloids evolve asexually but exchange DNA horizontally both within and between species.
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Affiliation(s)
- Nicolas Debortoli
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Xiang Li
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - Diego Fontaneto
- Institute of Ecosystem Study, National Research Council, Largo Tonolli 50, 28922 Verbania Pallanza, Italy
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Cuong Q Tang
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jean-François Flot
- Evolutionary Biology & Ecology, Université Libre de Bruxelles, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium.
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology, URBE, NAXYS, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.
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Abstract
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.
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Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Nora Besansky
- Department of Biological Sciences and Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
| | - Matthew W. Hahn
- Department of Biology and School of Informatics and ComputingIndiana UniversityBloomingtonINUSA
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Sun BF, Li T, Xiao JH, Jia LY, Liu L, Zhang P, Murphy RW, He SM, Huang DW. Horizontal functional gene transfer from bacteria to fishes. Sci Rep 2015; 5:18676. [PMID: 26691285 PMCID: PMC4687049 DOI: 10.1038/srep18676] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 11/23/2015] [Indexed: 01/06/2023] Open
Abstract
Invertebrates can acquire functional genes via horizontal gene transfer (HGT) from bacteria but fishes are not known to do so. We provide the first reliable evidence of one HGT event from marine bacteria to fishes. The HGT appears to have occurred after emergence of the teleosts. The transferred gene is expressed and regulated developmentally. Its successful integration and expression may change the genetic and metabolic repertoire of fishes. In addition, this gene contains conserved domains and similar tertiary structures in fishes and their putative donor bacteria. Thus, it may function similarly in both groups. Evolutionary analyses indicate that it evolved under purifying selection, further indicating its conserved function. We document the first likely case of HGT of functional gene from prokaryote to fishes. This discovery certifies that HGT can influence vertebrate evolution.
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Affiliation(s)
- Bao-Fa Sun
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tong Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences
| | - Jin-Hua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ling-Yi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Li Liu
- Network &Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Robert W Murphy
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Shun-Min He
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Wei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong 271018, China
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Barraclough TG. How Do Species Interactions Affect Evolutionary Dynamics Across Whole Communities? ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054030] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Theories of how species evolve in changing environments mostly consider single species in isolation or pairs of interacting species. Yet all organisms live in diverse communities containing many hundreds of species. This review discusses how species interactions influence the evolution of constituent species across whole communities. When species interactions are weak or inconsistent, evolutionary dynamics should be predictable by factors identified by single-species theory. Stronger species interactions, however, can alter evolutionary outcomes and either dampen or promote evolution of constituent species depending on the number of species and the distribution of interaction strengths across the interaction network. Genetic interactions, such as horizontal gene transfer, might also affect evolutionary outcomes. These evolutionary mechanisms in turn affect whole-community properties, such as the level of ecosystem functioning. Successful management of both ecosystems and focal species requires new understanding of evolutionary interactions across whole communities.
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Affiliation(s)
- Timothy G. Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, United Kingdom
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Identification of xenobiotic biodegradation and metabolism-related genes in the copepod Tigriopus japonicus whole transcriptome analysis. Mar Genomics 2015; 24 Pt 3:207-8. [DOI: 10.1016/j.margen.2015.05.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 05/15/2015] [Accepted: 05/15/2015] [Indexed: 11/20/2022]
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69
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Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A 2015; 112:15976-81. [PMID: 26598659 DOI: 10.1073/pnas.1510461112] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on a draft genome of a tardigrade, Hypsibius dujardini. Tardigrades are microscopic eight-legged animals that are famous for their ability to survive extreme conditions. Genome sequencing, direct confirmation of physical linkage, and phylogenetic analysis revealed that a large fraction of the H. dujardini genome is derived from diverse bacteria as well as plants, fungi, and Archaea. We estimate that approximately one-sixth of tardigrade genes entered by HGT, nearly double the fraction found in the most extreme cases of HGT into animals known to date. Foreign genes have supplemented, expanded, and even replaced some metazoan gene families within the tardigrade genome. Our results demonstrate that an unexpectedly large fraction of an animal genome can be derived from foreign sources. We speculate that animals that can survive extremes may be particularly prone to acquiring foreign genes.
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70
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Murray GGR, Weinert LA, Rhule EL, Welch JJ. The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Syst Biol 2015; 65:265-79. [PMID: 26559010 PMCID: PMC4748751 DOI: 10.1093/sysbio/syv084] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 11/04/2015] [Indexed: 11/14/2022] Open
Abstract
Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.
