SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.

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Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes

BMC Evolutionary Biology ◽

10.1186/1471-2148-11-276 ◽

2011 ◽

Vol 11 (1) ◽

Cited By ~ 86

Author(s):

Huiquan Liu ◽

Yanping Fu ◽

Bo Li ◽

Xiao Yu ◽

Jiatao Xie ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Single Stranded Dna ◽

Dna Viruses ◽

Eukaryotic Genomes

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Shaping the Landscape of Eukaryotic Gene Expression: Horizontal Gene Transfer

Asian Journal of Medical Sciences ◽

10.3126/ajms.v12i10.39643 ◽

2021 ◽

Vol 12 (10) ◽

pp. 1-2

Author(s):

Ruby Dhar ◽

Arun Kumar ◽

Subhradip Karmakar

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Human Genome ◽

Genetic Information ◽

Antibiotic Resistance Genes ◽

Ion Binding ◽

Gene Expressions ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Eukaryotic Genomes

Horizontal gene transfer (HGT) in prokaryotes refers to the movement of genes and genetic information between two organisms. This usually results in the spread of antibiotic resistance genes among bacteria. Vertical gene transfer(VGT), on the other hand, refers to the flow of genetic information from parents to offsprings. Until recently, HGT was an exclusive prerogative of the prokaryotes. These are obvious due to the distinct nuclear membrane enclosure of eukaryote genomes that are shielded from outside interferences. VGT can cross species barriers and may even allow the transmission of genes across the kingdoms of life. HGT is now an emerging idea in eukaryotic genomes, challenging previous assertions that HGT is restricted to prokaryotes. It is now accepted that HGT can profoundly influence host metabolic pathways and alter gene expressions even in eukaryotes. HGT, is also fundamentally important during development, origin of human diseases, such as cancer, and neurodegenerative disorders. It may also influence therapeutic outcome by promoting resistant phenotypes. HGT is recently documented in prokaryote to eukaryote HGT is the tardigrade case though an analysis of a draft tardigrade genome suggested that HGT contributed to up to ~17 % of the gene. Further analysis performed after whole genome pair-wise alignments between human genome as well as 53 vertebrate genomes, it was observed that nearly 1500 human genome regions involving 642 known genes, most of which are enriched with ion binding to be conserved with non-mammals than with most mammals. This indicated horizontal gene transfer is more common than we expected in the human genome. It’s a matter of time or maybe a tip of iceberg to know the full extent and implications of HGT. Surprisingly its seems that the eukaryotic genome has many more ways to update itself to vastly expand its repertoire of expression and usability. HGT is just another feather in the crown.

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Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes

Journal of Virology ◽

10.1128/jvi.00955-10 ◽

2010 ◽

Vol 84 (22) ◽

pp. 11876-11887 ◽

Cited By ~ 144

Author(s):

Huiquan Liu ◽

Yanping Fu ◽

Daohong Jiang ◽

Guoqing Li ◽

Jiatao Xie ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Rna Viruses ◽

Host Cells ◽

Double Stranded Rna ◽

New Genes ◽

Viral Genes ◽

Nuclear Genomes ◽

Eukaryotic Organisms ◽

Eukaryotic Genomes

ABSTRACT Horizontal gene transfer commonly occurs from cells to viruses but rarely occurs from viruses to their host cells, with the exception of retroviruses and some DNA viruses. However, extensive sequence similarity searches in public genome databases for various organisms showed that the capsid protein and RNA-dependent RNA polymerase genes from totiviruses and partitiviruses have widespread homologs in the nuclear genomes of eukaryotic organisms, including plants, arthropods, fungi, nematodes, and protozoa. PCR amplification and sequencing as well as comparative evidence of junction coverage between virus and host sequences support the conclusion that these viral homologs are real and occur in eukaryotic genomes. Sequence comparison and phylogenetic analysis suggest that these genes were likely transferred horizontally from viruses to eukaryotic genomes. Furthermore, we present evidence showing that some of the transferred genes are conserved and expressed in eukaryotic organisms and suggesting that these viral genes are also functional in the recipient genomes. Our findings imply that horizontal transfer of double-stranded RNA viral genes is widespread among eukaryotes and may give rise to functionally important new genes, thus entailing that RNA viruses may play significant roles in the evolution of eukaryotes.

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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2009974118 ◽

2021 ◽

Vol 118 (4) ◽

pp. e2009974118

Author(s):

Richard G. Dorrell ◽

Adrien Villain ◽

Benoît Perez-Lamarque ◽

Guillemette Audren de Kerdrel ◽

Giselle McCallum ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Large Scale ◽

Single Gene ◽

Gene Trees ◽

Reference Tree ◽

In Silico Modeling ◽

Genes Encoding ◽

Eukaryotic Genomes ◽

Algal Evolution

Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum. Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.

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