Horizontal gene transfer: building the web of life

Soucy, Shannon M.; Huang, Jinling; Gogarten, J. Peter

doi:10.1038/nrg3962

Cited by 1,096 publications

(976 citation statements)

References 114 publications

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“…The phylogenetic effect we observed is also unlikely to be explained by reduced opportunities of HTT between phylogenetically distant species, because these are not more geographically distant on average. Instead, as proposed for HGT and HTT in bacteria (1,25,26), compatibility between TEs and recipient host cells may decrease as genetic distance from source lineages increases. Transposition is known to involve a number of interactions between TEs and host cellular factors (e.g., transcription factors and chromatin), which, depending on the type of TE, may be limited or very intricate (27)(28)(29)(30).…”

Section: Significancementioning

confidence: 99%

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Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

200

236

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Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.horizontal transfer | transposable elements | insects | genome evolution | biogeography H orizontal transfer (HT) is the transmission of genetic material between organisms through a mechanism other than reproduction. In prokaryotes, HT is pervasive, its mechanisms are well understood, and it is now viewed as one of the main forces shaping genome architecture and evolution (1, 2). In contrast, the study of HT in eukaryotes is less documented, but has been increasingly investigated. The majority of genes horizontally acquired by eukaryotes come from bacteria, but the extent to which these transfers have contributed to eukaryote evolution is still unclear (3, 4). Gene transfers from eukaryote to eukaryote appear to be largely limited to filamentous organisms, such as oomycetes and fungi (5, 6).In animals and plants, very few cases of such horizontal gene transfers (HGTs) have been reported so far (7,8). In fact, most of the genetic material that is horizontally transferred in animals and plants consists of transposable elements (TEs) (9-11), which are pieces of DNA able to move from a chromosomal locus to another (12). The greater ability of TEs to move between organisms certainly relates to their intrinsic ability to transpose within genomes, which genes cannot do. HT of TEs (HTT) may allow these elements to enter naive genomes, which they invade by making copies of themselves, and then escape before they become fully silenced by anti-TE defenses (13). A growing number of studies have identified such HTT (11,[14][15][16]. However, a common drawback of these studies has been the inclusion of a limited set of TEs (11) or organisms (16), which hampers our understanding of the breadth of HTT, its contribution to genome evolution, and of the factors and barriers shaping these transfe...

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Section: Significancementioning

confidence: 99%

“…In prokaryotes, HT is pervasive, its mechanisms are well understood, and it is now viewed as one of the main forces shaping genome architecture and evolution (1,2). In contrast, the study of HT in eukaryotes is less documented, but has been increasingly investigated.…”

mentioning

confidence: 99%

Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

200

236

View full text Add to dashboard Cite

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“…Horizontal gene transfer across phylogenetic boundaries is another natural process that results in genetic variation in plants (Bock, 2010;Soucy et al, 2015), including transfer of DNA from bacteria, viruses, and unrelated plants (Bergthorsson et al, 2003;Staginnus et al, 2007;Liu et al, 2012;El Baidouri et al, 2014;Geering et al, 2014;Kyndt et al, 2015). One recent example was a study demonstrating that a wide selection of sweet potato [Ipomoea batatas (L.) Lam.…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 99%

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

et al. 2017

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Commercial‐scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders. During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial‐scale breeders have implemented extensive plant selection practices to identify the top‐performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years. Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes.

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“…HGT involving prokaryotes (1) has been repeatedly associated with adaptive evolution (2), such as the acquisition of antibiotic resistance (3), resistance to heavy metal (4), and pesticide degradation (5). Although there was a massive endosymbiotic transfer of genes into the nuclear genome from eubacterial ancestors of plastids (6) and mitochondria (7), relatively few cases of functional eukaryote-to-eukaryote HGTs have been detected or studied in detail (8).…”

mentioning

confidence: 99%

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

Yang

Zhang

Wafula

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Horizontal gene transfer (HGT) is the transfer of genetic material across species boundaries and has been a driving force in prokaryotic evolution. HGT involving eukaryotes appears to be much less frequent, and the functional implications of HGT in eukaryotes are poorly understood. We test the hypothesis that parasitic plants, because of their intimate feeding contacts with host plant tissues, are especially prone to horizontal gene acquisition. We sought evidence of HGTs in transcriptomes of three parasitic members of Orobanchaceae, a plant family containing species spanning the full spectrum of parasitic capabilities, plus the free-living Lindenbergia. Following initial phylogenetic detection and an extensive validation procedure, 52 highconfidence horizontal transfer events were detected, often from lineages of known host plants and with an increasing number of HGT events in species with the greatest parasitic dependence. Analyses of intron sequences in putative donor and recipient lineages provide evidence for integration of genomic fragments far more often than retro-processed RNA sequences. Purifying selection predominates in functionally transferred sequences, with a small fraction of adaptively evolving sites. HGT-acquired genes are preferentially expressed in the haustorium-the organ of parasitic plants-and are strongly biased in predicted gene functions, suggesting that expression products of horizontally acquired genes are contributing to the unique adaptive feeding structure of parasitic plants.

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Horizontal gene transfer: building the web of life

Cited by 1,096 publications

References 114 publications

Massive horizontal transfer of transposable elements in insects

Massive horizontal transfer of transposable elements in insects

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

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