Abstract
Horizontal gene transfer (HGT) has been traditionally assumed as limited in eukaryotes in contrast with its high frequency observed in prokaryotes. Although this event remains controversial in eukaryotic cells, evidences suggest that HGT is a relevant mechanism in eukaryotic genome development, as an evolutionary shortcut, triggering the appearance of new capabilities in the involved organisms. The best well-known transfer comes from endosymbionts to the host nuclear genome, often called endosymbiotic gene transfer, which represents an intracellular transference. Moreover, due to fungal inherent characteristics, as chitin cell walls and osmotrophic feeding, these organisms are considered as the most recalcitrant to allow gene transfer to them. However, the exponential number of genome sequences available on the databases has boosted the number of described gene transference events. Thus, the detection of the transferred genes, as well as their putative mechanisms of transference, is under study as a trending topic. Initially, genes from bacteria to fungi were the first detected candidates. Secondly, some complete bacterial metabolic pathways have been detected as transferred. Nowadays, the transference has been noticed from fungi to fungi or even from fungi to other eukaryotic organisms as aphids and plants or endosymbionts. This fact is opening the skyline to new unexpected gene or cluster movements.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Alexander WG, Wisecaver JH, Rokas A, Hittinger CT (2016) Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc Natl Acad Sci 113:4116–4121. https://doi.org/10.1073/pnas.1517242113
Altincicek B, Kovacs JL, Gerardo NM (2012) Horizontally transferred fungal carotenoid genes in the two-spotted spider mite Tetranychus urticae. Biol Lett 8:253–257. https://doi.org/10.1098/rsbl.2011.0704
Andersson JO (2005) Lateral gene transfer in eukaryotes. Cell Mol Life Sci 62:1182–1197. https://doi.org/10.1007/s00018-005-4539-z
Andersson JO, Sjögren AM, Davis LAM et al (2003) Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol 13:94–104
Andersson JO, Sjögren AM, Horner DS et al (2007) A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 8:51. https://doi.org/10.1186/1471-2164-8-51
Barredo J, García-Estrada C, Kosalkova K, Barreiro C (2017) Biosynthesis of astaxanthin as a main carotenoid in the heterobasidiomycetous yeast Xanthophyllomyces dendrorhous. J Fungi 3:44. https://doi.org/10.3390/jof3030044
Barreiro C, Barredo J (2018) Carotenoids production: a healthy and profitable industry. In: Barreiro C, Barredo J (eds) Microbial carotenoids: methods and protocols. Springer Science+Business Media, New York, NY, pp 45–55
Belbahri L, Calmin G, Mauch F, Andersson JO (2008) Evolution of the cutinase gene family: evidence for lateral gene transfer of a candidate Phytophthora virulence factor. Gene 408:1–8. https://doi.org/10.1016/j.gene.2007.10.019
Bowler C, Allen AE, Badger JH et al (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature 456:239–244. https://doi.org/10.1038/nature07410
Brinkman FS, Macfarlane EL, Warrener P, Hancock RE (2001) Evolutionary relationships among virulence-associated histidine kinases. Infect Immun 69:5207–5211. https://doi.org/10.1128/IAI.69.8.5207-5211.2001
Bryon A, Kurlovs AH, Dermauw W et al (2017) Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause in Tetranychus urticae. Proc Natl Acad Sci 114:E5871–E5880. https://doi.org/10.1073/pnas.1706865114
Bull JJ, Springman R, Molineux IJ (2007) Compensatory evolution in response to a novel RNA polymerase: orthologous replacement of a central network gene. Mol Biol Evol 24:900–908. https://doi.org/10.1093/molbev/msm006
Bundock P, den Dulk-Ras A, Beijersbergen A, Hooykaas PJ (1995) Trans-kingdom T-DNA transfer from Agrobacterium tumefaciens to Saccharomyces cerevisiae. EMBO J 14:3206–3214
