Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna

Biotechnology Research and Innovation - Tập 2 - Trang 9-18 - 2018
Nidhi Shukla1,2, Himani Kuntal1, Asheesh Shanker3, Satyendra Nath Sharma2
1Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
2Seed Technology Research, Rajasthan Agricultural Research Institute, Jaipur 302018, Rajasthan, India
3Department of Bioinformatics, Central University of South Bihar, Gaya, Bihar, India

Tài liệu tham khảo

Brondani, 2003, Transferability of microsatellite and sequence tagged site markers in Oryza species, Hereditas, 138, 187, 10.1034/j.1601-5223.2003.01656.x

Cao, 2005, Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates, BMC Bioinformatics, 6, 190, 10.1186/1471-2105-6-190

Cardle, 2000, Computational and experimental characterization of physically clustered simple sequence repeats in plants, Genetics, 156, 847, 10.1093/genetics/156.2.847

Cavagnaro, 2010, Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.), BMC Genomics, 11, 1, 10.1186/1471-2164-11-569

Chagne, 2004, Cross-species transferability and mapping of genomic and cDNA SSRs in pines, Theoretical and Applied Genetics, 109, 1204, 10.1007/s00122-004-1683-z

Chapman, 2009, Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.), Theoretical and Applied Genetics, 120, 85, 10.1007/s00122-009-1161-8

Chen, 2015, Transcriptome sequencing of mung bean (Vigna radiata L.) genes and the identification of EST-SSR markers, PLoS ONE, 10, 1

Cheng, 2016, A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in capsicum, Scientific Reports, 6, 18919, 10.1038/srep18919

Diehl, 2007, Ontology development for biological systems: Immunology, Bioinformatics, 23, 913, 10.1093/bioinformatics/btm029

Han, 2005, A genetic linkage map for azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi], Theoretical and Applied Genetics, 111, 1278, 10.1007/s00122-005-0046-8

Jansen, 2005, Methods for obtaining and analyzing whole chloroplast genome sequences, Methods in Enzymology, 395, 348, 10.1016/S0076-6879(05)95020-9

Kaila, 2016, Chloroplast genome sequence of pigeon pea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome organization and comparison with other legumes, Frontiers in Plant Science, 7, 1, 10.3389/fpls.2016.01847

Kang, 2014, Genome sequence of mungbean and insights into evolution within Vigna species, Nature Communications, 5, 1, 10.1038/ncomms6443

Kapil, 2014, ChloroSSRdb: A repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants, Database (Oxford), 10.1093/database/bau107

Kumar, 2014, MitoSatPlant: Mitochondrial microsatellites database of viridiplantae, Mitochondrion, 19, 334, 10.1016/j.mito.2014.02.002

Li, 2001, Determining genetic similarities and relationships among cowpea breeding lines and cultivars by microsatellite markers, Crop Science, 41, 189, 10.2135/cropsci2001.411189x

Mariotti, 2010, Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison, BMC Plant Biology, 10, 211, 10.1186/1471-2229-10-211

Mnejja, 2005, Development and transportability across Prunus species of 42 polymorphic almond microsatellites, Molecular Ecology Notes, 5, 531, 10.1111/j.1471-8286.2005.00977.x

Moe, 2011, Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mung bean, Journal of Integrative Plant Biology, 53, 63, 10.1111/j.1744-7909.2010.01012.x

Morgante, 1993, PCR-Amplified microsatellites as markers in plant genetics, The Plant Journal, 3, 175, 10.1046/j.1365-313X.1993.t01-9-00999.x

Mun, 2006, Distribution of microsatellites in the genome of Medicago truncatula: A resource of genetic markers that integrate genetic and physical maps, Genetics, 172, 2541, 10.1534/genetics.105.054791

Oliveira, 2006, Origin, evolution and genome distribution of microsatellites, Genetics and Molecular Biology, 29, 294, 10.1590/S1415-47572006000200018

Olmstead, 1994, Chloroplast DNA systematics: A review of methods and data analysis, American Journal of Botany, 81, 1205, 10.1002/j.1537-2197.1994.tb15615.x

Provan, 2001, Chloroplast microsatellites: New tools for studies in plant ecology and evolution, Trends in Ecology and Evolution, 16, 142, 10.1016/S0169-5347(00)02097-8

Qin, 2015, Evolution analysis of simple sequence repeats in plant genome, PLoS ONE, 10, 1, 10.1371/journal.pone.0144108

Rajendrakumar, 2007, Simple sequence repeats in organellar genomes of rice: Frequency and distribution in genic and intergenic regions, Bioinformatics, 23, 1, 10.1093/bioinformatics/btl547

Sangiri, 2007, Genetic diversity of the mungbean (Vigna radiata, Leguminosae) gene pool on the basis of microsatellite analysis, Australian Journal of Botany, 55, 837, 10.1071/BT07105

Shanker, 2007, Bioinformatically mined simple sequence repeats in UniGene of Citrus sinensis, Scientia Horticulturae, 113, 353, 10.1016/j.scienta.2007.04.011

Shanker, 2011, Phylogenomic evidence of bryophytes’ monophyly using complete and incomplete data sets from chloroplast proteomes, Journal of Plant Biochemistry and Biotechnology, 20, 288, 10.1007/s13562-011-0054-5

Shanker, 2013, Paraphyly of bryophytes inferred using chloroplast sequences, Archive for Bryology, 163, 1

Shanker, 2013, Inference of bryophytes paraphyly using mitochondrial genomes, Archive for Bryology, 165, 1

Shanker, 2013, Combined data from chloroplast and mitochondrial genome sequences showed paraphyly of bryophytes, Archive for Bryology, 171, 1

Shanker, 2013, Identification of microsatellites in chloroplast genome of Anthoceros formosae, Archive for Bryology, 191, 1

Sharma, 2011, A modified DNA extraction protocol and its utility in seed genetic purity assessment, Seed Science and Technology, 39, 236, 10.15258/sst.2011.39.1.24

Sonah, 2011, Genome-Wide distribution and organization of microsatellites in plants: An insight into marker development in Brachypodium, PLoS ONE, 6, 1, 10.1371/journal.pone.0021298

Srivastava, 2015, Mining of simple sequence repeats in chloroplast genome sequence of Cocos nucifera, Applied Research Journal, 1, 51

Tambarussi, 2009, In-silico analysis of simple sequence repeats from chloroplast genomes of Solanaceae species, Crop Breeding and Applied Biotechnology, 9, 344, 10.12702/1984-7033.v09n04a09

Tautz, 1989, Hypervariability of simple sequences as a general source for polymorphic DNA markers, Nucleic Acids Research, 17, 6463, 10.1093/nar/17.16.6463

Yi, 2012, Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L, PLoS ONE, 7, 10.1371/journal.pone.0035872

Zane, 2002, Strategies for microsatellite isolation: A review, Molecular Ecology, 11, 1, 10.1046/j.0962-1083.2001.01418.x

Zapiola, 2010, Development of novel chloroplast microsatellite markers to identify species in the Agrostis complex (Poaceae) and related genera, Molecular Ecology Resources, 10, 738, 10.1111/j.1755-0998.2009.02828.x

Zou, 2012, Distribution and characterization of simple sequence repeats in Gossypium raimondii genome, Bioinformation, 8, 801, 10.6026/97320630008801