In Silico chloroplast SSRs mining of Olea species

Filiz E, Koc E. 2012. In Silico chloroplast SSRs mining of Olea species. Biodiversitas 13: 114-117. Simple sequence repeat (SSR) markers are highly informative and have been widely applied as molecular markers in genetic studies. The purpose of present study is to analyze the occurrence and distribution of chloroplast SSRs in genic and intergenic regions from Olea species viz., Olea europaea, Olea europaea subsp. cuspidate, Olea europaea subsp. europaea, Olea europaea subsp. maroccana, Olea woodiana subsp. woodiana by using bioinformatics tools. We identified 1149 chloroplast SSRs (cpSSRs) in all genome and a total of 340 (29.6%) was located in genic regions. It was observed that the most abundant repeat types were found mononucleotide SSR (66.7 %) followed by trinucleotide SSR (28.3 %), dinucleotide (2.7%), tetranucleotide (1.5%) and pentanucleotide (0.8%). cpSSRs located in genic regions were identified only mono- and trinucleotide motifs, the most abundant of which was trinucleotide (16.2%) followed by mononucleotide (14.3%). All types of repeat motif (mono-, di-, tri-, tetra- and pentanucleotide) were detected except hexanucleotide motifs. According to SSRs analysis, the most abundant observed motifs were identified for mono-, di-, tri-, tetra- and pentanucleotide cpSSRs A/T, AT/TA, AAG/CTT, AAAG/AGTTT, and AATCC/ATTGG respectively. This study results provided scientific base for phylogenetics, evolutionary genetics and diversity studies on different Olea species in future.Key words: Olea, olive, chloroplast SSRs, SSR mining, in silico analysis

[1]  G. Besnard,et al.  Combination of chloroplast and mitochondrial DNA polymorphisms to study cytoplasm genetic differentiation in the olive complex (Olea europaea L.) , 2002, Theoretical and Applied Genetics.

[2]  D. Cavalieri,et al.  IDENTIFICATION OF OLIVE TREE CULTIVARS BY USING RANDOM AMPLIFIED POLYMORPHIC DNA , 1993 .

[3]  John M. Hancock,et al.  Simple sequence repeats in proteins and their significance for network evolution. , 2005, Gene.

[4]  Sumit G. Gandhi,et al.  Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family , 2010, Bioinformation.

[5]  J. Kadereit,et al.  The colonization history of Olea europaea L. in Macaronesia based on internal transcribed spacer 1 (ITS‐1) sequences, randomly amplified polymorphic DNAs (RAPD), and intersimple sequence repeats (ISSR) , 2000, Molecular ecology.

[6]  H. Carrer,et al.  In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species. , 2009 .

[7]  W. Powell,et al.  Chloroplast microsatellites: new tools for studies in plant ecology and evolution. , 2001, Trends in ecology & evolution.

[8]  D. Bassi,et al.  SSR marker based DNA fingerprinting of Tunisian olive (Olea europaea L.) varieties , 2008 .

[9]  João Lopes,et al.  Assessing Genetic Diversity in Olea europaea L. Using ISSR and SSR Markers , 2009, Plant Molecular Biology Reporter.

[10]  R. Jansen,et al.  A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. , 2007, American journal of botany.

[11]  M. Buiatti,et al.  Chloroplast DNA polymorphisms as molecular markers to identify cultivars of Olea europaea L. , 2007 .

[12]  A. Angiolillo,et al.  SNP-based markers for discriminating olive (Olea europaea L.) cultivars. , 2006, Genome.

[13]  A. Belaj,et al.  Genetic structure of wild and cultivated olives in the central Mediterranean basin. , 2006, Annals of botany.

[14]  M. Morgante,et al.  Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes , 2002, Nature Genetics.

[15]  M. Sugiura.  The chloroplast genome , 1992, Plant Molecular Biology.

[16]  Ashok Sharma,et al.  Analysis of Unigene Derived Microsatellite Markers in Family Solanaceae , 2010 .

[17]  Sezai Ercisli,et al.  SSR Marker-Based DNA Fingerprinting and Cultivar Identification of Olives (Olea europaea) , 2011, Biochemical Genetics.

[18]  E. Nevo,et al.  Microsatellites within genes: structure, function, and evolution. , 2004, Molecular biology and evolution.

[19]  Vinay Sharma,et al.  Microsatellite analysis in organelle genomes of Chlorophyta , 2012, Bioinformation.

[20]  T. Wood,et al.  Complete Chloroplast Genome Sequence of Glycine max and Comparative Analyses with other Legume Genomes , 2005, Plant Molecular Biology.

[21]  M. Gazzah,et al.  Genetic Relationships between Cultivated and Wild Olive Trees (Olea Europaea L. Var. Europaea and Var. Sylvestris) Based on Nuclear and Chloroplast SSR Markers , 2010 .

[22]  Thomas Thiel,et al.  In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. , 2002, Cellular & molecular biology letters.

[23]  H. Carrer,et al.  Characterization of chloroplast DNA microsatellites from Saccharum spp and related species. , 2011, Genetics and molecular research : GMR.

[24]  A. Belaj,et al.  Using RAPD and AFLP markers to distinguish individuals obtained by clonal selection of 'Arbequina' and 'Manzanilla de Sevilla' olive , 2004 .

[25]  M. Ramaswamy,et al.  Microsatellites in palm (Arecaceae) sequences , 2011, Bioinformation.

[26]  Passoupathy Rajendrakumar,et al.  Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions , 2007, Bioinform..

[27]  Passoupathy Rajendrakumar,et al.  In silicoAnalysis of Microsatellites in Organellar Genomes of Major Cereals for Understanding Their Phylogenetic Relationships , 2008, Silico Biol..

[28]  M. Rai,et al.  Microsatellite markers: an overview of the recent progress in plants , 2011, Euphytica.

[29]  C. Birky.  Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[30]  D. Cooke,et al.  On the origin of the invasive olives (Olea europaea L., Oleaceae) , 2007, Heredity.

[31]  L. Zane,et al.  Strategies for microsatellite isolation: a review , 2002, Molecular ecology.

[32]  N. Bahrman,et al.  Comparison of genetic differentiation in maritime pine (Pinus pinaster Ait.) estimated using isozyme, total protein and terpenic loci , 1995, Heredity.

[33]  J. Tomkins,et al.  Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes , 2006, Theoretical and Applied Genetics.

[34]  F. Cellini,et al.  Identification of simple sequence repeats (SSRs) in olive (Olea europaea L.) , 2002, Theoretical and Applied Genetics.