Calvo AM, Wilson RA, Bok JW, Keller NP (2002) Relationship between secondary metabolism and fungal development. Microbiol Mol Biol Rev 66:447–459
Campoy S, Pérez F, Martín JF et al (2003) Stable transformants of the azaphilone pigment-producing Monascus purpureus obtained by protoplast transformation and Agrobacterium-mediated DNA transfer. Curr Genet 43:447–452. https://doi.org/10.1007/s00294-003-0417-0
Cardoza RE, Vizcaino JA, Hermosa MR et al (2006) A comparison of the phenotypic and genetic stability of recombinant Trichoderma spp. generated by protoplast- and Agrobacterium-mediated transformation. J Microbiol 44:383–395
Chen X, Stone M, Schlagnhaufer C, Romaine CP (2000) A fruiting body tissue method for efficient Agrobacterium-mediated transformation of Agaricus bisporus. Appl Environ Microbiol 66:4510–4513
Cheng C, Qin J, Wu C et al (2018) Suppressing a plant-parasitic nematode with fungivorous behavior by fungal transformation of a Bt cry gene. Microb Cell Factories 17:116. https://doi.org/10.1186/s12934-018-0960-5
Cobbs C, Heath J, Stireman JO, Abbot P (2013) Carotenoids in unexpected places: Gall midges, lateral gene transfer, and carotenoid biosynthesis in animals. Mol Phylogenet Evol 68:221–228. https://doi.org/10.1016/j.ympev.2013.03.012
Coelho MA, Gonçalves C, Sampaio JP, Gonçalves P (2013) Extensive intra-kingdom horizontal gene transfer converging on a fungal fructose transporter gene. PLoS Genet 9:e1003587. https://doi.org/10.1371/journal.pgen.1003587
Cohen O, Gophna U, Pupko T (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol 28:1481–1489. https://doi.org/10.1093/molbev/msq333
Collado IG, Sánchez AJM, Hanson JR (2007) Fungal terpene metabolites: biosynthetic relationships and the control of the phytopathogenic fungus Botrytis cinerea. Nat Prod Rep 24:674–686. https://doi.org/10.1039/b603085h
Coyne RS, Lhuillier-Akakpo M, Duharcourt S (2012) RNA-guided DNA rearrangements in ciliates: is the best genome defence a good offence? Biol Cell 104:309–325. https://doi.org/10.1111/boc.201100057
Cuomo CA, Birren BW (2010) The fungal genome initiative and lessons learned from genome sequencing. Methods Enzymol 470:833–855. https://doi.org/10.1016/S0076-6879(10)70034-3
Dagan T, Artzy-Randrup Y, Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci USA 105:10039–10044. https://doi.org/10.1073/pnas.0800679105
Danchin EGJ, Rosso M-N, Vieira P et al (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci USA 107:17651–17656. https://doi.org/10.1073/pnas.1008486107
Daskalov A, Heller J, Herzog S et al (2017) Molecular mechanisms regulating cell fusion and heterokaryon formation in filamentous fungi. Microbiol Spectr 5. https://doi.org/10.1128/microbiolspec.FUNK-0015-2016
De Barro PJ, Liu S-S, Boykin LM, Dinsdale AB (2011) Bemisia tabaci: a statement of species status. Annu Rev Entomol 56:1–19. https://doi.org/10.1146/annurev-ento-112408-085504
de Groot MJ, Bundock P, Hooykaas PJ, Beijersbergen AG (1998) Agrobacterium tumefaciens-mediated transformation of filamentous fungi. Nat Biotechnol 16:839–842. https://doi.org/10.1038/nbt0998-839
de Sena Filho JG, Quin MB, Spakowicz DJ et al (2016) Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway. Fungal Biol 120:1050–1063. https://doi.org/10.1016/j.funbio.2016.04.001
Doolittle WF (1999a) Lateral genomics. Trends Cell Biol 9:M5–M8
Doolittle WF (1999b) Phylogenetic classification and the universal tree. Science 284:2124–2129
Druzhinina IS, Chenthamara K, Zhang J et al (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet 14:e1007322. https://doi.org/10.1371/journal.pgen.1007322
Dujon B, Sherman D, Fischer G et al (2004) Genome evolution in yeasts. Nature 430:35–44. https://doi.org/10.1038/nature02579
Dumesic PA, Natarajan P, Chen C et al (2013) Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 152:957–968. https://doi.org/10.1016/j.cell.2013.01.046
Dunning Hotopp JC, Clark ME, Oliveira DCSG et al (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753–1756. https://doi.org/10.1126/science.1142490