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Affiliation(s)
- Gemma G R Murray
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Emma L Rhule
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
| | - John J Welch
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; and
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Eyres I, Boschetti C, Crisp A, Smith TP, Fontaneto D, Tunnacliffe A, Barraclough TG. Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats. BMC Biol 2015; 13:90. [PMID: 26537913 PMCID: PMC4632278 DOI: 10.1186/s12915-015-0202-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/20/2015] [Indexed: 11/26/2022] Open
Abstract
Background Although prevalent in prokaryotes, horizontal gene transfer (HGT) is rarer in multicellular eukaryotes. Bdelloid rotifers are microscopic animals that contain a higher proportion of horizontally transferred, non-metazoan genes in their genomes than typical of animals. It has been hypothesized that bdelloids incorporate foreign DNA when they repair their chromosomes following double-strand breaks caused by desiccation. HGT might thereby contribute to species divergence and adaptation, as in prokaryotes. If so, we expect that species should differ in their complement of foreign genes, rather than sharing the same set of foreign genes inherited from a common ancestor. Furthermore, there should be more foreign genes in species that desiccate more frequently. We tested these hypotheses by surveying HGT in four congeneric species of bdelloids from different habitats: two from permanent aquatic habitats and two from temporary aquatic habitats that desiccate regularly. Results Transcriptomes of all four species contain many genes with a closer match to non-metazoan genes than to metazoan genes. Whole genome sequencing of one species confirmed the presence of these foreign genes in the genome. Nearly half of foreign genes are shared between all four species and an outgroup from another family, but many hundreds are unique to particular species, which indicates that HGT is ongoing. Using a dated phylogeny, we estimate an average of 12.8 gains versus 2.0 losses of foreign genes per million years. Consistent with the desiccation hypothesis, the level of HGT is higher in the species that experience regular desiccation events than those that do not. However, HGT still contributed hundreds of foreign genes to the species from permanently aquatic habitats. Foreign genes were mainly enzymes with various annotated functions that include catabolism of complex polysaccharides and stress responses. We found evidence of differential loss of ancestral foreign genes previously associated with desiccation protection in the two non-desiccating species. Conclusions Nearly half of foreign genes were acquired before the divergence of bdelloid families over 60 Mya. Nonetheless, HGT is ongoing in bdelloids and has contributed to putative functional differences among species. Variation among our study species is consistent with the hypothesis that desiccating habitats promote HGT. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0202-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isobel Eyres
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.,Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
| | - Chiara Boschetti
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Alastair Crisp
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Thomas P Smith
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK
| | - Diego Fontaneto
- National Research Council, Institute of Ecosystem Study, Largo Tonolli 50, 28922, Verbania Pallanza, Italy
| | - Alan Tunnacliffe
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, UK.
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72
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Abstract
The high prevalence of sexual reproduction is considered a paradox mainly for two reasons. First, asexuals should enjoy various growth benefits because they seemingly rid themselves of the many inefficiencies of sexual reproduction-the so-called costs of sex. Second, there seems to be no lack of asexual origins because losses of sexual reproduction have been described in almost every larger eukaryotic taxon. Current attempts to resolve this paradox concentrate on a few hypotheses that provide universal benefits that would compensate for these costs and give sexual reproduction a net advantage. However, are new asexual lineages really those powerful invaders that could quickly displace their sexual ancestors? Research on the costs of sex indicates that sex is often stabilized by highly lineage-specific mechanisms. Two main categories can be distinguished. First are beneficial traits that evolved within a particular species and became tightly associated with sex (e.g., a mating system that involves sexual selection, or a sexual diapausing stage that allows survival through harsh periods). If such traits are absent in asexuals, simple growth efficiency considerations will not capture the fitness benefits gained by skipping sexual reproduction. Second, lineage-specific factors might prevent asexuals from reaching their full potential (e.g., dependence on fertilization in sperm-dependent parthenogens). Such observations suggest that the costs of sex are highly variable and often lower than theoretical considerations suggest. This has implications for the magnitude of universal benefits required to resolve the paradox of sex.
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73
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Abstract
Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.
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74
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Luan JB, Chen W, Hasegawa DK, Simmons AM, Wintermantel WM, Ling KS, Fei Z, Liu SS, Douglas AE. Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects. Genome Biol Evol 2015; 7:2635-47. [PMID: 26377567 PMCID: PMC4607527 DOI: 10.1093/gbe/evv170] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction.
