To obtain information of Periplaneta americana, we analyzed the distribution characteristics of microsatellite sequences in the P.americana transcriptome (229 MB) by using MSDBv2.4. The total number of perfect microsatellite sequences was 38,082 and covered about 0.3 % of P. americana transcriptome. The cumulative length of microsatellites was 618,138 bp, and the density of microsatellites was 2978.54 bp/Mb. In the different repeat types of the microsatellites, the number of the mononucleotide repeats was 20,002 (accounting for 52.52 %), which obviously was the most abundant type. While the trinucleotide, tetranucleotide, dinucleotide,pentanucleotide and hexanucleotide repeats accounted for 24.51, 12.97, 8.1, 1.61 and 0.26 %, respectively. The kind of different repeat copy categories in each repeat type was also quite different, such as the A in mononucleotide repeat type, the AG in dinucleotide, the AAT in trinucleotide, AAAT in tetranucleotide, the AAGAA in pentanucleotide, and the CAGTAG in hexanucleotide were the most of each category. The A, T, AC, AG, AT, GT, AAG, AAT, ATC, ATG, ATT, CTT, AAAG and AAAT were the dominant repeat copy categories, the total number of all these types was 29,933, accounting for 78.6 % in the total number of microsatellite sequences. These results based on a foundation for developing high polymorphic microsatellites to research the functional genomics, population genetic structure and genetic diversity of P. americana.
Keywords: Periplaneta americana; transcriptome; microsatellite; tetranucleotide repeat types
Full text and supplemented materials
References
Chung, H.S., Yu, T.H., Kim, B.J., et al., Expressed sequence tags analysis of Blattella germanica, Korean J. Parasitol., 2005, vol. 43, no. 4, p. 149.
Du, L., Li, Y., Zhang, X., et al., MSDB: a user-friendly program for reporting distribution and building databases of microsatellites from genome sequences, J. Hered., 2013, vol. 104, no. 1, p. 154.
Emrich, S.J., Barbazuk, W.B., Li, L., et al., Gene discovery and annotation using LCM-454 transcriptome sequencing, Genome Res., 2007, vol. 17, no. 1, p. 69.
Eujayl, I., Sledge, M.K., Wang, L., et al., Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp., Theor. Appl. Genet., 2004, vol. 108, no. 3, pp. 414–422.
Gao, Z., Wang, W., and Zhou, X., DNA marker technologies and their applications in aquaculture genetics, Biotechnol. Bull., 2007, vol. 238, no. 1, pp. 1–37.
Gao, X., Han, J., Lu, Z., et al., RETRACTED: Characterization of the spotted seal Phoca largha transcriptome using Illumina paired-end sequencing and development of SSR markers, Comp. Biochem. Physiol., Part D: Genomics Proteomics, 2012, vol. 7, no. 3, pp. 277–284.
Gavery, M.R. and Roberts, S.B., Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas, Comp. Biochem. Physiol., Part D: Genomics Proteomics, 2012, vol. 7, no. 2, pp. 94–99.
Hamada, H., Petrino, M.G., and Kakunaga, T., A novel repeated element with Z-DNA-forming potential is widely found in evolutionarily diverse eukaryotic genomes, Proc. Natl. Acad. Sci. U. S. A., 1982, vol. 79, no. 21, pp. 6465–6469.
Huang, Q., Sun, P., Zhou, X., et al., Characterization of head transcriptome and analysis of gene expression involved in caste differentiation and aggression in Odontotermes formosanus (Shiraki), PloS One, 2012, vol. 7, no. 11, p. e50383.
Jaramillo-Ramirez, G.I., Cardenas-Henao, H., Gonzalez-Obando, R., et al., Genetic variability of five Periplaneta Americana L. (Dyctioptera: Blattidae) populations in southwestern Colombia using the AFLP molecular marker technique, Neotrop. Entomol., 2010, vol. 39, no. 3, p. 371.
Jing, S., Liu, B., Peng, L., et al., Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugens Stål), Bull. Entomol. Res., 2012, vol. 102, no. 1, p. 113.
Kashi, Y. and King, D.G., Simple sequence repeats as advantageous mutators in evolution, Trends Genet., 2006, vol. 22, no. 5, pp. 253–259.
Li, Y.C., Korol, A.B., Fahima, T., et al., Microsatellites within genes: structure, function, and evolution, Mol. Biol. Evol., 2004, vol. 21, no. 6, pp. 991–1007.
Li, H., He, C., Yang, Q., et al., Characterization of single nucleotide polymorphisms from expressed sequence tags of Chinese mitten crab Eriocheir sinensis, Aquat. Biol., 2010, vol. 11, pp. 193–199.
Li, Y., Korol, A.B., Fahima, T., et al., Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review, Mol. Ecol., 2010, vol. 11, no. 12, pp. 2453–2465.
