title: Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect.
abstract: Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola, of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia-ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia-ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia-ALF is most closely related to Zinderia, the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia/Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs >200 Ma, and possibly since the origin of the Auchenorrhyncha, >260 Ma.
authors.affiliation: Department of Ecology and Evolutionary Biology & Microbial Diversity Institute, Yale University.
authors.forename: Gordon M
authors.initials: GM
authors.lastname: Bennett
authors.forename: Nancy A
authors.initials: NA
authors.lastname: Moran
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000235:genetics; D001483:Base Sequence; D019143:Evolution, Molecular; D005247:Feeding Behavior; D016680:Genome, Bacterial; D006430:Hemiptera / Q000235:genetics* / Q000382:microbiology / Q000502:physiology; D052585:Phloem; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013559:Symbiosis / Q000235:genetics*
keywords: Nasuia deltocephalinicola; Sulcia muelleri; gene loss; genome evolution; leafhopper; nutritional symbioses
references.citation: Genome Biol Evol. 2013;5(5):783-93
references.pmid: 23542079
references.citation: Annu Rev Microbiol. 2003;57:579-608
references.pmid: 14527292
references.citation: Appl Environ Microbiol. 2013 Aug;79(16):5013-22
references.pmid: 23770905
references.citation: Proc Natl Acad Sci U S A. 1985 Apr;82(8):2306-9
references.pmid: 3887399
references.citation: Genome Biol Evol. 2010;2:708-18
references.pmid: 20829280
references.citation: J Biol Chem. 1982 Oct 10;257(19):11468-73
references.pmid: 6749840
references.citation: J Biol Chem. 2001 Oct 19;276(42):39186-91
references.pmid: 11504719
references.citation: Annu Rev Entomol. 1998;43:17-37
references.pmid: 15012383
references.citation: Curr Biol. 2011 Aug 23;21(16):1366-72
references.pmid: 21835622
references.citation: Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14240-5
references.pmid: 15377794
references.citation: Nat Rev Microbiol. 2011 Nov 08;10(1):13-26
references.pmid: 22064560
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9
references.pmid: 15980563
references.citation: Appl Environ Microbiol. 2005 Dec;71(12):8802-10
references.pmid: 16332876
references.citation: Bioinformatics. 2007 Mar 15;23(6):673-9
references.pmid: 17237039
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2849-54
references.pmid: 21282658
references.citation: Mol Biol Evol. 2013 Apr;30(4):772-80
references.pmid: 23329690
references.citation: J Bacteriol. 2009 Jun;191(12):4041-3
references.pmid: 19376855
references.citation: BMC Microbiol. 2009 Jul 20;9:143
references.pmid: 19619300
references.citation: Appl Environ Microbiol. 2011 Feb;77(4):1423-35
references.pmid: 21183640
references.citation: Bioinformatics. 2009 Aug 1;25(15):1966-7
references.pmid: 19497933
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8627-33
references.pmid: 17494762
references.citation: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37
references.pmid: 21593126
references.citation: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19392-7
references.pmid: 18048332
references.citation: J Biol Chem. 1980 Nov 25;255(22):10984-90
references.pmid: 6776124
references.citation: PLoS Biol. 2006 Jun;4(6):e188
references.pmid: 16729848
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5
references.pmid: 17526522
references.citation: Bioinformatics. 2009 Jan 1;25(1):119-20
references.pmid: 18990721
references.citation: J Bacteriol. 2008 Sep;190(17):6026-9
references.pmid: 18586942
references.citation: Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15394-9
references.pmid: 19706397
references.citation: Genome Biol Evol. 2013;5(2):338-50
references.pmid: 23345457
references.citation: Environ Microbiol. 2003 Feb;5(2):116-26
references.pmid: 12558594