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Affiliation(s)
- Jun-Bo Luan
- Department of Entomology, Cornell University
| | - Wenbo Chen
- Boyce Thompson Institute for Plant Research, Cornell University
| | - Daniel K Hasegawa
- Boyce Thompson Institute for Plant Research, Cornell University USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina
| | - Alvin M Simmons
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina
| | - William M Wintermantel
- USDA-Agricultural Research Service, Crop Improvement and Protection Research, Salinas, California
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, China
| | - Angela E Douglas
- Department of Entomology, Cornell University Department of Molecular Biology and Genetics, Cornell University
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75
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Suzuki K, Moriguchi K, Yamamoto S. Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers. Res Microbiol 2015; 166:753-63. [PMID: 26291765 DOI: 10.1016/j.resmic.2015.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 11/15/2022]
Abstract
Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.
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76
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Casane D, Fumey J, Laurenti P. [ENCODE apophenia or a panglossian analysis of the human genome]. Med Sci (Paris) 2015; 31:680-6. [PMID: 26152174 DOI: 10.1051/medsci/20153106023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.
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Affiliation(s)
- Didier Casane
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
| | - Julien Fumey
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France
| | - Patrick Laurenti
- Laboratoire Évolution, génomes, comportement, écologie, CNRS université Paris-Sud UMR 9191, IRD UMR 247, Avenue de la Terrasse, bâtiment 13, boîte postale 1, 91198 Gif-sur-Yvette, France - Université Paris-Diderot, Sorbonne Paris-Cité, Paris, France
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Against All Odds: Trehalose-6-Phosphate Synthase and Trehalase Genes in the Bdelloid Rotifer Adineta vaga Were Acquired by Horizontal Gene Transfer and Are Upregulated during Desiccation. PLoS One 2015; 10:e0131313. [PMID: 26161530 PMCID: PMC4498783 DOI: 10.1371/journal.pone.0131313] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/31/2015] [Indexed: 01/15/2023] Open
Abstract
The disaccharide sugar trehalose is essential for desiccation resistance in most metazoans that survive dryness; however, neither trehalose nor the enzymes involved in its metabolism have ever been detected in bdelloid rotifers despite their extreme resistance to desiccation. Here we screened the genome of the bdelloid rotifer Adineta vaga for genes involved in trehalose metabolism. We discovered a total of four putative trehalose-6-phosphate synthase (TPS) and seven putative trehalase (TRE) gene copies in the genome of this ameiotic organism; however, no trehalose-6-phosphate phosphatase (TPP) gene or domain was detected. The four TPS copies of A. vaga appear more closely related to plant and fungi proteins, as well as to some protists, whereas the seven TRE copies fall in bacterial clades. Therefore, A. vaga likely acquired its trehalose biosynthesis and hydrolysis genes by horizontal gene transfers. Nearly all residues important for substrate binding in the predicted TPS domains are highly conserved, supporting the hypothesis that several copies of the genes might be functional. Besides, RNAseq library screening showed that trehalase genes were highly expressed compared to TPS genes, explaining probably why trehalose had not been detected in previous studies of bdelloids. A strong overexpression of their TPS genes was observed when bdelloids enter desiccation, suggesting a possible signaling role of trehalose-6-phosphate or trehalose in this process.
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78
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Szydlowski L, Boschetti C, Crisp A, Barbosa E, Tunnacliffe A. Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae. Gene 2015; 566:125-37. [DOI: 10.1016/j.gene.2015.04.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
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79
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Bruto M, Prigent-Combaret C, Luis P, Moënne-Loccoz Y, Muller D. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes. Proc Biol Sci 2015; 281:20140848. [PMID: 24990676 DOI: 10.1098/rspb.2014.0848] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes-as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.
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Affiliation(s)
- Maxime Bruto
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Patricia Luis
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, Lyon 69622, France Université Lyon 1, Villeurbanne, France CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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80
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Fontaneto D, Barraclough TG. Do Species Exist in Asexuals? Theory and Evidence from Bdelloid Rotifers. Integr Comp Biol 2015; 55:253-63. [PMID: 25912362 DOI: 10.1093/icb/icv024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The possibility for independently evolving entities to form and persist in the absence of sexual recombination in eukaryotes has been questioned; nevertheless, there are organisms that are known to be asexual and that have apparently diversified into multiple species as recognized by taxonomists. These organisms have therefore been identified as an evolutionary paradox. We explore three alternative hypotheses attempting to solve the apparent paradox, focusing on bdelloid rotifers, the most studied group of organisms in which all species are considered asexual: (1) they may have some hidden form of sex; (2) species do not represent biological entities but simply convenient names; and (3) sex may not be a necessary requirement for speciation. We provide ample evidence against the first two hypotheses, reporting several studies supporting (1) bdelloids asexuality from different approaches, and (2) the existence of species from genetics, jaw morphology, ecology, and physiology. Thus, we (3) explore the role of sex in speciation comparing bdelloid and monogonont rotifers, and conclude with some caveats that could still change our understanding of bdelloid species.