Eichinger L, Pachebat JA, Glöckner G et al (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43–57. https://doi.org/10.1038/nature03481
Eisen JA (2000) Assessing evolutionary relationships among microbes from whole-genome analysis. Curr Opin Microbiol 3:475–480
Fast NM, Law JS, Williams BAP, Keeling PJ (2003) Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution. Eukaryot Cell 2:1069–1075
Fischer MJC, Rustenhloz C, Leh-Louis V, Perrière G (2015) Molecular and functional evolution of the fungal diterpene synthase genes. BMC Microbiol 15:221. https://doi.org/10.1186/s12866-015-0564-8
Fitzpatrick DA, Logue ME, Butler G (2008) Evidence of recent interkingdom horizontal gene transfer between bacteria and Candida parapsilosis. BMC Evol Biol 8:181. https://doi.org/10.1186/1471-2148-8-181
Fraser PD, Bramley PM (2004) The biosynthesis and nutritional uses of carotenoids. Prog Lipid Res 43:228–265. https://doi.org/10.1016/j.plipres.2003.10.002
Garcia-Vallvé S, Romeu A, Palau J (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res 10:1719–1725
Gladyshev E (2017) Repeat-induced point mutation and other genome defense mechanisms in fungi. Microbiol Spectr 5. https://doi.org/10.1128/microbiolspec.FUNK-0042-2017
Gladyshev EA, Meselson M, Arkhipova IR (2008) Massive horizontal gene transfer in bdelloid rotifers. Science 320:1210–1213. https://doi.org/10.1126/science.1156407
Glass NL, Jacobson DJ, Shiu PK (2000) The genetics of hyphal fusion and vegetative incompatibility in filamentous ascomycete fungi. Annu Rev Genet 34:165–186. https://doi.org/10.1146/annurev.genet.34.1.165
Gogarten JP, Townsend JP (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687. https://doi.org/10.1038/nrmicro1204
Gojković Z, Knecht W, Zameitat E et al (2004) Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol Gen Genomics 271:387–393. https://doi.org/10.1007/s00438-004-0995-7
Gonzalez P, Barroso G, Labarère J (1998) Molecular analysis of the split cox1 gene from the Basidiomycota Agrocybe aegerita: relationship of its introns with homologous Ascomycota introns and divergence levels from common ancestral copies. Gene 220:45–53
Graham LA, Lougheed SC, Ewart KV, Davies PL (2008) Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS One 3:e2616. https://doi.org/10.1371/journal.pone.0002616
Hall C, Dietrich FS (2007) The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics 177:2293–2307. https://doi.org/10.1534/genetics.107.074963
Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4:1102–1115. https://doi.org/10.1128/EC.4.6.1102-1115.2005
Hane JK, Williams AH, Taranto AP et al (2015) Repeat-induced point mutation: a fungal-specific, endogenous mutagenesis process. In: van den Berg M, Maruthachalam K (eds) Genetic transformation systems in fungi, vol 2. Springer, pp 55–68
Haney SL, Wills VS, Wiemer DF, Holstein SA (2017) Recent advances in the development of mammalian geranylgeranyl diphosphate synthase inhibitors. Molecules 22:886. https://doi.org/10.3390/molecules22060886
Hayashi K-I, Kawaide H, Notomi M et al (2006) Identification and functional analysis of bifunctional ent-kaurene synthase from the moss Physcomitrella patens. FEBS Lett 580:6175–6181. https://doi.org/10.1016/j.febslet.2006.10.018
Heinemann JA, Sprague GF (1989) Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340:205–209. https://doi.org/10.1038/340205a0
Heinig U, Jennewein S (2009) Taxol: a complex diterpenoid natural product with an evolutionarily obscure origin. J Biotechnol 8:1370–1385. https://doi.org/10.4314/ajb.v8i8.60130
Hoekstra RF (1994) Population genetics of filamentous fungi. Antonie Van Leeuwenhoek 65:199–204
Huang J, Mullapudi N, Lancto CA et al (2004) Phylogenomic evidence supports past endosymbiosis, intracellular and horizontal gene transfer in Cryptosporidium parvum. Genome Biol 5:R88. https://doi.org/10.1186/gb-2004-5-11-r88
Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806
