title: Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta).
abstract: The majority of our knowledge about mitochondrial genomes of Viridiplantae comes from land plants, but much less is known about their green algal relatives. In the green algal order Sphaeropleales (Chlorophyta), only one representative mitochondrial genome is currently available-that of Acutodesmus obliquus. Our study adds nine completely sequenced and three partially sequenced mitochondrial genomes spanning the phylogenetic diversity of Sphaeropleales. We show not only a size range of 25-53 kb and variation in intron content (0-11) and gene order but also conservation of 13 core respiratory genes and fragmented ribosomal RNA genes. We also report an unusual case of gene arrangement convergence in Neochloris aquatica, where the two rns fragments were secondarily placed in close proximity. Finally, we report the unprecedented usage of UCG as stop codon in Pseudomuriella schumacherensis. In addition, phylogenetic analyses of the mitochondrial protein-coding genes yield a fully resolved, well-supported phylogeny, showing promise for addressing systematic challenges in green algae.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut karolina.fucikova@uconn.edu.
authors.forename: Karolina
authors.initials: K
authors.lastname: Fučíková
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut.
authors.forename: Paul O
authors.initials: PO
authors.lastname: Lewis
authors.affiliation: Instituto de Fisiología Celular, Departamento de Genética Molecular Universidad Nacional Autónoma de México, Ciudad de México, Mexico.
authors.forename: Diego
authors.initials: D
authors.lastname: González-Halphen
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Connecticut.
authors.forename: Louise A
authors.initials: LA
authors.lastname: Lewis
mesh_terms: D000460:Chlorophyta / Q000235:genetics*; D018388:Codon, Terminator / Q000235:genetics; D023061:Gene Order; D020459:Genes, rRNA; D005815:Genetic Code; D054629:Genome, Mitochondrial; D007438:Introns; D010802:Phylogeny
chemical_list: D018388:Codon, Terminator
keywords: collinearity; gene fragmentation; genome rearrangements; green algae; rRNA
references.citation: J Mol Evol. 1998 Oct;47(4):431-40
references.pmid: 9767688
references.citation: Gene. 2000 Jul 25;253(1):13-8
references.pmid: 10925198
references.citation: BMC Genomics. 2007 Jul 04;8:213
references.pmid: 17610731
references.citation: Genome Res. 2000 Jun;10(6):819-31
references.pmid: 10854413
references.citation: Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9905-12
references.pmid: 12119382
references.citation: BMC Evol Biol. 2008 Jul 25;8:218
references.pmid: 18655698
references.citation: BMC Evol Biol. 2006 Apr 25;6:37
references.pmid: 16638149
references.citation: Mol Biol Evol. 2008 Mar;25(3):487-96
references.pmid: 18222946
references.citation: Genome Res. 2009 Jun;19(6):1117-23
references.pmid: 19251739
references.citation: Syst Biol. 2013 Jan 1;62(1):121-33
references.pmid: 22962005
references.citation: Mol Biol Evol. 1998 Jun;15(6):690-701
references.pmid: 9615450
references.citation: BMC Evol Biol. 2006 Feb 09;6:13
references.pmid: 16469102
references.citation: BMC Genomics. 2009 Mar 26;10:132
references.pmid: 19323823
references.citation: Mol Genet Genomics. 2006 Nov;276(5):464-77
references.pmid: 16944205
references.citation: Genome Biol Evol. 2013;5(10):1817-35
references.pmid: 24022472
references.citation: Mol Phylogenet Evol. 2003 Dec;29(3):380-95
references.pmid: 14615181
references.citation: PLoS One. 2011;6(10):e25836
references.pmid: 21998706
references.citation: Trends Genet. 2007 Mar;23(3):119-25
references.pmid: 17280737
references.citation: Curr Genet. 1996 Jun;30(1):29-33
references.pmid: 8662206
references.citation: Science. 2010 Jul 9;329(5988):223-6
references.pmid: 20616280
references.citation: Bioinformatics. 2004 Nov 22;20(17):3252-5
references.pmid: 15180927
references.citation: Mol Biol Evol. 2013 Apr;30(4):793-7
references.pmid: 23300255
references.citation: Genome Biol Evol. 2010 Jul 12;2:240-56
references.pmid: 20624729
references.citation: Curr Genet. 2004 Sep;46(3):123-39
references.pmid: 15300404
references.citation: Curr Genet. 2007 Nov;52(5-6):267-74
references.pmid: 17957369
references.citation: Mol Phylogenet Evol. 2012 Jul;64(1):166-76
references.pmid: 22724135
references.citation: Genome Res. 2004 Jul;14(7):1394-403
references.pmid: 15231754
references.citation: Curr Genet. 2010 Oct;56(5):427-38
references.pmid: 20574726
references.citation: J Biol Chem. 2001 Apr 6;276(14):11302-9
references.pmid: 11094061
references.citation: Plant Mol Biol. 1998 Jan;36(2):285-95
references.pmid: 9484440
references.citation: Mol Biol Evol. 1997 May;14(5):506-17
references.pmid: 9159928
references.citation: J Phycol. 2014 Feb;50(1):14-25
references.pmid: 26988005
references.citation: Mol Biol Evol. 2012 Jun;29(6):1695-701
references.pmid: 22319168
references.citation: Mol Phylogenet Evol. 2012 Jan;62(1):109-16
references.pmid: 22056605
references.citation: J Mol Evol. 1988 Dec-1989 Feb;28(1-2):87-97
references.pmid: 3148746
references.citation: BMC Genomics. 2008 Jun 16;9:290
references.pmid: 18558012