Examples of inter-phylum adaptive horizontal DNA transfers based on genomic data
Donor	Recipient	Function(s)	Reference(s)
Prokaryote-prokaryote (Koonin 2016)
Bacteria	Methanogenic Archaea (early Haloarchaea)	1,089 transfers, carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I-IV of the eubacterial respiratory chain; converted strictly anaerobic, chemolithoautotrophic methanogen into heterotrophic, oxygen-respiring haloarchaeal common ancestor.	(Nelson-Sathi, Dagan et al. 2012)
Bacteria	Methanogenic Archaea Methosarcina spp.	~5-11% of genetic loci, including gluconeogenesis, proline biosynthesis, transport processes, DNA-repair, environmental sensing, gene regulation, and stress response, such as the bacterial GroEL/GroES chaperone system and the presence of tetrahydrofolate-dependent enzymes	(Deppenmeier, Johann et al. 2002; Garushyants, Kazanov et al. 2015)
Bacteria	Mesophilic clades descended from thermophilic Archaea: Thaumarchaeota, MG II/III euryarchaeotes, Halobacteriales	Mesophilic metabolic activites (energy conversion, amino acid transport and metabolism, and lipid or membrane biogenesis): Thaumarchaeota (937 loci), MG II/III euryarchaeotes (1677 loci), Halobacteriales (1047 loci)	(Deschamps, Zivanovic et al. 2014; Lopez-Garcia, Zivanovic et al. 2015)
Bacteria	Early Archaeal progenitors	“13 archaeal higher taxa…correspond to 2,264 group-specific gene acquisitions from bacteria”	(Nelson-Sathi, Sousa et al. 2015; Groussin, Boussau et al. 2016)
Prokaryote-eukaryote microbe (Marcet-Houben and Gabaldon 2009; Soanes and Richards 2014)
Actinobacterium	Basidiomycete Agaricomycotina	Alpha-amylase		(Da Lage, Binder et al. 2013)
Bacteria	Plant pathogenic fungi Pyrenophora teres and Pyrenophora tritici-repentis	Extracellular proteins, interference with plant defense-response, degradation of plant cell walls, carbohydrate metabolism		(Sun, Xiao et al. 2013; Soanes and Richards 2014)
Bacteria (40%), fungi (25%), and viruses (22%)	Animal pathogenic fungus Aspergillus fumigatus	Central and intermediary metabolism, virulence (including lipase, 4 peptide transporters, gliotoxin synthesis)		(Mallet, Becq et al. 2010)
Bacteria and Archaea	Red alga Galdieria sulphuraria	Growth in high temperature, toxic metal-rich, acidic environments		(Schonknecht, Chen et al. 2013)
Bacteria	Red alga Porphyridium purpureum	Non-plastid functions encoded in nuclear genome		(Qiu, Yoon et al. 2013)
Actinobacteria, proteobacteria, archaea	Chromalveolates (dinoflagellates of the genera Karenia and Karlodinium)	Energy metabolism, sugar and amino acid metabolism, cell membrane biosynthesis, substrate transport, DNA repair		(Nosenko and Bhattacharya 2007)
Proteobacteria, cyanobacteria and archaea	Diatom Phaeodactylum tricornutum	7.5% of genetic loci (784 loci); organic carbon and nitrogen utilization (xylanases and glucanases, prismane, carbon-nitrogen hydrolase, amidohydrolase), diatom urea cycle (carbamoyl transferase, carbamate kinase, ornithine cyclodeaminase) and polyamine metabolism related to diatom cell wall silicification (S-adenosylmethionine (SAM)-dependent decarboxylases and methyltransferases); also cell wall component synthesis, unorthodox DNA replication, repair and recombination mechanisms		(Bowler, Allen et al. 2008)
Bacteria, archaea	Rumen ciliates	Catabolism of complex carbohydrates		(Ricard, McEwan et al. 2006)
Actinobacteria	Plant pathogenic fungal Phytophthora species	Cutinase		(Belbahri, Calmin et al. 2008)
Bacteria	Fish ciliate scuticociliatosis pathogen Pseudocohnilembus persalinus	Cell adhesion, hemolysis and heme utilization		(Xiong, Wang et al. 2015)