Li, H., Liang, Y., Sui, L., et al., Characterization of 10 polymorphic microsatellite markers for Mediterranean blue mussel Mytilus galloprovincialis by EST database mining and cross-species amplification, J. Genet., 2011, vol. 90, no. 1, p. e30.
Li, H.J., Liu, W.D., Gao, X.G., et al., Identification of host-defense genes and development of microsatellite markers from ESTs of hard clam Meretrix meretrix, Mol. Biol. Rep., 2011, vol. 38, no. 2, pp. 769–775.
Marta, M., Cavagnaro, P.F., Megan, B., et al., De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity, BMC Genomics, 2011, vol. 12, no. 1, p. 389.
Omar, H. and Ahmad, A., Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs), Parasites Vectors, 2011, vol. 4, no. 1, p. 189.
Powell, W., Morgante, M., Andre, C., et al., The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis, Mol. Breed., 1996, vol. 2, no. 3, pp. 225–238.
Saha, M.C., Cooper, J.D., Mian, M.A., et al., Tall fescue genomic SSR markers: development and transferability across multiple grass species, Theor. Appl. Genet., 2006, vol. 113, no. 8, pp. 1449–1458.
Santure, A.W., Gratten, J., Mossman, J.A., et al., Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing, BMC Genomics, 2011, vol. 12, no. 1, p. 283.
Schlötterer, C., The evolution of molecular markers–just a matter of fashion, Nat. Rev. Genet., 2004, vol. 5, no. 1, pp. 63–69.
Sharma, P.C., Grover, A., and Kahl, G., Mining microsatellites in eukaryotic genomes, Trends Biotechnol., 2007, vol. 25, no. 11, pp. 490–498.
Shen, Y., Catchen, J., Garcia, T., et al., Identification of transcriptome SNPs between Xiphophorus, lines and species for assessing allele specific gene expression within F1, interspecies hybrids, Comp. Biochem. Physiol., Part C: Pharmacol., Toxicol. Endocrinol., 2012, vol. 155, no. 1, pp. 102–108.
Simbaqueba, J., Sánchez, P., Sanchez, E., et al., Development and characterization of microsatellite markers for the cape gooseberry Physalis peruviana, PloS One, 2011, vol. 6, no. 10, p. e26719.
Sun, L., Chen, M., Yang, H, et al., Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicas, Comp. Biochem. Physiol., Part D: Genomics Proteomics, 2015, vol. 6, no. 2, pp. 195–205.
Tautz, D. and Renz, M., Simple sequences are ubiquitous repetitive components of eukaryotic genomes, Nucleic Acids Res., 1984, vol. 12, no. 10, pp. 4127–4138.
Tóth, G., Gáspári, Z., and Jurka, J., Microsatellites in different eukaryotic genomes: survey and analysis, Genome Res., 2000, vol. 10, no. 7, p. 967.
Varshney, R.K., Graner, A., et al., Genic microsatellite markers in plants: features and applications, Trends Biotechnol., 2005, vol. 23, no. 1, pp. 48–55.
Wang, B., Ekblom, R., Castoe, T.A., et al., Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development, Open Biol., 2012, vol. 2, no. 4, p. 120054.
Wang, P., Ma, Y., Ma, L., et al., Development and characterization of EST-SSR markers for Catalpa bungei (Bignoniaceae), Appl. Plant Sci., 2016, vol. 4, no. 4, p. 1500117.
Wei, W., Qi, X., Wang, L., et al., Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers, BMC Genomics, 2011, vol. 12, no. 1, p. 451.
Wen, M., Wang, H., Xia, Z., et al., Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L., BMC Res. Notes, 2010, vol. 3, no. 1, p. 42.
Xie, W., Meng, Q.S., Wu, Q.J., et al., Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance, PloS One, 2012, vol. 7, no. 4, p. e35181.
Xu, Y., Zhou, W., Zhou, Y., et al., Transcriptome and comparative gene expression analysis of Sogatella furcifera (Horváth) in response to southern rice black-streaked dwarf virus, PloS One, 2012, vol. 7, no. 4, p. e36238.
Zhang, L.Y., Bernard, M., Leroy, P., et al., High transferability of bread wheat EST-derived SSRs to other cereals, Theor. Appl. Genet., 2005, vol. 111, no. 4, pp. 677–687.
Zhou, X., Qian, K., Tong, Y., et al., De Novo transcriptome of the hemimetabolous German cockroach (Blattella germanica), PloS One, 2014, vol. 9, no. 9, p. e106932.
Zhu, J.Y., Li, Y.H., Yang, S., et al., De novo assembly and characterization of the global transcriptome for Rhyacionia leptotubula using Illumina paired-end sequencing, PloS One, 2013, vol. 8, no. 11, p. e81096.
Zhu, J.Y., Wu, G.X., and Yang, B., High-throughput discovery of SSR genetic markers in the yellow mealworm beetle, Tenebrio molitor (Coleoptera: Tenebrionidae), from its transcriptome database, Acta Entomol. Sin., 2013, vol. 56, no. 7, pp. 724–728.