title: Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea).
abstract: In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes.
authors.affiliation: Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063; Laboratory of Protozoology, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Gao
authors.forename: Weibo
authors.initials: W
authors.lastname: Song
authors.forename: Laura A
authors.initials: LA
authors.lastname: Katz
mesh_terms: D017398:Alternative Splicing; D016798:Ciliophora / Q000235:genetics*; D019143:Evolution, Molecular; D048648:Macronucleus / Q000235:genetics; D048631:Micronucleus, Germline / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D017422:Sequence Analysis, DNA; D059467:Transcriptome; D014404:Tubulin / Q000235:genetics
chemical_list: D014404:Tubulin
keywords: Alternative processing; ciliate; gene family; genome evolution; macronucleus; micronucleus
references.citation: Int Rev Cytol. 2007;262:219-51
references.pmid: 17631190
references.citation: Syst Biol. 2008 Oct;57(5):758-71
references.pmid: 18853362
references.citation: Int J Syst Evol Microbiol. 2001 Jul;51(Pt 4):1587-1592
references.pmid: 11491362
references.citation: Genetics. 1987 Jan;115(1):207-13
references.pmid: 3557113
references.citation: Mol Biol Evol. 2001 Jul;18(7):1372-7
references.pmid: 11420375
references.citation: J Mol Evol. 2011 Dec;73(5-6):266-72
references.pmid: 22258433
references.citation: Microbiol Rev. 1994 Jun;58(2):233-67
references.pmid: 8078435
references.citation: Annu Rev Genet. 2011;45:227-46
references.pmid: 21910632
references.citation: Ann N Y Acad Sci. 1999 May 18;870:349-50
references.pmid: 10415495
references.citation: Trends Genet. 2012 Aug;28(8):382-8
references.pmid: 22622227
references.citation: Biochim Biophys Acta. 2008 Nov;1783(11):2130-6
references.pmid: 18706458
references.citation: Gene. 2000 Dec 23;259(1-2):45-52
references.pmid: 11163960
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Mol Biol Evol. 2010 Feb;27(2):221-4
references.pmid: 19854763
references.citation: Gene. 2003 Oct 2;315:15-9
references.pmid: 14557060
references.citation: Annu Rev Genomics Hum Genet. 2011;12:367-89
references.pmid: 21801022
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Science. 2000 Nov 10;290(5494):1151-5
references.pmid: 11073452
references.citation: Gene. 2012 Aug 10;504(2):303-8
references.pmid: 22588027
references.citation: Nat Rev Immunol. 2006 Oct;6(10):728-40
references.pmid: 16998507
references.citation: Bioessays. 2009 Jan;31(1):29-39
references.pmid: 19153999
references.citation: Matrix Biol. 1996 Nov;15(5):301-10; discussion 311-2
references.pmid: 8981326
references.citation: Curr Opin Microbiol. 2009 Dec;12(6):638-43
references.pmid: 19879799
references.citation: Genetics. 1995 Jan;139(1):421-8
references.pmid: 7705642
references.citation: PLoS Biol. 2008 Jul 29;6(7):e185
references.pmid: 18666832
references.citation: Results Probl Cell Differ. 1987;14:59-67
references.pmid: 3112879
references.citation: J Mol Evol. 1991 Jul;33(1):34-41
references.pmid: 1909373
references.citation: Mol Biol Evol. 2006 Sep;23(9):1681-7
references.pmid: 16760419
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22134-9
references.pmid: 20974970
references.citation: PLoS Biol. 2006 Sep;4(9):e286
references.pmid: 16933976
references.citation: Dev Genet. 1992;13(1):66-74
references.pmid: 1395144
references.citation: J Exp Zool B Mol Dev Evol. 2010 Sep 15;314(6):480-8
references.pmid: 20700892