Jaramillo ADA, Sukno SA, Thon MR (2015) Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics 16:1–16. https://doi.org/10.1186/1471-2164-16-2
Jennewein S, Wildung MR, Chau M et al (2004) Random sequencing of an induced Taxus cell cDNA library for identification of clones involved in Taxol biosynthesis. Proc Natl Acad Sci USA 101:9149–9154. https://doi.org/10.1073/pnas.0403009101
Karlin S, Mrázek J, Campbell AM (1998) Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 29:1341–1355
Kauserud H, Svegården IB, Decock C, Hallenberg N (2007) Hybridization among cryptic species of the cellar fungus Coniophora puteana (Basidiomycota). Mol Ecol 16:389–399. https://doi.org/10.1111/j.1365-294X.2006.03129.x
Keeling PJ, Palmer JD (2008) Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet 9:605–618. https://doi.org/10.1038/nrg2386
Kempken F (1995) Horizontal transfer of a mitochondrial plasmid. Mol Gen Genet 248:89–94
Kleine T, Maier UG, Leister D (2009) DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol 60:115–138. https://doi.org/10.1146/annurev.arplant.043008.092119
Kloesges T, Popa O, Martin W, Dagan T (2011) Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths. Mol Biol Evol 28:1057–1074. https://doi.org/10.1093/molbev/msq297
Koepp AE, Hezari M, Zajicek J et al (1995) Cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene is the committed step of taxol biosynthesis in Pacific yew. J Biol Chem 270:8686–8690
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742. https://doi.org/10.1146/annurev.micro.55.1.709
Kozák L, Szilágyi Z, Vágó B et al (2018) Inactivation of the indole-diterpene biosynthetic gene cluster of Claviceps paspali by Agrobacterium-mediated gene replacement. Appl Microbiol Biotechnol 102:3255–3266. https://doi.org/10.1007/s00253-018-8807-x
Lawrence JG (1999) Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 2:519–523
Lawrence JG, Ochman H (1997) Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 44:383–397
League GP, Slot JC, Rokas A (2012) The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces. FEMS Yeast Res 12:859–863. https://doi.org/10.1111/j.1567-1364.2012.00828.x
Li G, Köllner TG, Yin Y et al (2012) Nonseed plant Selaginella moellendorffi has both seed plant and microbial types of terpene synthases. Proc Natl Acad Sci USA 109:14711–14715. https://doi.org/10.1073/pnas.1204300109
Li F-W, Villarreal JC, Kelly S et al (2014) Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proc Natl Acad Sci USA 111:6672–6677. https://doi.org/10.1073/pnas.1319929111
Li M, Zhao J, Tang N et al (2018) Horizontal gene transfer from bacteria and plants to the arbuscular mycorrhizal fungus Rhizophagus irregularis. Front Plant Sci 9:1–13. https://doi.org/10.3389/fpls.2018.00701
Loftus B, Anderson I, Davies R et al (2005) The genome of the protist parasite Entamoeba histolytica. Nature 433:865–868. https://doi.org/10.1038/nature03291
Malmierca MG, Cardoza RE, Alexander NJ et al (2013) Relevance of trichothecenes in fungal physiology: disruption of tri5 in Trichoderm arundinaceum. Fungal Genet Biol 53:22–33. https://doi.org/10.1016/j.fgb.2013.02.001
Marcet-Houben M, Gabaldón T (2010) Acquisition of prokaryotic genes by fungal genomes. Trends Genet 26:5–8. https://doi.org/10.1016/j.tig.2009.11.007
Marsit S, Mena A, Bigey F et al (2015) Evolutionary advantage conferred by an eukaryote-to-eukaryote gene transfer event in wine yeasts. Mol Biol Evol 32:1695–1707. https://doi.org/10.1093/molbev/msv057
Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15:394–408. https://doi.org/10.1038/nrg3683
Médigue C, Rouxel T, Vigier P et al (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J Mol Biol 222:851–856
Medrano-Soto A, Moreno-Hagelsieb G, Vinuesa P et al (2004) Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Mol Biol Evol 21:1884–1894. https://doi.org/10.1093/molbev/msh202
