Simple sequence repeats in bryophyte mitochondrial genomes

References

• Arroyo-Garcia R, Lefort F, de Andres MT, Ibanez J, Borrego J, Jouve N, Cabello F, Martinez-Zapater JM. (2002). Chloroplast microsatellite polymorphisms in Vitis species. Genome 45:1142–9
   PubMed Web of Science ®Google Scholar
• Gandhi SG, Awasthi P, Bedi YS. (2010). Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family. Bioinformation 5:16–20
   PubMedGoogle Scholar
• Hall TA. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–8
   Google Scholar
• Karlin EF, Boles SB, Shaw AJ. (2008a). Resolving boundaries between species in Sphagnum section Subsecunda using microsatellite markers. Taxon 57:1189–200
   Web of Science ®Google Scholar
• Karlin EF, Boles SB, Shaw AJ. (2008b). Systematics of Sphagnum section Sphagnum in New Zealand: A microsatellite-based analysis. New Zeal J Bot 46:105–18
   Web of Science ®Google Scholar
• Kashi Y, King DJ. (2006). Simple sequence repeats as advantageous mutators in evolution. Trends Genet 22:253–9
   PubMed Web of Science ®Google Scholar
• King DG, Kashi Y. (2009). Heretical DNA sequences? Science 326:229–30
   PubMed Web of Science ®Google Scholar
• Kuntal H, Sharma V. (2011). In silico analysis of SSRs in mitochondrial genomes of plants. OMICS 15:783–9
   PubMed Web of Science ®Google Scholar
• Kuntal H, Sharma V, Daniell H. (2012). Microsatellite analysis in organelle genomes of Chlorophyta. Bioinformation 8:255–9
   PubMedGoogle Scholar
• Lawson MJ, Zhang L. (2006). Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 17:R14 (1–11)
   Google Scholar
• Li L, Wang B, Liu Y, Qiu YL. (2009). The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol 68:665–78
   PubMed Web of Science ®Google Scholar
• Li YC, Korol AB, Fahima T, Nevo E. (2004). Microsatellites within genes: Structure, function, and evolution. Mol Biol Evol 21:991–1007
   PubMed Web of Science ®Google Scholar
• Lin WH, Kussell E. (2012). Evolutionary pressures on simple sequence repeats in prokaryotic coding regions. Nucleic Acids Res 40:2399–413
   PubMed Web of Science ®Google Scholar
• Liu Y, Wang B, Li L, Qiu YL, Xue J. (2012). Conservative and dynamic evolution of mitochondrial genomes in early land plants. In: Bock R, Knoop V, editors. Genomics of chloroplasts and mitochondria. The Netherlands: Springer. p 159–74
   Google Scholar
• Liu Y, Xue JU, Wang B, Li L, Qiu YL. (2011). The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: Dynamic and conservative evolution. PLoS One 6:e25836
   PubMed Web of Science ®Google Scholar
• Magain N, Forrest LL, Serusiaux E, Goffinet B. (2010). Microsatellite primers in the Peltigera dolichorhiza complex (lichenized ascomycete, Peltigerales). Am J Bot 97:e102–4
   PubMed Web of Science ®Google Scholar
• Mayer C, Leese F, Tollrian R. (2010). Genome-wide analysis of tandem repeats in Daphnia pulex – A comparative approach. BMC Genomics 11:277
   PubMed Web of Science ®Google Scholar
• Nishikawa T, Vaughan DA, Kadowaki K. (2005). Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes. Theor Appl Genet 110:696–705
   PubMed Web of Science ®Google Scholar
• Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, et al. (1992). Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA – A primitive form of plant mitochondrial genome. J Mol Biol 223:1–7
   PubMed Web of Science ®Google Scholar
• Qiu YL, Li L, Wang B, Chen Z, Dombrovska O, Lee J, Kent L, et al. (2007). A non-flowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial and nuclear genes. Int J Plant Sci 168:691–708
   Web of Science ®Google Scholar
• Qiu YL, Li L, Wang B, Chen Z, Knoop V, Groth-Malonek M, Dombrovska O, et al. (2006). The deepest divergences in land plants inferred from phylogenomic evidence. Proc Natl Acad Sci USA 103:15511–16
   PubMed Web of Science ®Google Scholar
• Rajendrakumar P, Biswal AK, Balachandran SM, Srinivasarao K, Sundaram RM. (2007). Simple sequence repeats in organellar genomes of rice: Frequency and distribution in genic and intergenic regions. Bioinformatics 23:1–4
   PubMed Web of Science ®Google Scholar
• Rajendrakumar P, Biswal AK, Balachandran SM, Sundaram RM. (2008). In silico analysis of microsatellites in organellar genomes of major cereals for understanding their phylogenetic relationships. In Silico Biol 8:87–104
   PubMedGoogle Scholar
• Ronchetti E, Salvadori S, Deiana AM. (1995). Genome size and AT content in Anguilliformes. Eur J Histochem 39:259–64
   PubMed Web of Science ®Google Scholar
• Sawicki J, Kwasniewski M, Szczecinska M, Chwialkowska K, Milewicz M, Plasek V. (2012). Isolation and characterization of simple sequence repeats (SSR) markers from the moss genus Orthotrichum using a small throughput pyrosequencing machine. Int J Mol Sci 13:7586–93
   PubMed Web of Science ®Google Scholar
• Shaw AJ, Cao T, Wang LS, Flatberg KI, Flatberg B, Shaw B, Zhou P, et al. (2008). Genetic variation in three Chinese peat mosses (Sphagnum) based on microsatellite markers, with primer information and analysis of ascertainment bias. Bryologist 111:271–81
   Web of Science ®Google Scholar
• Subramanian S, Madgula VM, George R, Kumar S, Pandit MW, Singh L. (2003). SSRD: Simple sequence repeats database of the human genome. Comp Funct Genomics 4:342–5
   PubMedGoogle Scholar
• Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N. (2007). The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24:699–709
   PubMed Web of Science ®Google Scholar
• Thomas EE. (2005). Short, local duplications in eukaryotic genomes. Curr Opin Genet Dev 15:640–4
   PubMed Web of Science ®Google Scholar
• Ussery DW, Hallin PF. (2004). Genome update: AT content in sequenced prokaryotic genomes. Microbiology 150:749–52
   PubMed Web of Science ®Google Scholar
• Villarreal JC, Forrest LL, McFarland K, Goffinet B. (2012). Chloroplast, mitochondrial, and nuclear microsatellites from the Southern Appalachian hornwort, Nothoceros aenigmaticus (Dendrocerotaceae). Am J Bot 99:e88–90
   Google Scholar
• Wang B, Xue JY, Li L, Liu L, Qiu YL. (2009). The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet 55:601–9
   PubMed Web of Science ®Google Scholar
• Westberg J, Persson A, Holmberg A, Goesmann A, Lundeberg J, Johansson KE, Pettersson B, Uhlen M. (2004). The genome sequence of Mgcoplasma mycoides subsp mycoides SC type strain PG1(T), the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res 14:221–7
   PubMed Web of Science ®Google Scholar
• Xue JY, Liu Y, Li L, Wang B, Qiu YL. (2010). The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: Retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet 56:53–61
   PubMed Web of Science ®Google Scholar
• Yang JY, Motilal LA, Dempewolf H, Maharaj K, Cronk QCB. (2011). Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae. Am J Bot 98:E372–4
   Google Scholar
• Zhang L, Yuan D, Yu S, Li Z, Cao Y, Miao Z, Qian H, Tang K. (2004). Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana. Bioinformatics 20:1081–6
   PubMed Web of Science ®Google Scholar