satDNA Analyzer 1.2 as a Valuable Computing Tool for Evolutionary Analysis of Satellite-DNA Families: Revisiting Y-Linked Satellite-DNA Sequences of Rumex (Polygonaceae)

In a previous paper [1] we showed that Y-linked satellite-DNA sequences of Rumex (Polygonaceae) present reduced rates of evolution in relation to other autosomal satellite-DNA sequences. In the present paper, we re-analyze the same set of sequences by using the satDNA Analyzer 1.2 software, specifically developed by us for analysis of satellite DNA evolution. We do not only confirm our previous findings but also prove that the satDNA Analyzer 1.2 package constitutes a powerful tool for users interested in evolutionary analysis on satellite-DNA sequences. In fact, we are able to gather more accurate calculations regarding location of Strachan positions and evolutionary rates calculations, among others useful statistics. All results are displayed in a very comprehensive multicoloured graphic representation easy to use as an html file. Furthermore, satDNA Analyzer 1.2 is a time saving feature since every utility is automatized and collected in a single software package, so the user does not need to use different programs. Additionally, it significantly reduces the rate of data miscalculations due to human errors, very prone to occur specially in large files.

[1]  M. Garrido-Ramos,et al.  The evolution of reproductive systems and sex-determining mechanisms within rumex (polygonaceae) inferred from nuclear and chloroplastidial sequence data. , 2005, Molecular biology and evolution.

[2]  M. Garrido-Ramos,et al.  The origin and evolution of the variability in a Y-specific satellite-DNA of Rumex acetosa and its relatives. , 2006, Gene.

[3]  R. Devlin,et al.  Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences , 2002 .

[4]  T. Jukes.  CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[5]  J. Graves,et al.  Mammalian sex chromosomes: Evolution of organization and function , 1991, Chromosoma.

[6]  J. Bull.  Sex Determination in Reptiles , 1980, The Quarterly Review of Biology.

[7]  J. Parker,et al.  Cytogenetic and molecular analysis of the multiple sex chromosome system of Rumex acetosa , 1994, Heredity.

[8]  M. Garrido-Ramos,et al.  Cloning and characterization of a fish centromeric satellite DNA. , 1994, Cytogenetics and cell genetics.

[9]  D. Charlesworth,et al.  Plant sex determination and sex chromosomes , 2002, Heredity.

[10]  D. Filatov.  Substitution rates in a new Silene latifolia sex-linked gene, SlssX/Y. , 2005, Molecular biology and evolution.

[11]  J. Pons,et al.  Evolutionary dynamics of satellite DNA family PIM357 in species of the genus Pimelia (Tenebrionidae, Coleoptera). , 2002, Molecular biology and evolution.

[12]  T. Strachan,et al.  Transition stages of molecular drive in multiple‐copy DNA families in Drosophila , 1985, The EMBO journal.

[13]  B. Vissel,et al.  Evolution of alpha-satellite DNA on human acrocentric chromosomes. , 1989, Genomics.

[14]  M. Steinemann,et al.  The enigma of Y chromosome degeneration: TRAM, a novel retrotransposon is preferentially located on the Neo-Y chromosome of Drosophila miranda. , 1997, Genetics.

[15]  D. Bachtrog.  Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila , 2003, Nature Genetics.

[16]  M. Singer.  Highly repeated sequences in mammalian genomes. , 1982, International review of cytology.

[17]  G. Dover,et al.  Molecular drive: a cohesive mode of species evolution , 1982, Nature.

[18]  B. Charlesworth,et al.  The evolution of chromosomal sex determination and dosage compensation , 1996, Current Biology.

[19]  Wen-Hsiung Li,et al.  Contrasting rates of nucleotide substitution in the X-Linked and Y-Linked zinc finger genes , 1994, Journal of Molecular Evolution.

[20]  M. Hizume,et al.  Chromosome painting of Y chromosomes and isolation of a Y chromosome-specific repetitive sequence in the dioecious plant Rumex acetosa , 1999, Chromosoma.

[21]  Chris Tyler-Smith,et al.  The human Y chromosome: an evolutionary marker comes of age , 2003, Nature Reviews Genetics.

[22]  H. Munro,et al.  Mammalian protein metabolism , 1964 .

[23]  M. Hizume,et al.  Differentiation and the Polymorphic Nature of the Y Chromosomes Revealed by Repetitive Sequences in the Dioecious Plant, Rumex Acetosa , 2004, Chromosome Research.

[24]  H. Ellegren,et al.  Evolution of the avian sex chromosomes from an ancestral pair of autosomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[25]  Wolfgang Stephan,et al.  The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.

[26]  D. Charlesworth,et al.  Low variability in a Y-linked plant gene and its implications for Y-chromosome evolution , 2000, Nature.

[27]  M. Garrido-Ramos,et al.  Reduced Rates of Sequence Evolution of Y-Linked Satellite DNA in Rumex (Polygonaceae) , 2005, Journal of Molecular Evolution.

[28]  Jirí Macas,et al.  PlantSat: a specialized database for plant satellite repeats , 2002, Bioinform..

[29]  T. Graves,et al.  The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes , 2003, Nature.

[30]  D. Bachtrog.  Accumulation of Spock and Worf, two novel non-LTR retrotransposons, on the neo-Y chromosome of Drosophila miranda. , 2003, Molecular biology and evolution.

[31]  F. Marec,et al.  Sex Chromatin in Lepidoptera , 1996, The Quarterly Review of Biology.

[32]  M. Hizume,et al.  Molecular cytogenetic analysis of supernumerary heterochromatic segments in Rumex acetosa. , 2000, Genome.