Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria

BMC Genomics

Iliana B Baums¹  Dannise V Ruiz-Ramos¹ 

[1] Department of Biology, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA

关键词: Comparative genomics;    Simple sequence repeats;    Ancestral metazoan;    Microsatellites;    Cnidaria;   

Others  :  1130607
DOI  :  10.1186/1471-2164-15-939

 received in 2013-07-24, accepted in 2014-10-16,  发布年份 2014

【 摘 要 】

Background

Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria.

Results

Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group.

Conclusions

Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

【 授权许可】

   
2014 Ruiz-Ramos and Baums; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Ball EE, Hayward DC, Saint R, Miller DJ: A simple plan - Cnidarians and the origins of developmental mechanisms. Nat Rev Genet 2004, 5(8):567-577.
• [2]Buss LW: Evolution, development and the units of selection. Proc Natl Acad Sci U S A 1982, 80:1387-1391.
• [3]Shick JM: Ultraviolet Stress. Berkeley and Los Angeles: University of California Press; 2007.
• [4]Wolfe BE, Tulloss RE, Pringle A: The irreversible loss of a decomposition pathway marks the single origin of an ectomycorrhizal symbiosis. PLoS One 2012, 7(7):e39597.
• [5]Steele RE, David CN, Technau U: A genomic view of 500 million years of cnidarian evolution. Trends Genet 2011, 27(1):7-13.
• [6]Galtier N, Jobson RW, Nabholz B, Glémin S, Blier PU: Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution. Biol Lett 2009, 5(3):413-416.
• [7]Hancock JM: Microsatellites and other simple sequences: genomic context and mutational mechanisms. In Microsatellites: Evolution and Applications. Edited by Goldstein DB, Schlötterer C. NY: Oxford University Press; 1998:1-9.
• [8]Ellegren H: Microsatellites: simple sequences with complex evolution. Nat Rev Genet 2004, 5(6):435-445.
• [9]Kelkar YD, Eckert KA, Chiaromonte F, Makova KD: A matter of life or death: how microsatellites emerge in and vanish from the human genome. Genome Res 2011, 21(12):2038-2048.
• [10]Toth G, Gaspari Z, Jurka J: Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 2000, 10(7):967-981.
• [11]Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD: The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res 2008, 18(1):30-38.
• [12]Neff BD, Gross MR: Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution 2001, 55(9):1717-1733.
• [13]Gemayel R, Vinces MD, Legendre M, Verstrepen KJ: Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 2010, 44:445-477.
• [14]Sreenu V, Kumar P, Nagaraju J, Nagarajaram H: Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity. BMC Genomics 2006, 7(1):78-88. BioMed Central Full Text
• [15]Hammock EAD, Young LJ: Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 2005, 308(5728):1630-1634.
• [16]Katti MV, Ranjekar PK, Gupta VS: Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 2001, 18(7):1161-1167.
• [17]Ross CL, Dyer KA, Erez T, Miller SJ, Jaenike J, Markow TA: Rapid divergence of microsatellite abundance among species of Drosophila. Mol Biol Evol 2003, 20(7):1143-1157.
• [18]Meglecz E, Neve G, Biffin E, Gardner MG: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species. PLoS One 2012, 7(7):e40861.
• [19]Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS: Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 2007, 317(5834):86-94.
• [20]Chapman JA, Kirkness EF, Simakov O, Hampson SE, Mitros T, Weinmaier T, Rattei T, Balasubramanian PG, Borman J, Busam D, Disbennett K, Pfannkoch C, Sumin N, Sutton GG, Viswanathan LD, Walenz B, Goodstein DM, Hellsten U, Kawashima T, Prochnik SE, Putnam NH, Shu SQ, Blumberg B, Dana CE, Gee L, Kibler DF, Law L, Lindgens D, Martinez DE, Peng JS, et al.: The dynamic genome of Hydra. Nature 2010, 464(7288):592-596.
• [21]Suzuki R, Shimodaira H: Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 2006, 22(12):1540-1542.
