程晓凤,黄福江,刘明典,等. 2011. 454测序技术开发微卫星标记的研究进展.生物技术通报, (8):82-90. (Cheng X F, Huang F J, Liu M D, et al. 2011. Development of microsatellite markers using 454 pyrosequencing. Biotechnology Bulletin, (8):82-90.[in Chinese]) 齐明. 2008.杉木远交亲本群体遗传多样性研究.植物研究, 28(3):299-303. (Qi M. 2008. Genetic diversity of wide cross population of Cunninghamia lanceolata and Platycladus orientalis. Bulletin of Botanical Research, 28(3):299-303.[in Chinese]) 徐阳,陈金慧,李亚,等. 2014.杉木EST-SSR与基因组SSR引物开发.南京林业大学学报, 38(1):9-14. (Xu Y, Chen J H, Li Y, et al. 2014. Development of EST-SSR and genomic-SSR in Chinese fir. Journal of Nanjing Forestry University, 38(1):9-14.[in Chinese]) 尤勇,洪菊生.1998. RAPD标记在杉木种源遗传变异上的应用.林业科学, 34(4):33-38. (You Y, Hong J S. 1998. Application of RAPD marker of genetic variation of Chinese fir provenances. Scientia Silvae Sinicae, 34(4):33-38.[in Chinese]) 张圣,黄华宏,林二培,等. 2013.杉木与台湾杉EST-SSR标记的开发与应用.林业科学, 49(10):173-180. (Zhang S, Huang H H, Lin E P, et al. 2013. Development and application of EST-SSR markers for Cunninghamia lanceolata and Taiwania cryptomerioides. Scientia Silvae Sinicae, 49(10):173-180.[in Chinese]) Altschul S F, Gish W, Miller W, et al. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-410. Bérubé Y, Zhuang J, Rungis D, et al. 2007. Characterization of EST-SSRs in loblolly pine and spruce. Tree Genetics and Genomes, 3(3):251-259. Blacket M J, Robin C, Good R T, et al. 2012. Universal primers for fluorescent labelling of PCR fragments-an efficient and cost-effective approach to genotyping by fluorescence. Molecular Ecology Resources, 12(3):456-463. Bräutigam A, Mullick T, Schliesky S, et al. 2011. Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C3 and C4 species. Journal of Experimental Botany, 62(9):3093-3102. Buschiazzo E, Gemmell N J. 2006. The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays, 28(10):1040-1050. Castoe T A, Poole A W, de Koning A P J, et al. 2012. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE, 7(2):e30953. Chung J D, Lin T P, Tan Y C, et al. 2004. Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan:a comparison with Cunninghamia lanceolata, a mainland species in China. Molecular Phylogenetics and Evolution, 33(3):792-801. da Maia L C, Palmieri D A, de Souza V Q, et al. 2008. SSRLocator:tool for simple sequence repeat discovery integrated with primer design and PCR simulation. International Journal of Plant Genomics, doi:10.1155/2008/412696. Davey J W, Hohenlohe P A, Etter P D, et al. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics, 12(7):499-510. Duran C, Singhania R, Raman H, et al. 2013. Predicting polymorphic EST-SSRs in silico. Molecular Ecology Resources, 13(3):538-545. Glenn T C, Schable N A. 2005. Isolating microsatellite DNA loci. Methods in Enzymology, 395:202-222. Hamilton M B, Pincus E L, Di-Fiore A, et al. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. BioTechniques, 27(3):500-507. He C, Poysa V, Yu K. 2003. Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical and Applied Genetics, 106(2):363-373. Hoffman J I, Nichols H J. 2011. A novel approach for mining polymorphic microsatellite markers in silico. PLoS ONE, 6(8):e23283. Jarne P, Lagoda P J L. 1996. Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution, 11(10):424-429. Li W, Godzik A. 2006. Cd-hit:a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22:1658-1659. Meglécz E, Costedoat C, Dubut V, et al. 2010. QDD:a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics, 26(3):403-404. O'Neill E M, Schwartz R, Bullock C T, et al. 2013. Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex. Molecular Ecology, 22(1):111-129. Pandey G, Misra G, Kumari K, et al. 2013. Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet[Setaria italica (L.)]. DNA Research, 20(2):197-207. Peakall R, Smouse P E. 2006. GENALEX 6:genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1):288-295. Qiu Z B, Wan L C, Chen T, et al. 2013. The regulation of cambial activity in Chinese fir (Cunninghamia lanceolata) involves extensive transcriptome remodeling. New Phytologist, 199(3):708-719. Rozen S, Skaletsky H J. 2000. Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols, 132:365-386. Sarmah R, Sahu J, Dehury B, et al. 2012. ESMP:a high-throughput computational pipeline for mining SSR markers from ESTs. Bioinformation, 8(4):206-208. Slater G S, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics, 6(4):31. Smulders M J M, Bredemeijer G, Rus-Kortekaas W, et al. 1997. Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theoretical and Applied Genetics, 94(2):264-272. Tang J F, Baldwin S J, Jacobs J M E, et al. 2008. Large-scale identification of polymorphic microsatellites using an in silico approach. BMC Bioinformatics, 9:374. Thiel T, Michalek W, Varshney R, et al. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L). Theoretical and Applied Genetics, 106(3):411-422. Ueno S, Moroguchi Y, Uchiyama K, et al. 2012. A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics, 13:136. Victoria F C, da Maia L C, de Oliveira A C. 2011. In silico comparative analysis of SSR markers in plants. BMC Plant Biology, 11:15. Wen Y, Ueno S, Han W, et al. 2013. Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on tranxcriptome sequences. Silave Gentica, 62(3):137-141. Yu J N, Won C, Jun J, et al. 2011. Fast and cost-effective mining of microsatellite markers using NGS technology:an example of a Korean water deer Hydropotes inermis argyropus. PLoS ONE, 6:e26933. Zalapa J E, Cuevas H, Zhu H Y, et al. 2012. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. American Journal of Botany, 99(2):193-208. Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation:A review. Molecular Ecology, 11(1):1-16. |