Mehrabi R, Bahkali AH, Abd-Elsalam KA et al (2011) Horizontal gene and chromosome transfer in plant pathogenic fungi affecting host range. FEMS Microbiol Rev 35:542–554. https://doi.org/10.1111/j.1574-6976.2010.00263.x
Michielse CB, Salim K, Ragas P et al (2004) Development of a system for integrative and stable transformation of the zygomycete Rhizopus oryzae by Agrobacterium-mediated DNA transfer. Mol Gen Genomics 271:499–510. https://doi.org/10.1007/s00438-004-1003-y
Mitreva M, Smant G, Helder J (2009) Role of horizontal gene transfer in the evolution of plant parasitism among nematodes. Methods Mol Biol 532:517–535. https://doi.org/10.1007/978-1-60327-853-9_30
Mondo SJ, Lastovetsky OA, Gaspar ML et al (2017) Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi. Nat Commun 8. https://doi.org/10.1038/s41467-017-02052-8
Moran NA, Jarvik T (2010) Lateral transfer of genes from fungi underlies carotenoid production in aphids. Science 328:624–627. https://doi.org/10.1126/science.1187113
Moreira D, Deschamps P (2014) What was the real contribution of endosymbionts to the eukaryotic nucleus? Insights from photosynthetic eukaryotes. Cold Spring Harb Perspect Biol 6:a016014. https://doi.org/10.1101/cshperspect.a016014
Moriguchi K, Yamamoto S, Tanaka K et al (2013) Trans-kingdom horizontal DNA transfer from bacteria to yeast is highly plastic due to natural polymorphisms in auxiliary nonessential recipient genes. PLoS One 8:e74590. https://doi.org/10.1371/journal.pone.0074590
Moszer I, Rocha EP, Danchin A (1999) Codon usage and lateral gene transfer in Bacillus subtilis. Curr Opin Microbiol 2:524–528
Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760–766. https://doi.org/10.1038/ng1381
Nakjang S, Williams TA, Heinz E et al (2013) Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Genome Biol Evol 5:2285–2303. https://doi.org/10.1093/gbe/evt184
Naranjo-Ortíz MA, Brock M, Brunke S et al (2016) Widespread inter- and intra-domain horizontal gene transfer of d-amino acid metabolism enzymes in eukaryotes. Front Microbiol 7:2001. https://doi.org/10.3389/fmicb.2016.02001
Nevoigt E, Fassbender A, Stahl U (2000) Cells of the yeast Saccharomyces cerevisiae are transformable by DNA under non-artificial conditions. Yeast 16:1107–1110. https://doi.org/10.1002/1097-0061(20000915)16:12<1107::AID-YEA608>3.0.CO;2-3
Nikoh N, McCutcheon JP, Kudo T et al (2010) Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host. PLoS Genet 6:e1000827. https://doi.org/10.1371/journal.pgen.1000827
Nováková E, Moran NA (2012) Diversification of genes for carotenoid biosynthesis in aphids following an ancient transfer from a fungus. Mol Biol Evol 29:313–323. https://doi.org/10.1093/molbev/msr206
Novo M, Bigey F, Beyne E et al (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci USA 106:16333–16338. https://doi.org/10.1073/pnas.0904673106
Ochman H, Bergthorsson U (1998) Rates and patterns of chromosome evolution in enteric bacteria. Curr Opin Microbiol 1:580–583
Pál C, Papp B, Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37:1372–1375. https://doi.org/10.1038/ng1686
Park S-Y, Jeong M-H, Wang H-Y et al (2013) Agrobacterium tumefaciens-mediated transformation of the lichen fungus, Umbilicaria muehlenbergii. PLoS One 8:e83896. https://doi.org/10.1371/journal.pone.0083896
Partida-Martinez LP, Monajembashi S, Greulich K-O, Hertweck C (2007) Endosymbiont-dependent host reproduction maintains bacterial-fungal mutualism. Curr Biol 17:773–777. https://doi.org/10.1016/j.cub.2007.03.039
Pawlowska TE, Gaspar ML, Lastovetsky OA et al (2018) Biology of fungi and their bacterial endosymbionts. Annu Rev Phytopathol 56:289–309
Pennisi E (2004) Microbiology. Researchers trade insights about gene swapping. Science 305:334–335. https://doi.org/10.1126/science.305.5682.334
Proctor RH, McCormick SP, Kim H-S et al (2018) Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi. PLoS Pathog 14:e1006946. https://doi.org/10.1371/journal.ppat.1006946