references.citation: Proc Natl Acad Sci U S A. 1967 Sep;58(3):1144-51
references.pmid: 5233840
references.citation: Genome Res. 2008 May;18(5):821-9
references.pmid: 18349386
references.citation: Cell Mol Life Sci. 2011 Apr;68(8):1297-309
references.pmid: 21390549
references.citation: Nat Rev Genet. 2001 Jan;2(1):49-58
references.pmid: 11253070
references.citation: Environ Microbiol Rep. 2013 Aug;5(4):499-505
references.pmid: 23864562
references.citation: J Bacteriol. 2001 Mar;183(6):1853-61
references.pmid: 11222582
references.citation: BMC Genomics. 2008 Feb 08;9:75
references.pmid: 18261238
references.citation: Mol Biol Evol. 2013 Jun;30(6):1258-62
references.pmid: 23519313
references.citation: Environ Microbiol. 2013 Jul;15(7):2073-81
references.pmid: 23574391
references.citation: Tissue Cell. 2008 Aug;40(4):231-42
references.pmid: 18272191
references.citation: Curr Microbiol. 2013 Sep;67(3):263-70
references.pmid: 23549902
references.citation: BMC Evol Biol. 2012 Jun 14;12:87
references.pmid: 22697166
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90
references.pmid: 21097882
references.citation: J Bacteriol. 1996 Oct;178(19):5563-7
references.pmid: 8824597
references.citation: Biol Lett. 2012 Dec 23;8(6):986-9
references.pmid: 22977066
references.citation: Annu Rev Entomol. 2010;55:207-25
references.pmid: 19725772
references.citation: Annu Rev Microbiol. 2005;59:155-89
references.pmid: 16153167
references.citation: Bioinformatics. 2011 Apr 15;27(8):1164-5
references.pmid: 21335321
references.citation: PLoS One. 2010 Apr 23;5(4):e10314
references.pmid: 20428247
references.citation: Genome Res. 2011 Sep;21(9):1552-60
references.pmid: 21690186
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9388-93
references.pmid: 12886019
references.citation: Science. 2006 Oct 13;314(5797):312-3
references.pmid: 17038625
references.citation: Annu Rev Genet. 2008;42:165-90
references.pmid: 18983256
references.citation: Mol Biol Evol. 2012 Dec;29(12):3781-92
references.pmid: 22821013
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D226-32
references.pmid: 23125362
references.citation: Nucleic Acids Res. 1980 Sep 11;8(17):3865-74
references.pmid: 6255421
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: PLoS Genet. 2011 May;7(5):e1002064
references.pmid: 21589895
references.citation: Mol Ecol. 2006 Nov;15(13):4175-91
references.pmid: 17054511
references.citation: Genome Biol. 2011;12(2):R18
references.pmid: 21338519
references.citation: Bioinformatics. 2009 Sep 1;25(17):2271-8
references.pmid: 19561336
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 17;106(46):19521-6
references.pmid: 19880743
references.citation: BMC Evol Biol. 2007 Oct 01;7:181
references.pmid: 17908294
references.citation: Mol Biol Evol. 2003 Sep;20(9):1513-20
references.pmid: 12832650
references.citation: PLoS Genet. 2009 Jul;5(7):e1000565
references.pmid: 19609354
references.citation: Nature. 2000 Sep 7;407(6800):81-6
references.pmid: 10993077
references.citation: Science. 2006 Oct 13;314(5797):267
references.pmid: 17038615
references.citation: Trends Genet. 1988 Jul;4(7):191-8
references.pmid: 3070867
references.citation: Insect Mol Biol. 2006 Oct;15(5):563-76
references.pmid: 17069632
references.citation: Insect Mol Biol. 2010 Mar;19 Suppl 2:249-58
references.pmid: 20482655
references.citation: Mol Cell Proteomics. 2011 Jun;10(6):M110.007039
references.pmid: 21421797
references.citation: J Econ Entomol. 2011 Dec;104(6):1800-15
references.pmid: 22299339
references.citation: FEMS Microbiol Rev. 1998 Dec;22(5):503-21
references.pmid: 9990727
references.citation: Nucleic Acids Res. 2007;35(9):3100-8
references.pmid: 17452365
references.citation: Methods Enzymol. 2013;531:445-64
references.pmid: 24060132
references.citation: Cell Microbiol. 2005 Feb;7(2):293-305
references.pmid: 15659072
references.citation: Plant Physiol. 1981 Sep;68(3):619-25
references.pmid: 16661968
references.citation: Environ Microbiol. 2013 Jul;15(7):1988-99
references.pmid: 23279075