• [22]Romiguier J, Ranwez V, Douzery EJP, Galtier N: Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes. Genome Res 2010, 20(8):1001.
• [23]Ponting CP: The functional repertoires of metazoan genomes. Nat Rev Genet 2008, 9(9):689-698.
• [24]Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ: Rise of the machines – recommendations for ecologists when using next generation sequencing for microsatellite development. Mol Ecol Resour 2011, 11(6):1093-1101.
• [25]Stolle E, Kidner JH, Moritz RFA: Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in hymenoptera than in diptera. Genome Biol Evol 2013, 5(1):151-162.
• [26]Jurka J, Pethiyagoda C: Simple repetitive DNA-sequences from primates- compilation and analysis. J Mol Evol 1995, 40(2):120-126.
• [27]Venn AA, Loram JE, Trapido-Rosenthal HG, Joyce DA, Douglas AE: Importance of time and place: patterns in abundance of Symbiodinium clades A and B in the tropical sea anemone Condylactis gigantea. Biol Bull 2008, 215:243-252.
• [28]Jones RJ: Changes in zooxanthellar densities and chlorophyll concentrations in corals during and after a bleaching event. Mar Ecol Prog Ser 1997, 158:51-59.
• [29]Shoguchi E, Shinzato C, Kawashima T, Gyoja F, Mungpakdee S, Koyanagi R, Takeuchi T, Hisata K, Tanaka M, Fujiwara M: Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr Biol 2013, 23(15):1399-1408.
• [30]Davy SK, Allemand D, Weis VM: Cell biology of cnidarian-dinoflagellate symbiosis. Microbiol Mol Biol Rev 2012, 76(2):229-261.
• [31]France SC, Hoover LL: Analysis of variation in mitochondrial DNA sequences (ND3, ND4L, MSH) among Octocorallia (=Alcyonaria)(Cnidaria: Anthozoa). Bull Biol Soc Washington 2001, 10:110-118.
• [32]Hellberg M: No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evol Biol 2006, 6(1):24. BioMed Central Full Text
• [33]Shearer TL, Van Oppen MJH, Romano SL, Wörheide G: Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Mol Ecol 2002, 11(12):2475-2487.
• [34]Baums IB: A restoration genetics guide for coral reef conservation. Mol Ecol 2008, 17(12):2796-2811.
• [35]Van Oppen MJH, Worheide G, Takabayashi M: Nuclear markers in evolutionary and population genetic studies of scleractinian corals and sponges. Proc 9th Int Coral Reef Symposium 2000, 1:131-138.
• [36]Vera JC, Wheat CW, Fescemyer HW, Frilander MK, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647.
• [37]Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K, Tanaka M, Fujie M, Fujiwara M, Koyanagi R, Ikuta T, Fujiyama A, Miller DJ, Satoh N: Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 2011, 08(18):320-323.
• [38]Bayer T, Aranda M, Sunagawa S, Yum LK, DeSalvo MK, Lindquist E, Coffroth MA, Voolstra CR, Medina M: Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PLoS One 2012, 7(4):e35269.
• [39]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
• [40]Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997, 25:3398-3402.
• [41]Benson G: Tandem repeat finder: a program to analyze DNA sequences. Nucleic Acid Res 1999, 27(2):573-580.
• [42]Kofler R, Schlötterer C, Lelley T: SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics 2007, 23(13):1683-1685.
• [43]Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT: Direct comparisons of illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 2012, 7(2):e30087.
• [44]R Development Core Team: R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2008.
• [45]Harismendy O, Ng P, Strausberg R, Wang X, Stockwell T, Beeson K, Schork N, Murray S, Topol E, Levy S, Frazer K: Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009, 10(3):R32. BioMed Central Full Text
• [46]Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A: Geneious v5.1. 2010.
• [47]Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
• [48]Drummond AJ, Suchard MA, Xie D, Rambaut A: Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012, 29(8):1969-1973.
• [49]Pagel M, Meade A, Barker D: Bayesian estimation of ancestral character states on phylogenies. Syst Biol 2004, 53(5):673-684.