title: Evolutionary dynamics of the 5S rDNA gene family in the mussel Mytilus: mixed effects of birth-and-death and concerted evolution.
abstract: In higher eukaryotes, the gene family encoding the 5S ribosomal RNA (5S rRNA) has been used (together with histones) to showcase the archetypal example of a gene family subject to concerted evolution. However, recent studies have revealed conspicuous features challenging the predictions of this model, including heterogeneity of repeat units, the presence of functional 5S gene variants as well as the existence of 5S rDNA divergent pseudogenes lacking traces of homogenization. In the present work, we have broadened the scope in the evolutionary study of ribosomal gene families by studying the 5S rRNA family in mussels, a model organism which stands out among other animals due to the heterogeneity it displays regarding sequence and organization. To this end, 48 previously unknown 5S rDNA units (coding and spacer regions) were sequenced in five mussel species, leading to the characterization of two new types of units (referred to here as small-beta 5S rDNA and gamma-5S rDNA) coexisting in the genome with alpha and beta rDNA units. The intense genetic dynamics of this family is further supported by the first description of an association between gamma-5S rDNA units and tRNA genes. Molecular evolutionary and phylogenetic analyses revealed an extensive lack of homology among spacer sequences belonging to different rDNA types, suggesting the presence of independent evolutionary pathways leading to their differentiation. Overall, our results suggest that the long-term evolution of the 5S rRNA gene family in mussels is most likely mediated by a mixed mechanism involving the generation of genetic diversity through birth-and-death, followed by a process of local homogenization resulting from concerted evolution in order to maintain the genetic identities of the different 5S units, probably after their transposition to independent chromosomal locations.
authors.affiliation: XENOMAR Group, Departamento de Biología Celular y Molecular, Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira s/n, A Coruña, Spain.
authors.forename: Ruth
authors.initials: R
authors.lastname: Freire
authors.forename: Alberto
authors.initials: A
authors.lastname: Arias
authors.forename: Ana M
authors.initials: AM
authors.lastname: Insua
authors.forename: Josefina
authors.initials: J
authors.lastname: Méndez
authors.forename: José M
authors.initials: JM
authors.lastname: Eirín-López
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D004247:DNA / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D049878:Mytilus / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011401:Promoter Regions, Genetic; D012341:RNA, Ribosomal, 5S / Q000235:genetics*; D012347:RNA, Transfer, Arg / Q000737:chemistry / Q000235:genetics
chemical_list: D012341:RNA, Ribosomal, 5S; D012347:RNA, Transfer, Arg; D004247:DNA
references.citation: Nucleic Acids Res. 2008 Oct;36(18):5832-44
references.pmid: 18790808
references.citation: Mol Biol Evol. 1995 Mar;12(2):319-33
references.pmid: 7700156
references.citation: Mol Phylogenet Evol. 2009 Oct;53(1):34-44
references.pmid: 19527789
references.citation: Annu Rev Genet. 2005;39:121-52
references.pmid: 16285855
references.citation: Cytogenet Cell Genet. 1997;76(1-2):101-6
references.pmid: 9154136
references.citation: Nucleic Acids Res. 1984 Oct 25;12(20):7617-32
references.pmid: 6093044
references.citation: Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):5084-9
references.pmid: 15784739
references.citation: Genetics. 1995 May;140(1):325-43
references.pmid: 7635297
references.citation: Genomics. 1989 Apr;4(3):376-83
references.pmid: 2714796
references.citation: Genetika. 2000 Sep;36(9):1206-20
references.pmid: 11042807
references.citation: J Mol Evol. 2004 Feb;58(2):131-44
references.pmid: 15042333
references.citation: Cytogenet Genome Res. 2002;98(1):78-85
references.pmid: 12584446
references.citation: J Mol Evol. 1980 Dec;16(2):111-20
references.pmid: 7463489
references.citation: Mol Biol Evol. 1995 May;12(3):481-93
references.pmid: 7739390
references.citation: Cell. 1987 Jan 16;48(1):91-100
references.pmid: 3791417
references.citation: J Mol Evol. 1985;22(2):160-74
references.pmid: 3934395
references.citation: Nucleic Acids Res. 1993 Aug 11;21(16):3631-6
references.pmid: 8367278
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Annu Rev Biochem. 1980;49:727-64
references.pmid: 6996571
references.citation: Chromosome Res. 2001;9(6):495-505
references.pmid: 11592484
references.citation: Mol Biol Evol. 1996 Apr;13(4):605-11
references.pmid: 8882503
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: Genome. 2005 Jun;48(3):427-42
references.pmid: 16121240
references.citation: Mol Biol Evol. 2008 Jul;25(7):1253-6
references.pmid: 18397919
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: Mol Biol Evol. 2007 Aug;24(8):1586-91
references.pmid: 17483113
references.citation: Mol Cell Biol. 1988 Mar;8(3):1266-74
references.pmid: 3130565
references.citation: Genetica. 2009 Apr;135(3):355-65
references.pmid: 18648989
references.citation: Genome. 2005 Apr;48(2):247-56
references.pmid: 15838547
references.citation: J Mol Evol. 2003 Dec;57(6):731-6
references.pmid: 14745542
references.citation: Nucleic Acids Res. 1983 Nov 25;11(22):7735-41
references.pmid: 6196721
references.citation: Nucleic Acids Res. 2000 Mar 15;28(6):1283-98
references.pmid: 10684922
references.citation: Hereditas. 2008 Feb;145(1):9-19
references.pmid: 18439229
references.citation: Trends Genet. 1993 Dec;9(12):407
references.pmid: 8122306
references.citation: Mol Biol Evol. 2007 Aug;24(8):1596-9
references.pmid: 17488738
references.citation: J Biochem. 1986 Aug;100(2):369-74
references.pmid: 3782056
references.citation: Genome. 2006 Jan;49(1):79-86
references.pmid: 16462904
references.citation: Science. 2010 Feb 5;327(5966):693-6
references.pmid: 20133573
references.citation: Evolution. 1985 Jul;39(4):783-791
references.pmid: 28561359
references.citation: Genetica. 2006 May;127(1-3):243-52
references.pmid: 16850228
references.citation: Nature. 1980 Apr 3;284(5755):426-30
references.pmid: 6987539
references.citation: Genetics. 1988 Apr;118(4):685-91
references.pmid: 2835290
references.citation: Nucleic Acids Res. 1979 Nov 24;7(6):1513-23
references.pmid: 388356
references.citation: Nucleic Acids Res. 1982 Aug 11;10(15):4679-85
references.pmid: 7133995
references.citation: Biochem Genet. 2009 Dec;47(11-12):775-88
references.pmid: 19633947
references.citation: Biochem Genet. 2009 Oct;47(9-10):635-44
references.pmid: 19633948
references.citation: J Mol Evol. 1996 Jun;42(6):685-705
references.pmid: 8662014
references.citation: Nucleic Acids Res. 1997 Dec 15;25(24):4876-82
references.pmid: 9396791
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Genome. 2005 Dec;48(6):1116-9
references.pmid: 16391680
references.citation: Nature. 1982 Sep 9;299(5879):111-7
references.pmid: 7110332
references.citation: Nucleic Acids Res. 2006 Apr 05;34(6):1816-35
references.pmid: 16600899