Bacteria, eukaryotes Dictyostelium discoideum, Entamoeba histolytica, Gibberella zeae, Mastigamoeba balamuthi	Diplomonad fish parasite Spironucleus salmonicida	Amino acid metabolism, DNA repair, protein folding, membrane transport, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate metabolism, pentose phosphate pathway, pyruvate metabolism, starch and sucrose metabolism, nitrogen metabolism, oxidative phosphorylation, purine and pyrimidine metabolism		(Andersson, Sjogren et al. 2007)
β,γ-Proteobacteria, Chlamydiae, other bacteria	Red alga Cyanidioschyzon	Amino acid, vitamin, lipid, porphyrin biosynthesis; ATP/ADP transport; RNA processing, translation		(Huang and Gogarten 2008)
Arthrobacter	Ascomycete fungi Penicillium canescens and Scopulariopsis sp	Beta-glucuronidase (enables utilization of glucuronides in vertebrate urine)		(Wenzl, Wong et al. 2005)
Rumen bacteria Fibrobacter succinogenes	Rumen fungus Orpinomyces joyonii	Endoglucanase (polysaccharide digestion)		(Garcia-Vallve, Romeu et al. 2000)
Bacteria	Eukaryotic unicellular parasites (Entamoeba histolytica, E. dispar, Trichomonas vaginalis, Giardia lamblia, Trypanosoma brucei, T. cruzi, Plasmodium falciparum)	Amino acid, sugar, nucleotide, lipid, and, energy metabolism, host glycan degradation, vitamin and membrane biosynthesis, translation		(Loftus, Anderson et al. 2005; Alsmark, Sicheritz-Ponten et al. 2009; Alsmark, Foster et al. 2013; Strese, Backlund et al. 2014; Hirt, Alsmark et al. 2015)
Eukaryote microbe–eukaryote microbe (Andersson 2009; Andersson 2009; Soanes and Richards 2014)
Phytopathogenic fungi in genera Magnaporthiopsis  or Colletotrichum	Phytopathogenic fungi in genera Magnaporthiopsis  or Colletotrichum	33-90 horizontally transferred loci enriched for plant cell wall degrading enzymes		(Qiu, Cai et al. 2016)
Fungi	Plant parasitic oomycetes, e.g., Phytophthora ramorum	Secreted proteins for plant cell wall digestion, resisting plant defenses, effector functions		(Richards, Soanes et al. 2011)
Filamentous plant pathogenic Ascomycete fungus Magnaporthe grisea	Filamentous plant Oomycete pathogen Phytophthora sp.	Sugar-transporter, purine permease, extracellular dioxygenase/Protocatechuate 3,4-dioxygenase β-subunit, aldose 1-epimerase (osmotropic lifestyle)		(Richards, Dacks et al. 2006)
Fungal pathogen Stagonospora nodorum	Fungal pathogen Pyrenophora tritici-repentis	ToxA virulence factor, extends host range		(Mehrabi, Bahkali et al. 2011)
Algae, bacteria	Choanoflagellate Monosiga brevicollis	405 genetic loci (4.4% nuclear genome); carbohydrate and amino acid metabolism, 45 transporters, responses to oxidative, osmotic, antibiotic, or heavy metal stresses, biosynthesis of vitamins C and K12, porphyrins and phospholipids.		(Nedelcu, Miles et al. 2008) (Yue, Sun et al. 2013) (Tucker 2013) (Sun, Yang et al. 2010)
Prokaryote-animal (Dunning Hotopp 2011; Alegado and King 2014; Boto 2014)
Bacteria, likely including some related to marine species Vibrio campbellii, Desulfovibrio hydrothermalis, and Arcobacter nitrofigilis	Sponge Amphimedon queenslandica, a model metazoan ancestor (Srivastava, Simakov et al. 2010)	227 loci transferred, including metallopeptidase, carbohydrate metabolism, polymer degradation, transport, proteolysis, nitrogen metabolism, extracellular matrix biosynthesis		(Conaco, Tsoulfas et al. 2016)
Mainly bacteria, but also fungi, protists, and algae	Bdelloid rotifers	8-9% of genetic loci, including toxin degradation, biosynthesis of antioxidants and key metabolites, amino acid metabolism, non-ribosomal peptide synthetases		(Gladyshev, Meselson et al. 2008; Boschetti, Carr et al. 2012; Eyres, Boschetti et al. 2015)