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Affiliation(s)
- Diego Fontaneto
- *National Research Council, Institute of Ecosystem Study, Largo Tonolli 50, 28922 Verbania Pallanza, Italy;
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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81
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Strakova A, Murchison EP. The cancer which survived: insights from the genome of an 11000 year-old cancer. Curr Opin Genet Dev 2015; 30:49-55. [PMID: 25867244 DOI: 10.1016/j.gde.2015.03.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/04/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
Abstract
The canine transmissible venereal tumour (CTVT) is a transmissible cancer that is spread between dogs by the allogeneic transfer of living cancer cells during coitus. CTVT affects dogs around the world and is the oldest and most divergent cancer lineage known in nature. CTVT first emerged as a cancer about 11000 years ago from the somatic cells of an individual dog, and has subsequently acquired adaptations for cell transmission between hosts and for survival as an allogeneic graft. Furthermore, it has achieved a genome configuration which is compatible with long-term survival. Here, we discuss and speculate on the evolutionary processes and adaptions which underlie the success of this remarkable lineage.
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Affiliation(s)
- Andrea Strakova
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Elizabeth P Murchison
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
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82
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Crisp A, Boschetti C, Perry M, Tunnacliffe A, Micklem G. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes. Genome Biol 2015; 16:50. [PMID: 25785303 PMCID: PMC4358723 DOI: 10.1186/s13059-015-0607-3] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 02/04/2015] [Indexed: 01/17/2023] Open
Abstract
Background A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans. Results We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens or hundreds of active ‘foreign’ genes, largely concerned with metabolism. Our analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes throughout their evolution, humans and other primates have gained relatively few since their common ancestor. We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes. Conclusions We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0607-3) contains supplementary material, which is available to authorized users.
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83
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Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Front Microbiol 2015; 6:161. [PMID: 25784900 PMCID: PMC4347624 DOI: 10.3389/fmicb.2015.00161] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Metabolic gene clusters (MGCs), physically co-localized genes participating in the same metabolic pathway, are signature features of fungal genomes. MGCs are most often observed in specialized metabolism, having evolved in individual fungal lineages in response to specific ecological needs, such as the utilization of uncommon nutrients (e.g., galactose and allantoin) or the production of secondary metabolic antimicrobial compounds and virulence factors (e.g., aflatoxin and melanin). A flurry of recent studies has shown that several MGCs, whose functions are often associated with fungal virulence as well as with the evolutionary arms race between fungi and their competitors, have experienced horizontal gene transfer (HGT). In this review, after briefly introducing HGT as a source of gene innovation, we examine the evidence for HGT's involvement on the evolution of MGCs and, more generally of fungal metabolism, enumerate the molecular mechanisms that mediate such transfers and the ecological circumstances that favor them, as well as discuss the types of evidence required for inferring the presence of HGT in MGCs. The currently available examples indicate that transfers of entire MGCs have taken place between closely related fungal species as well as distant ones and that they sometimes involve large chromosomal segments. These results suggest that the HGT-mediated acquisition of novel metabolism is an ongoing and successful ecological strategy for many fungal species.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University Nashville, TN, USA
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84
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Lee BY, Kim HS, Hwang DS, Won EJ, Choi BS, Choi IY, Park HG, Rhee JS, Lee JS. Whole transcriptome analysis of the monogonont rotifer Brachionus koreanus provides molecular resources for developing biomarkers of carbohydrate metabolism. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 14:33-41. [PMID: 25746681 DOI: 10.1016/j.cbd.2015.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/05/2015] [Accepted: 02/13/2015] [Indexed: 11/28/2022]
Abstract
Rotifers (phylum Rotifera) are the most common non-arthropod animal. Species in the monogonont rotifer Brachionus are widely distributed in coastal areas and play an important role in aquatic food webs as secondary producers. Brachionus koreanus is currently being developed as a model system for ecotoxicological research. We sequenced the whole transcriptome of B. koreanus using RNA-seq technology. De novo sequence assembly by Trinity integrated with TransDecoder produced 36,918 contigs, including putative alternatively spliced variants. A total of 13,784 genes were identified based on Blast analysis. KEGG pathway analysis detected transcripts annotated as coding for enzymes involved in metabolic pathways, the immune system, translation, and signal transduction. Most identified enzymes and pathways were involved in carbohydrate metabolism, such as the tricarboxylic acid (TCA) cycle and glycolysis. We anticipate that the availability of whole transcriptome data for B. koreanus will provide insights into rotifer biology and physiology and facilitate the development of biomarkers for ecotoxicology studies.
