title: High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporter/ammonia permease gene family.
abstract: BACKGROUND
  Horizontal gene transfer has shaped the evolution of the ammonium transporter/ammonia permease gene family. Horizontal transfers of ammonium transporter/ammonia permease genes into the fungi include one transfer from archaea to the filamentous ascomycetes associated with the adaptive radiation of the leotiomyceta. The horizontally transferred gene has subsequently been lost in most of the group but has been selectively retained in lichenizing fungi. However, some groups of lichens appear to have secondarily lost the archaeal ammonium transporter. Definitive assessment of gene loss can only be made via whole genome sequencing.
  
  
  RESULTS
  Ammonium transporter/ammonia permease gene sequences were recovered from the assembled genomes of eight lichenizing fungi in key clades including the Caliciales, the Peltigerales, the Ostropomycetidae, the Acarosporomycetidae, the Verrucariales, the Arthoniomycetidae and the Lichinales. The genes recovered were included in a refined phylogenetic analysis. The hypothesis that lichens symbiotic with a nitrogen-fixing cyanobacterium as a primary photobiont or lichens living in high nitrogen environments lose the plant-like ammonium transporters was upheld, but did not account for additional losses of ammonium transporters/ammonia permeases in the lichens from the Acarosporomycetidae, Chaetotheriomycetes and Arthoniomycetes. In addition, the four ammonium transporter/ammonia permease genes from Cladonia grayi were shown to be functional by expressing the lichen genes in a strain of Saccharomyces cerevisiae in which all three native ammonium transporters were deleted, and assaying for growth on limiting ammonia as a sole nitrogen source.
  
  
  CONCLUSIONS
  Given sufficient coverage, next-generation sequencing technology can definitively address the loss of a gene in a genome when using environmental DNA isolated from lichen thalli collected from their natural habitats. Lichen-forming fungi have been losing ammonium transporters/ammonia permease genes at a slower rate than the most closely related non-lichenized lineages. These horizontally transferred genes in the Cladonia grayi genome encode functional ammonium transporters/ammonia permeases.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA. mcdo0264@umn.edu
authors.forename: Tami R
authors.initials: TR
authors.lastname: McDonald
authors.forename: Olaf
authors.initials: O
authors.lastname: Mueller
authors.forename: Fred S
authors.initials: FS
authors.lastname: Dietrich
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
mesh_terms: D017753:Ecosystem; D022761:Gene Transfer, Horizontal; D005800:Genes, Fungal / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008011:Lichens / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D026901:Membrane Transport Proteins / Q000235:genetics* / Q000378:metabolism*; D009584:Nitrogen / Q000494:pharmacology; D000644:Quaternary Ammonium Compounds / Q000378:metabolism*; D013045:Species Specificity; D013559:Symbiosis
chemical_list: D026901:Membrane Transport Proteins; D000644:Quaternary Ammonium Compounds; D009584:Nitrogen
references.citation: Int J Syst Evol Microbiol. 2000 Mar;50 Pt 2:511-516
references.pmid: 10758854
references.citation: Nat Protoc. 2007;2(1):35-7
references.pmid: 17401335
references.citation: Eukaryot Cell. 2002 Feb;1(1):85-94
references.pmid: 12455974
references.citation: Gene. 1995 Apr 14;156(1):119-22
references.pmid: 7737504
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: IMA Fungus. 2011 Dec;2(2):143-53
references.pmid: 22679599
references.citation: Fungal Genet Biol. 2002 Jun;36(1):22-34
references.pmid: 12051892
references.citation: BMC Genomics. 2008 Dec 11;9:597
references.pmid: 19077236
references.citation: Mol Microbiol. 2000 Nov;38(3):552-64
references.pmid: 11069679
references.citation: Mycol Res. 2007 May;111(Pt 5):509-47
references.pmid: 17572334
references.citation: EMBO J. 1994 Aug 1;13(15):3464-71
references.pmid: 8062823
references.citation: Syst Biol. 2009 Apr;58(2):224-39
references.pmid: 20525580
references.citation: Am J Bot. 2004 Mar;91(3):449-64
references.pmid: 21653401
references.citation: New Phytol. 2007;174(1):137-150
references.pmid: 17335504
references.citation: Science. 2004 Sep 10;305(5690):1587-94
references.pmid: 15361618
references.citation: Fungal Genet Biol. 2006 Feb;43(2):102-10
references.pmid: 16386437
references.citation: Environ Microbiol. 2012 Jan;14(1):147-61
references.pmid: 21906220
references.citation: Stand Genomic Sci. 2009 Jul 20;1(1):38-45
references.pmid: 21304635