Bacteria, fungi	Bdelloid rotifer, Adineta ricciae	16 cellulolytic enzymes		(Szydlowski, Boschetti et al. 2015)
Bacteria	Sponge Astrosclera willeyana	Biomineralization		(Jackson, Macis et al. 2011)
Bacteria	Starlet sea anemone, Nematostella vectensis	Shikimic acid biosynthesis, glyoxylate cycle		(Kondrashov, Koonin et al. 2006; Starcevic, Akthar et al. 2008)
Bacteria	Cnidarian Hydra magnipapillata	Carbohydrate, lipid, nucleotide, amino acid, cofactor, vitamin and xenobiotic metabolism, glycan biosynthesis; transamination, methylation, and acetylation of sugars, polysaccharides, or glycoproteins; bacterial lipopolysaccharide (LPS) biosynthetic pathway		(Chapman, Kirkness et al. 2010)
Bacteria	Filarial nematode parasite Onchocerca flexuosa	Independence from Wolbachia endosymbionts; synthesis of riboflavin, heme and nucleotides; inosine monophosphate and uridine monophosphate biosynthesis		(McNulty, Foster et al. 2010; McNulty, Abubucker et al. 2012)
Bacteria, chiefly rhizobacteria, and fungi	Plant parasitic nematodes	Cellulose and phytopolymer digestion (multiple transfers to distinct nematode lineages), B vitamin biosynthesis, plant resistance-breaking effector proteins		(Bird, Opperman et al. 2003; Craig, Bekal et al. 2008; Opperman, Bird et al. 2008; Craig, Bekal et al. 2009; Mitreva, Smant et al. 2009; Danchin 2011; Haegeman, Jones et al. 2011; Mayer, Schuster et al. 2011; Scholl and Bird 2011; Paganini, Campan-Fournier et al. 2012; Eves-van den Akker, Laetsch et al. 2016)
Bacteria	Stick and Leaf Insects	Pectinases		(Shelomi, Danchin et al. 2016)
Bacteria	Phytophagous mites and Lepidoptera	Detoxification of plant defense cyanogenic glucosides		(Wybouw, Dermauw et al. 2014)
Bacteria and fungi	Asian longhorned beetle Anoplophora glabripennis	Enzymes involved in digestion of woody plant tissues and detoxification of plant allelochemicals		(McKenna, Scully et al. 2016)
Bacteria and fungi	Herbivorous arthropods (>20 distinct insect and chelicerate species)	Overcoming plant defenses, assimilation of intracellular plant metabolites, digestion of plant cell walls		(Wybouw, Pauchet et al. 2016)
Bacteria	Coffee berry borer beetle, Hypothenemus hampe	Glycosyl hydrolase (galactomannan, major coffee storage polymer, is the substrate)		(Acuna, Padilla et al. 2012)
Bacteria	Silkworm Bombyx mori and related Lepidoptera	Glycosyl hydrolase family, oxidoreductase family, and amino acid metabolism		(Li, Shen et al. 2011)
Archaea, Bacteria, Fungi, Protists, and Plants	26 animal species (4 Caenorhabditis, 12 Drosophila, and 10 primates)	Multiple metabolic functions (biosynthetic and degradative), innate immunity responses, antioxidant activities		(Crisp, Boschetti et al. 2015)
Bacteria	Arthropods, echinoderms, and vertebrates, including platypus and opossum, but not in splacental mammals	Glyoxylate cycle		(Kondrashov, Koonin et al. 2006)
Bacteria, Archaea, fungi and plants	Tardigrade Hypsibius dujardini (desiccation-resistant animals subject to oxidative stress)	17.5% of tardigrade genetic loci, particularly oxidative stress tolerance functions: catalases; DNA repair functions, including recombination proteins and translesion polymerases; polyamine biosynthesis; heat shock chaperones		(Boothby, Tenlen et al. 2015)
Bacteria	Urochordate Ciona intestinalis	Cellulose synthase		(Nakashima, Yamada et al. 2004)
Eukaryotic microbe-animal (Boto 2014)
Fungi	Pea aphid, two-spotted spider mite Tetranychus urticae	Carotenoid pigment biosynthesis, cyanate metabolism		(Moran and Jarvik 2010; Altincicek, Kovacs et al. 2012; Wybouw, Balabanidou et al. 2012)