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Affiliation(s)
- Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Eun-Ji Won
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Beom-Soon Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea
| | - Jae-Sung Rhee
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 406-772, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
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85
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Schwander T, Marais G, Roze D. Sex uncovered: the evolutionary biology of reproductive systems. J Evol Biol 2015; 27:1287-91. [PMID: 24975885 DOI: 10.1111/jeb.12424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- T Schwander
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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86
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Hespeels B, Knapen M, Hanot-Mambres D, Heuskin AC, Pineux F, LUCAS S, Koszul R, Van Doninck K. Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation. J Evol Biol 2015; 27:1334-45. [PMID: 25105197 DOI: 10.1111/jeb.12326] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The bdelloid rotifer lineage Adineta vaga inhabits temporary habitats subjected to frequent episodes of drought. The recently published draft sequence of the genome of A. vaga revealed a peculiar genomic structure incompatible with meiosis and suggesting that DNA damage induced by desiccation may have reshaped the genomic structure of these organisms. However, the causative link between DNA damage and desiccation has never been proven to date in rotifers. To test for the hypothesis that desiccation induces DNA double-strand breaks (DSBs), we developed a protocol allowing a high survival rate of desiccated A. vaga. Using pulsed-field gel electrophoresis to monitor genomic integrity, we followed the occurrence of DSBs in dried bdelloids and observed an accumulation of these breaks with time spent in dehydrated state. These DSBs are gradually repaired upon rehydration. Even when the genome was entirely shattered into small DNA fragments by proton radiation, A. vaga individuals were able to efficiently recover from desiccation and repair a large amount of DSBs. Interestingly, when investigating the influence of UV-A and UV-B exposure on the genomic integrity of desiccated bdelloids, we observed that these natural radiations also caused important DNA DSBs, suggesting that the genome is not protected during the desiccated stage but that the repair mechanisms are extremely efficient in these intriguing organisms.
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87
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Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJ, Orlando L, Willerslev E. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130383. [PMID: 25487334 PMCID: PMC4275890 DOI: 10.1098/rstb.2013.0383] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Affiliation(s)
- Mikkel Winther Pedersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Søren Overballe-Petersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - James Haile
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Trace and Environmental DNA Laboratory, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Micaela Hellstrom
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Johan Spens
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Department of Wildlife, Fish and Environmental Studies, SLU, Umeå S-901 83, Sweden
| | - Philip Francis Thomsen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Kristine Bohmann
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Enrico Cappellini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ida Bærholm Schnell
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nathan A Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Astrid M Z Schmidt
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
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88
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Gahan PB. The Biology of CNAPS. ADVANCES IN PREDICTIVE, PREVENTIVE AND PERSONALISED MEDICINE 2015. [DOI: 10.1007/978-94-017-9168-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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89
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Zhang J, Lou X, Zellmer L, Liu S, Xu N, Liao DJ. Just like the rest of evolution in Mother Nature, the evolution of cancers may be driven by natural selection, and not by haphazard mutations. Oncoscience 2014; 1:580-90. [PMID: 25594068 PMCID: PMC4278337 DOI: 10.18632/oncoscience.83] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022] Open
Abstract
Sporadic carcinogenesis starts from immortalization of a differentiated somatic cell or an organ-specific stem cell. The immortalized cell incepts a new or quasinew organism that lives like a parasite in the patient and usually proceeds to progressive simplification, constantly engendering intermediate organisms that are simpler than normal cells. Like organismal evolution in Mother Nature, this cellular simplification is a process of Darwinian selection of those mutations with growth- or survival-advantages, from numerous ones that occur randomly and stochastically. Therefore, functional gain of growth- or survival-sustaining oncogenes and functional loss of differentiation-sustaining tumor suppressor genes, which are hallmarks of cancer cells and contribute to phenotypes of greater malignancy, are not drivers of carcinogenesis but are results from natural selection of advantageous mutations. Besides this mutation-load dependent survival mechanism that is evolutionarily low and of an asexual nature, cancer cells may also use cell fusion for survival, which is an evolutionarily-higher mechanism and is of a sexual nature. Assigning oncogenes or tumor suppressor genes or their mutants as drivers to induce cancer in animals may somewhat coerce them to create man-made oncogenic pathways that may not really be a course of sporadic cancer formations in the human.