Qiu H, Cai G, Luo J et al (2016) Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol 14:1–11. https://doi.org/10.1186/s12915-016-0264-3
Quin MB, Flynn CM, Wawrzyn GT et al (2013) Mushroom hunting by using bioinformatics: application of a predictive framework facilitates the selective identification of sesquiterpene synthases in basidiomycota. Chembiochem 14:2480–2491. https://doi.org/10.1002/cbic.201300349
Ragan MA, McInerney JO, Lake JA (2009) The network of life: genome beginnings and evolution. Introduction. Philos Trans R Soc Lond Ser B Biol Sci 364:2169–2175. https://doi.org/10.1098/rstb.2009.0046
Ricard G, McEwan NR, Dutilh BE et al (2006) Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7:22. https://doi.org/10.1186/1471-2164-7-22
Richards TA, Soanes DM, Foster PG et al (2009) Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21:1897–1911. https://doi.org/10.1105/tpc.109.065805
Richards TA, Leonard G, Soanes DM, Talbot NJ (2011a) Gene transfer into the fungi. Fungal Biol Rev 25:98–110. https://doi.org/10.1016/j.fbr.2011.04.003
Richards TA, Soanes DM, Jones MDM et al (2011b) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc Natl Acad Sci USA 108:15258–15263. https://doi.org/10.1073/pnas.1105100108
Richardson AO, Palmer JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9. https://doi.org/10.1093/jxb/erl148
Rodriguez PA, Bos JIB (2013) Toward understanding the role of aphid effectors in plant infestation. Mol Plant-Microbe Interact 26:25–30. https://doi.org/10.1094/MPMI-05-12-0119-FI
Rossignol JL, Faugeron G (1994) Gene inactivation triggered by recognition between DNA repeats. Experientia 50:307–317
Sandmann G, Misawa N (2002) Fungal carotenoids. In: Osiewacz HD (ed) Industrial applications. Springer, Berlin, pp 247–262
Scholl EH, Thorne JL, McCarter JP, Bird DM (2003) Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol 4:R39. https://doi.org/10.1186/gb-2003-4-6-r39
Sibley LD (2011) Invasion and intracellular survival by protozoan parasites. Immunol Rev 240:72–91. https://doi.org/10.1111/j.1600-065X.2010.00990.x
Sieiro C, Poza M, de Miguel T, Villa TG (2003) Genetic basis of microbial carotenogenesis. Int Microbiol 6:11–16. https://doi.org/10.1007/s10123-003-0097-0
Sivasithamparam K, Ghisalberti E (1998) Secondary metabolism in Trichoderma and Gliocladium. In: Kubicek C, Harman G (eds) Trichoderma and Gliocladium. Taylor & Francis, London, pp 139–191
Sloan DB, Moran NA (2012) Endosymbiotic bacteria as a source of carotenoids in whiteflies. Biol Lett 8:986–989
Slot JC, Rokas A (2011) Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr Biol 21:134–139. https://doi.org/10.1016/j.cub.2010.12.020
Soucy SM, Huang J, Gogarten JP (2015) Horizontal gene transfer: building the web of life. Nat Rev Genet 16:472–482. https://doi.org/10.1038/nrg3962
Stern DL (2008) Aphids. Curr Biol 18:R504–R505. https://doi.org/10.1016/j.cub.2008.03.034
Stierle A, Strobel G, Stierle D (1993) Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science 260:214–216
Szklarczyk D, Franceschini A, Wyder S et al (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452. https://doi.org/10.1093/nar/gku1003
Szklarczyk D, Gable AL, Lyon D et al (2018) STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47:D607–D613. https://doi.org/10.1093/nar/gky1131
Treangen TJ, Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7:e1001284. https://doi.org/10.1371/journal.pgen.1001284
Tunjic M, Korac P (2013) Vertical and horizontal gene transfer in lichens. Period Biol 115:321–329
Ugolini I, Halic M (2018) Fidelity in RNA-based recognition of transposable elements. Philos Trans R Soc Lond Ser B Biol Sci 373. https://doi.org/10.1098/rstb.2018.0168
Uo T, Yoshimura T, Tanaka N et al (2001) Functional characterization of alanine racemase from Schizosaccharomyces pombe: a eucaryotic counterpart to bacterial alanine racemase. J Bacteriol 183:2226–2233. https://doi.org/10.1128/JB.183.7.2226-2233.2001