Algae and other photosynthetic eukaryotes	Tunicate Ciona intestinalis	Molecule transport, cellular regulation and methylation signaling		(Ni, Yue et al. 2012)
Animal-eukaryotic microbe
Arthropod	Microsporidia intracellular parasites Encephalitozoon intestinalis and Encephalitozoon cuniculi	Purine nucleotide phosphorylase, folylpolyglutamate synthase		(Selman, Pombert et al. 2011; Pombert, Selman et al. 2012)
Prokaryote-plant (non-plastid)
Bacteria, Archaea, viruses, and sea anemones	Moss Physcomitrella patens (primitive land plant)	Xylem formation, plant defense, nitrogen recycling, plus biosynthesis of starch, polyamines, hormones and glutathione; actinoporin water stress adaptation		(Hoang, Cho et al. 2009; Yue, Hu et al. 2012)
Bacteria, fungi	Plants	Shikimate biosynthesis, phenylpropanoid pathway leading to synthesis of flavonoids and lignin, TAL transaldolase involved in vascular biogenesis		(Emiliani, Fondi et al. 2009; Yang, Zhou et al. 2015)
Eukarote microbe-plant
Fungi	Plants (Bryophyte Physcomitrella patens and Lycophyte Selaginella moellendorffil)	L-fucose permease sugar transporter, , membrane transporter, bifunctional iucA/iucC siderophore biosynthesis protein, phospholipase/carboxylesterase family protein. Both cases that involve HGT from a fungus to the bryophyte moss P. patens, the HGT is positioned next to a putative transposable element.		(Richards, Soanes et al. 2009)
Plant-microbe
Plants	Bacteria, fungi, amoebozoa	Expansins (plant cell-wall loosening proteins)		(Nikolaidis, Doran et al. 2014)
Plants	Fungi (Basidiomycete Laccaria bicolor, Chytrydiomycete Bhatrachochytrium dendrobatidis, Ascomycete Sclerotinia sclerotiorum)	Phosphate-responsive protein, zinc binding alcohol dehydrogenase, DUF239 domain protein, zinc finger (C2H2 type) protein		(Richards, Soanes et al. 2009)
Plant-plant (Bock 2009; Gao, Ren et al. 2014)
Parasitic plant (Cuscuta sp.)	Host plant (Plantago sp.)	Mitochondrial loci atp1, atp6 and matR		(Mower, Stefanovic et al. 2004; Mower, Stefanovic et al. 2010)
Tetrastigma rafflesiae Miq (obligate host)	Parasitic flowering plant Rafflesia cantleyi Solms-Laubach	Respiration, carbohydrate metabolism, mitochondrial translation, and protein turnover; mitochondrial sequences		(Davis and Wurdack 2004; Xi, Bradley et al. 2012) (Xi, Wang et al. 2013)
Grasses, Panicoideae genera	16 diploid barley (Hordeum) species	Ribosomal RNA (rDNA) sequences		(Mahelka, Krak et al. 2017)
Bryophyte hornworts	Fern	Novel chimeric photoreceptor--neochrome		(Li, Villarreal et al. 2014)
Andropogoneae, Cenchrinae (2 species), and Melinidinae C4 plants	Grass lineage Alloteropsis (4 independent transfers)	C4 photosynthesis activities (phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase)		(Christin, Edwards et al. 2012)
Plant	Plants (Amborella and others)	Mitochondrial genomes		(Bergthorsson, Adams et al. 2003; Bergthorsson, Richardson et al. 2004; Rice, Alverson et al. 2013; Gandini and Sanchez-Puerta 2017)
Papilionoid legume	Phelipanche aegyptiaca, parasitic species of family Orobanchaceae	albumin 1 KNOTTIN-like proteins		(Zhang, Fernandez-Aparicio et al. 2013)
Brassicaceae host plant	Root parasitic plant Orobanche aegyptiaca, shoot parasitic plant Cuscuta australis	Strictosidine synthase (independent transfers)		(Zhang, Qi et al. 2014)
Animal-animal	(Boto 2014)
Fish (herring or sea raven)	Rainbow smelt, Osmerus mordax	Type II anti-freeze protein		(Graham, Lougheed et al. 2008; Graham, Li et al. 2012)
Eukaryote-prokaryote  (Doolittle, Feng et al. 1990)