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Affiliation(s)
- Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Xiaomin Lou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Lucas Zellmer
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Siqi Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Ningzhi Xu
- Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P.R. China
| | - D Joshua Liao
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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90
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Overballe-Petersen S, Willerslev E. Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction. Bioessays 2014; 36:1005-10. [PMID: 25143190 PMCID: PMC4255686 DOI: 10.1002/bies.201400035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Horizontal gene transfer in the form of long DNA fragments has changed our view of bacterial evolution. Recently, we discovered that such processes may also occur with the massive amounts of short and damaged DNA in the environment, and even with truly ancient DNA. Although it presently remains unclear how often it takes place in nature, horizontal gene transfer of short and damaged DNA opens up the possibility for genetic exchange across distinct species in both time and space. In this essay, we speculate on the potential evolutionary consequences of this phenomenon. We argue that it may challenge basic assumptions in evolutionary theory; that it may have distant origins in life's history; and that horizontal gene transfer should be viewed as an evolutionary strategy not only preceding but causally underpinning the evolution of sexual reproduction.
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91
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Zhang D, Qi J, Yue J, Huang J, Sun T, Li S, Wen JF, Hettenhausen C, Wu J, Wang L, Zhuang H, Wu J, Sun G. Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer. BMC PLANT BIOLOGY 2014; 14:19. [PMID: 24411025 PMCID: PMC3893544 DOI: 10.1186/1471-2229-14-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/08/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important for species evolution and adaption to new ecological niches. Parasitic systems expectedly allow the occurrence of HGT at relatively high frequencies due to their long-term physical contact. In plants, a number of HGT events have been reported between the organelles of parasites and the hosts, but HGT between host and parasite nuclear genomes has rarely been found. RESULTS A thorough transcriptome screening revealed that a strictosidine synthase-like (SSL) gene in the root parasitic plant Orobanche aegyptiaca and the shoot parasitic plant Cuscuta australis showed much higher sequence similarities with those in Brassicaceae than with those in their close relatives, suggesting independent gene horizontal transfer events from Brassicaceae to these parasites. These findings were strongly supported by phylogenetic analysis and their identical unique amino acid residues and deletions. Intriguingly, the nucleus-located SSL genes in Brassicaceae belonged to a new member of SSL gene family, which were originated from gene duplication. The presence of introns indicated that the transfer occurred directly by DNA integration in both parasites. Furthermore, positive selection was detected in the foreign SSL gene in O. aegyptiaca but not in C. australis. The expression of the foreign SSL genes in these two parasitic plants was detected in multiple development stages and tissues, and the foreign SSL gene was induced after wounding treatment in C. australis stems. These data imply that the foreign genes may still retain certain functions in the recipient species. CONCLUSIONS Our study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.
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Affiliation(s)
- Dale Zhang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
- College of Life Science, Henan University, 85 Minglun Street, Kaifeng 475001, Henan, China
| | - Jinfeng Qi
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jipei Yue
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jinling Huang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Suoping Li
- College of Life Science, Henan University, 85 Minglun Street, Kaifeng 475001, Henan, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang East Road, Kunming 650223, Yunnan, China
| | - Christian Hettenhausen
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jinsong Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Lei Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Huifu Zhuang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming 650201, Yunnan, China
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Abstract
Horizontal gene transfer is accepted as an important evolutionary force modulating the evolution of prokaryote genomes. However, it is thought that horizontal gene transfer plays only a minor role in metazoan evolution. In this paper, I critically review the rising evidence on horizontally transferred genes and on the acquisition of novel traits in metazoans. In particular, I discuss suspected examples in sponges, cnidarians, rotifers, nematodes, molluscs and arthropods which suggest that horizontal gene transfer in metazoans is not simply a curiosity. In addition, I stress the scarcity of studies in vertebrates and other animal groups and the importance of forthcoming studies to understand the importance and extent of horizontal gene transfer in animals.