Valdivia RH, Heitman J (2007) Endosymbiosis: The Evil within. Curr Biol 17:408–410. https://doi.org/10.1016/j.cub.2007.04.001
van Diepeningen AD, Debets AJ, Hoekstra RF (1998) Intra- and interspecies virus transfer in Aspergilli via protoplast fusion. Fungal Genet Biol 25:171–180. https://doi.org/10.1006/fgbi.1998.1096
Walton JD (2000) Horizontal gene transfer and the evolution of secondary metabolite gene clusters in fungi: an hypothesis. Fungal Genet Biol 30:167–171. https://doi.org/10.1006/fgbi.2000.1224
Wang J-Y, Li H-Y (2008) Agrobacterium tumefaciens-mediated genetic transformation of the phytopathogenic fungus Penicillium digitatum. J Zhejiang Univ Sci B 9:823–828. https://doi.org/10.1631/jzus.B0860006
Wang J, Gao S, Mostovoy Y et al (2017) Comparative genome analysis of programmed DNA elimination in nematodes. Genome Res 27:2001–2014. https://doi.org/10.1101/gr.225730.117
Wani MC, Taylor HL, Wall ME et al (1971) Plant antitumor agents. VI. Isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus brevifolia. J Am Chem Soc 93:2325–2327. https://doi.org/10.1021/ja00738a045
Wellner A, Lurie MN, Gophna U (2007) Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biol 8:R156. https://doi.org/10.1186/gb-2007-8-8-r156
Wisecaver JH, Slot JC, Rokas A (2014) The evolution of fungal metabolic pathways. PLoS Genet 10:e1004816. https://doi.org/10.1371/journal.pgen.1004816
Xiong Z-Q, Yang Y-Y, Zhao N, Wang Y (2013) Diversity of endophytic fungi and screening of fungal paclitaxel producer from Anglojap yew, Taxus x media. BMC Microbiol 13:71. https://doi.org/10.1186/1471-2180-13-71
Yang Y, Zhao H, Barrero RA et al (2014) Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics 15:69. https://doi.org/10.1186/1471-2164-15-69
Yu Y, Gu J, Jin Y et al (2015) Panoramix enforces piRNA-dependent cotranscriptional silencing. Science 350:339–342. https://doi.org/10.1126/science.aab0700
Yue J, Hu X, Sun H et al (2012) Widespread impact of horizontal gene transfer on plant colonization of land. Nat Commun 3:1152. https://doi.org/10.1038/ncomms2148
Zaratiegui M, Castel SE, Irvine DV et al (2011) RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479:135–138. https://doi.org/10.1038/nature10501
Zhao C, Nabity PD (2017) Phylloxerids share ancestral carotenoid biosynthesis genes of fungal origin with aphids and adelgids. PLoS One 12:1–14. https://doi.org/10.1371/journal.pone.0185484
Zhong YH, Wang XL, Wang TH, Jiang Q (2007) Agrobacterium-mediated transformation (AMT) of Trichoderma reesei as an efficient tool for random insertional mutagenesis. Appl Microbiol Biotechnol 73:1348–1354. https://doi.org/10.1007/s00253-006-0603-3
Zofall M, Yamanaka S, Reyes-Turcu FE et al (2012) RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation. Science 335:96–100. https://doi.org/10.1126/science.1211651
Acknowledgements
We would like to thank for their collaboration to all the members of INBIOTEC and the Department of Molecular Biology of the University of León. Special thanks to the ERA-IB project ProWood (“Wood and derivatives protection by novel bio-coating solutions”, ERA IB seventh Joint Call) through the APCIN call of the Spanish Ministry of Economy and Competitiveness (MINECO, Spain) (Project ID: PCIN-2016-081) and to the Syntheroids project (“Synthetic biology for industrial production of steroids”; ERA CoBioTech first call) through the APCIN call of the Spanish Ministry of Science, Innovation and Universities (Project ID: PCI2018-093066).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Barreiro, C., Gutiérrez, S., Olivera, E.R. (2019). Fungal Horizontal Gene Transfer: A History Beyond the Phylogenetic Kingdoms. In: Villa, T., Viñas, M. (eds) Horizontal Gene Transfer. Springer, Cham. https://doi.org/10.1007/978-3-030-21862-1_13
Download citation
DOI: https://doi.org/10.1007/978-3-030-21862-1_13
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-21861-4
Online ISBN: 978-3-030-21862-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)