Eukaryotic cells (Impossible to identify because Legionella infects and grows in amoebae, protozoa, paramecium, macrophages, and many other eukaryotic cells)	Bacteria Legionella pneumophila	Eukaryote-like regulatory “effector” proteins injected in the course of infecting eukaryotic cells		(Lurie-Weinberger, Gomez-Valero et al. 2010; Gomez-Valero, Rusniok et al. 2011; de la Casa-Esperon 2012; Rolando and Buchrieser 2014; Burstein, Amaro et al. 2016)
Virus-prokaryote
Halovirus	Halobacterium salinarum (Archaea)	B-type DNA polymerase B1		(Filee, Forterre et al. 2002)
Virus-eukaryote
T3/T7 family bacteriophage	Ancestral eukaryote nuclear and mitochondrial genomes	A-type DNA polymerase Gamma of the mitochondrion (Opisthokonts only, metazoa and fungi), mitochondrial single-subunit RNA Polymerase (mt-ssRNAP), nucleus-encoded mitochondrial replicative helicase (all eukaryotes)		(Filee, Forterre et al. 2002; Filee and Forterre 2005; Shutt and Gray 2006)
Double-stranded RNA viruses (totiviruses and partitiviruses)	Eukaryote nuclear genomes (plants, arthropods, fungi, nematodes, and protozoa)	Capsid protein and RNA-dependent RNA polymerases		(Liu, Fu et al. 2010)
Circular single-stranded DNA viruses (geminiviruses, nanoviruses and circoviruses)	Eukaryotic nuclear genomes (plants, fungi, animals and protists)	Replication initiation protein (Rep)-related sequences		(Liu, Fu et al. 2011)
Cellular organisms-virus
Bacteria	Diverse temperate bacteriophages (bacterial viruses capable of insertion into “lysogen” bacterial genome as repressed prophage)	Expressed in lysogens: DNA adenine methylase, DNA cytosine methylase, porin (outer membrane transport), mammalian serum resistance, phage attack resistance, improved survival in Peyer's patches, mammalian cell binding, superoxide dismutase (lysogen more virulent in mice), mammalian cell ruffling and cell invasion, Shiga-like toxin (kills mammalian cells by damaging rRNA)		(Hendrix, Lawrence et al. 2000)
Bacteria (primarily, endosymbionts and parasites), bacteriophages, protists, animals	Nucleocytoplasmic large DNA viruses (NCLDVs), including Poxviruses and Iridoviruses infecting insects and vertebrates, Mimiviruses and Phycodnaviruses infecting amoebae, protists and algae	Small and large subunit rDNAs, DNA polymerase, two subunits of the DNA-dependent RNA polymerase, and two subunits of the ribonucleotide reductase, DNA ligase, dUTPase, serine/threonine kinase, thymidine kinase, ribonucleotide reductase, virus-specific signaling and regulatory domains, ubiquitin signaling; defenses against apoptosis, immune response (the MHC class I, interleukin-10, interleukin-24, interleukin-18, the interferon gamma receptor, and tumor necrosis factor receptor II), including growth factors and potential inhibitors of cytokine signaling, peptidases; glutaredoxin and glutathione peroxidase involved in resistance of cells to oxidative stress.		(Tidona and Darai 2000; Hughes and Friedman 2005; Iyer, Balaji et al. 2006; Filee, Siguier et al. 2007; Filee, Pouget et al. 2008; Colson and Raoult 2010; Aherfi, Colson et al. 2016)
Mammal	Influenza virus	28S rDNA insert in hemagglutinin sequence increases pathogenicity		(Becker 2000)
Gamma-proteobacteria and insects (viral hosts)	Baculovirus	DNA ligase, ribonucleotide reductase 1, SNF2 global transactivator, inhibitor of apoptosis, chitinase, and UDP-glucosyltransferase		(Hughes and Friedman 2003)
Marine phytoplankton prasinophytes	Prasinovirus	Glycosyltransferases, methyltransferases and amino acid synthesis enzymes		(Weynberg, Allen et al. 2017)

 

 

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