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Affiliation(s)
- Luis Boto
- Dpto. Biodiversidad y Biología Evolutiva, Museo Nacional Ciencias Naturales. CSIC, , C/ José Gutierrez Abascal 2, 28006 Madrid, Spain
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93
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Schönknecht G, Weber APM, Lercher MJ. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays 2013; 36:9-20. [DOI: 10.1002/bies.201300095] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Andreas P. M. Weber
- Institute of Plant Biochemistry; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
| | - Martin J. Lercher
- Cluster of Excellence on Plant Sciences (CEPLAS); Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
- Institute for Computer Science; Heinrich-Heine-Universität Düsseldorf; Düsseldorf Germany
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94
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Yue J, Sun G, Hu X, Huang J. The scale and evolutionary significance of horizontal gene transfer in the choanoflagellate Monosiga brevicollis. BMC Genomics 2013; 14:729. [PMID: 24156600 PMCID: PMC4046809 DOI: 10.1186/1471-2164-14-729] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/17/2013] [Indexed: 12/29/2022] Open
Abstract
Background It is generally agreed that horizontal gene transfer (HGT) is common in phagotrophic protists. However, the overall scale of HGT and the cumulative impact of acquired genes on the evolution of these organisms remain largely unknown. Results Choanoflagellates are phagotrophs and the closest living relatives of animals. In this study, we performed phylogenomic analyses to investigate the scale of HGT and the evolutionary importance of horizontally acquired genes in the choanoflagellate Monosiga brevicollis. Our analyses identified 405 genes that are likely derived from algae and prokaryotes, accounting for approximately 4.4% of the Monosiga nuclear genome. Many of the horizontally acquired genes identified in Monosiga were probably acquired from food sources, rather than by endosymbiotic gene transfer (EGT) from obsolete endosymbionts or plastids. Of 193 genes identified in our analyses with functional information, 84 (43.5%) are involved in carbohydrate or amino acid metabolism, and 45 (23.3%) are transporters and/or involved in response to oxidative, osmotic, antibiotic, or heavy metal stresses. Some identified genes may also participate in biosynthesis of important metabolites such as vitamins C and K12, porphyrins and phospholipids. Conclusions Our results suggest that HGT is frequent in Monosiga brevicollis and might have contributed substantially to its adaptation and evolution. This finding also highlights the importance of HGT in the genome and organismal evolution of phagotrophic eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-729) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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95
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Affiliation(s)
- Peter Gahan
- Anatomy & Human Sciences; King's College London; London Bridge London SE1 1UL UK
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96
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Mialet B, Majdi N, Tackx M, Azémar F, Buffan-Dubau E. Selective feeding of bdelloid rotifers in river biofilms. PLoS One 2013; 8:e75352. [PMID: 24073263 PMCID: PMC3779155 DOI: 10.1371/journal.pone.0075352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
In situ pigment contents of biofilm-dwelling bdelloid rotifers of the Garonne River (France) were measured by high performance liquid chromatography (HPLC) and compared with pigment composition of surrounding biofilm microphytobenthic communities. Among pigments that were detected in rotifers, the presence of carotenoids fucoxanthin and myxoxanthophyll showed that the rotifers fed on diatoms and cyanobacteria. Unexpectedly, while diatoms strongly dominated microphytobenthic communities in terms of biomass, HPLC results hinted that rotifers selectively ingested benthic filamentous cyanobacteria. In doing so, rotifers could daily remove a substantial fraction (up to 28%) of this cyanobacterial biomass. The possibility that the rotifers hosted symbiotic myxoxanthophyll-containing cyanobacteria was examined by localisation of chlorophyll fluorescence within rotifers using confocal laser scanning microscopy (CLSM). CLSM results showed an even distribution of quasi-circular fluorescent objects (FO) throughout rotifer bodies, whereas myxoxanthophyll is a biomarker pigment of filamentous cyanobacteria, so the hypothesis was rejected. Our results also suggest that rotifers converted β-carotene (provided by ingested algae) into echinenone, a photoprotective pigment. This study, which is the first one to detail in situ pigment contents of rotifers, clearly shows that the role of cyanobacteria as a food source for meiobenthic invertebrates has been underestimated so far, and deserves urgent consideration.