references.citation: Mol Phylogenet Evol. 2012 May;63(2):374-87
references.pmid: 22306043
references.citation: Plant Cell. 2009 Jul;21(7):1897-911
references.pmid: 19584142
references.citation: J Bacteriol. 2009 Sep;191(18):5877-8
references.pmid: 19617360
references.citation: EMBO J. 1994 Aug 1;13(15):3456-63
references.pmid: 8062822
references.citation: Mol Biol Evol. 2008 Jul;25(7):1253-6
references.pmid: 18397919
references.citation: Syst Biol. 2009 Jun;58(3):283-97
references.pmid: 20525584
references.citation: Appl Environ Microbiol. 2004 Apr;70(4):2079-88
references.pmid: 15066799
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9091-6
references.pmid: 15184674
references.citation: Plant Physiol. 2002 Dec;130(4):1788-96
references.pmid: 12481062
references.citation: Biochem J. 2002 Jun 1;364(Pt 2):527-35
references.pmid: 12023896
references.citation: Transfus Clin Biol. 2010 Sep;17(3):168-75
references.pmid: 20674437
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835-40
references.pmid: 11427726
references.citation: Mol Microbiol. 2003 Oct;50(1):259-75
references.pmid: 14507379
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19279-84
references.pmid: 18040042
references.citation: J Biol Chem. 2006 Dec 22;281(51):39492-8
references.pmid: 17040913
references.citation: Biochem J. 2006 Jun 15;396(3):431-7
references.pmid: 16499477
references.citation: Trends Biochem Sci. 1997 Dec;22(12):460-1
references.pmid: 9433124
references.citation: Fungal Genet Biol. 2002 Jun;36(1):35-46
references.pmid: 12051893
references.citation: Bioinformatics. 2007 May 1;23(9):1061-7
references.pmid: 17332020
references.citation: Proc Natl Acad Sci U S A. 2010 May 25;107(21):9638-43
references.pmid: 20457942
references.citation: Trends Microbiol. 2003 Feb;11(2):53-5
references.pmid: 12598122
references.citation: Cell. 1992 Mar 20;68(6):1077-90
references.pmid: 1547504
references.citation: EMBO J. 1998 Aug 10;17(5):1236-47
references.pmid: 9482721
references.citation: Mycologia. 2006 Nov-Dec;98(6):1018-28
references.pmid: 17486977
references.citation: Nucleic Acids Res. 2009 Jan;37(1):289-97
references.pmid: 19042974
references.citation: J Bacteriol. 1995 Dec;177(24):7050-9
references.pmid: 8522509
references.citation: Eukaryot Cell. 2008 Feb;7(2):237-46
references.pmid: 18055915
references.citation: Plant Mol Biol. 2003 Jan;51(1):99-108
references.pmid: 12602894
references.citation: FEBS Lett. 2000 Feb 11;467(2-3):273-8
references.pmid: 10675553
references.citation: Trends Genet. 2010 Jan;26(1):5-8
references.pmid: 19969385
references.citation: Biophys J. 2007 May 1;92(9):L82-4
references.pmid: 17351012
references.citation: Proc Natl Acad Sci U S A. 2004 Dec 7;101(49):17090-5
references.pmid: 15563598
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 18;102(42):14994-9
references.pmid: 16214888
references.citation: Transfus Clin Biol. 2006 Mar-Apr;13(1-2):103-10
references.pmid: 16563833
references.citation: Mol Cell Biol. 1997 Aug;17(8):4282-93
references.pmid: 9234685
references.citation: J Biol Chem. 2002 Apr 19;277(16):13548-55
references.pmid: 11821433
references.citation: Am J Bot. 2004 Oct;91(10):1446-80
references.pmid: 21652303
references.citation: Biotechniques. 1999 Jan;26(1):134-8, 140-1
references.pmid: 9894602
references.citation: Bioinformatics. 2005 Feb 15;21(4):456-63
references.pmid: 15608047
references.citation: Mol Biol Evol. 2002 Dec;19(12):2226-38
references.pmid: 12446813
references.citation: PLoS One. 2007 Oct 31;2(10):e1097
references.pmid: 17971860
references.citation: Science. 1966 Jan 14;151(3707):199-201
references.pmid: 17746338
references.citation: Appl Environ Microbiol. 2009 Jul;75(13):4599-615
references.pmid: 19429552
references.citation: Biophys J. 2007 Feb 1;92(3):877-85
references.pmid: 17098799
references.citation: Pflugers Arch. 2006 Mar;451(6):701-7
references.pmid: 16273393
references.citation: Extremophiles. 2002 Feb;6(1):39-44
references.pmid: 11878560
references.citation: Plant Biol (Stuttg). 2006 Jul;8(4):522-8
references.pmid: 16917981
references.citation: Int J Syst Bacteriol. 1999 Jul;49 Pt 3:1157-63
references.pmid: 10425774
references.citation: J Bacteriol. 2011 Dec;193(24):7003-4
references.pmid: 22123759
references.citation: Mol Biol Evol. 2012 Jan;29(1):51-60
references.pmid: 21680869
references.citation: Eukaryot Cell. 2006 Feb;5(2):226-37
references.pmid: 16467464
references.citation: Arch Mikrobiol. 1972;84(1):54-68
references.pmid: 4559703
references.citation: Biochim Biophys Acta. 1966 Oct 31;127(2):325-38
references.pmid: 5964977
references.citation: Nature. 2006 Oct 19;443(7113):818-22
references.pmid: 17051209