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Affiliation(s)
- Benoit Mialet
- Université de Toulouse, INP, UPS, Ecolab (Laboratoire d’Ecologie Fonctionnelle et Environnement), Toulouse, France
- Centre National de la Recherche Scientifique, Ecolab, Toulouse, France
- Université de la Rochelle, CNRS, UMR 7266 LIENSs (Littoral Environnement et Sociétés), La Rochelle, France
- * E-mail:
| | - Nabil Majdi
- Université de Toulouse, INP, UPS, Ecolab (Laboratoire d’Ecologie Fonctionnelle et Environnement), Toulouse, France
- Centre National de la Recherche Scientifique, Ecolab, Toulouse, France
| | - Micky Tackx
- Université de Toulouse, INP, UPS, Ecolab (Laboratoire d’Ecologie Fonctionnelle et Environnement), Toulouse, France
- Centre National de la Recherche Scientifique, Ecolab, Toulouse, France
| | - Frédéric Azémar
- Université de Toulouse, INP, UPS, Ecolab (Laboratoire d’Ecologie Fonctionnelle et Environnement), Toulouse, France
- Centre National de la Recherche Scientifique, Ecolab, Toulouse, France
| | - Evelyne Buffan-Dubau
- Université de Toulouse, INP, UPS, Ecolab (Laboratoire d’Ecologie Fonctionnelle et Environnement), Toulouse, France
- Centre National de la Recherche Scientifique, Ecolab, Toulouse, France
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Driscoll T, Gillespie JJ, Nordberg EK, Azad AF, Sobral BW. Bacterial DNA sifted from the Trichoplax adhaerens (Animalia: Placozoa) genome project reveals a putative rickettsial endosymbiont. Genome Biol Evol 2013; 5:621-45. [PMID: 23475938 PMCID: PMC3641634 DOI: 10.1093/gbe/evt036] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genome sequencing projects often yield bacterial DNA sequences, data typically considered as microbial contamination. However, these sequences may also indicate either symbiont genes or lateral gene transfer (LGT) to host genomes. These bacterial sequences can provide clues about eukaryote-microbe interactions. Here, we used the genome of the primitive animal Trichoplax adhaerens (Metazoa: Placozoa), which is known to harbor an uncharacterized Gram-negative endosymbiont, to search for the presence of bacterial DNA sequences. Bioinformatic and phylogenomic analyses of extracted data from the genome assembly (181 bacterial coding sequences [CDS]) and trace read archive (16S rDNA) revealed a dominant proteobacterial profile strongly skewed to Rickettsiales (Alphaproteobacteria) genomes. By way of phylogenetic analysis of 16S rDNA and 113 proteins conserved across proteobacterial genomes, as well as identification of 27 rickettsial signature genes, we propose a Rickettsiales endosymbiont of T. adhaerens (RETA). The majority (93%) of the identified bacterial CDS belongs to small scaffolds containing prokaryotic-like genes; however, 12 CDS were identified on large scaffolds comprised of eukaryotic-like genes, suggesting that T. adhaerens might have recently acquired bacterial genes. These putative LGTs may coincide with the placozoan's aquatic niche and symbiosis with RETA. This work underscores the rich, and relatively untapped, resource of eukaryotic genome projects for harboring data pertinent to host-microbial interactions. The nature of unknown (or poorly characterized) bacterial species may only emerge via analysis of host genome sequencing projects, particularly if these species are resistant to cell culturing, as are many obligate intracellular microbes. Our work provides methodological insight for such an approach.
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Affiliation(s)
- Timothy Driscoll
- Virginia Bioinformatics Institute at Virginia Polytechnic Institute and State University, USA
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98
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Abstract
The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.
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Affiliation(s)
- Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA; Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Gioti A, Stajich JE, Johannesson H. Neurospora and the dead-end hypothesis: genomic consequences of selfing in the model genus. Evolution 2013; 67:3600-16. [PMID: 24299411 DOI: 10.1111/evo.12206] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 06/24/2013] [Indexed: 12/24/2022]
Abstract
It is becoming increasingly evident that adoption of different reproductive strategies, such as sexual selfing and asexuality, greatly impacts genome evolution. In this study, we test theoretical predictions on genomic maladaptation of selfing lineages using empirical data from the model fungus Neurospora. We sequenced the genomes of four species representing distinct transitions to selfing within the history of the genus, as well as the transcriptome of one of these, and compared with available data from three outcrossing species. Our results provide evidence for a relaxation of purifying selection in protein-coding genes and for a reduced efficiency of transposable element silencing by Repeat Induced Point mutation. A reduction in adaptive evolution was also identified in the form of reduced codon usage bias in highly expressed genes of selfing Neurospora, but this result may be confounded by mutational bias. Potentially counteracting these negative effects, the nucleotide substitution rate and the spread of transposons is reduced in selfing species. We suggest that differences in substitution rate relate to the absence, in selfing Neurospora, of the asexual pathway producing conidia. Our results support the dead-end theory and show that Neurospora genomes bear signatures of both sexual and asexual reproductive mode.
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Affiliation(s)
- Anastasia Gioti
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
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100
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Wijayawardena BK, Minchella DJ, DeWoody JA. Hosts, parasites, and horizontal gene transfer. Trends Parasitol 2013; 29:329-38. [DOI: 10.1016/j.pt.2013.05.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 12/16/2022]
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