Development of polymorphic microsatellite markers by using de novo transcriptome assembly of Calanthe masuca and C. sinica (Orchidaceae)

[1]  Rolf Lohaus,et al.  The Apostasia genome and the evolution of orchids , 2017, Nature.

[2]  Yi-Gang Song,et al.  De novo transcriptome assembly and development of SSR markers of oaks Quercus austrocochinchinensis and Q. kerrii (Fagaceae) , 2016, Tree Genetics & Genomes.

[3]  Y. Lei,et al.  Genomic survey sequencing for development and validation of single-locus SSR markers in peanut (Arachis hypogaea L.) , 2016, BMC Genomics.

[4]  Y. van de Peer,et al.  The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution , 2016, Scientific Reports.

[5]  D. Pollock,et al.  Erratum: Rapid microsatellite identification from illumina paired-end genomic sequencing in two birds and a snake(PLoS ONE 7:2(e30953) 10.1371/journal.pone.0030953) , 2015 .

[6]  Liping Liu,et al.  Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis) , 2015, PloS one.

[7]  Xiaomei Sun,et al.  Development and Characterization of Polymorphic Genic-SSR Markers in Larix kaempferi , 2015, Molecules.

[8]  R. Visser,et al.  Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals , 2015, Molecular ecology resources.

[9]  Xun Xu,et al.  The genome sequence of the orchid Phalaenopsis equestris , 2014, Nature Genetics.

[10]  Guo-Qiang Zhang,et al.  A new phylogenetic analysis sheds new light on the relationships in the Calanthe alliance (Orchidaceae) in China. , 2014, Molecular phylogenetics and evolution.

[11]  S. Aceto,et al.  De Novo Transcriptome Assembly from Inflorescence of Orchis italica: Analysis of Coding and Non-Coding Transcripts , 2014, PloS one.

[12]  Xiaolan Zhao,et al.  Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development , 2013, BMC Genomics.

[13]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[14]  C. Jantasuriyarat,et al.  Development and transferability of EST-SSR and transferability of genomic SSR markers for genetic diversity assessment of Doritis , 2012 .

[15]  Huizhong Wang,et al.  Development and characterization of 110 novel EST-SSR markers for Dendrobium officinale (Orchidaceae). , 2012, American journal of botany.

[16]  H. Miao,et al.  Development and validation of genic-SSR markers in sesame by RNA-seq , 2012, BMC Genomics.

[17]  E. van de Weg,et al.  Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra) , 2012, BMC Genomics.

[18]  Todd A. Castoe,et al.  Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake , 2012, PloS one.

[19]  Linhai Wang,et al.  Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers , 2011, BMC Genomics.

[20]  C. Su,et al.  De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. , 2011, Plant & cell physiology.

[21]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[22]  Chuan-Yun Li,et al.  KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases , 2011, Nucleic Acids Res..

[23]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[24]  Jun Yu,et al.  KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies , 2010, Genom. Proteom. Bioinform..

[25]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[26]  M. Chase,et al.  Genome size diversity in orchids: consequences and evolution. , 2009, Annals of botany.

[27]  Jack A. M. Leunissen,et al.  Large-scale identification of polymorphic microsatellites using an in silico approach , 2008, BMC Bioinformatics.

[28]  D. Kliebenstein,et al.  Distinct Roles of Jasmonates and Aldehydes in Plant-Defense Responses , 2008, PloS one.

[29]  Gabriel Moreno-Hagelsieb,et al.  Choosing BLAST options for better detection of orthologs as reciprocal best hits , 2008, Bioinform..

[30]  B. Faircloth,et al.  msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design , 2008, Molecular ecology resources.

[31]  S. Kalinowski,et al.  Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment , 2007, Molecular ecology.

[32]  Q. Kong,et al.  Development of EST‐SSRs in Cucumis sativus from sequence database , 2006 .

[33]  Peer Bork,et al.  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments , 2006, Nucleic Acids Res..

[34]  Erik L. L. Sonnhammer,et al.  Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..

[35]  Markus Schuelke,et al.  An economic method for the fluorescent labeling of PCR fragments , 2000, Nature Biotechnology.

[36]  Yan P. Yuan,et al.  Predicting function: from genes to genomes and back. , 1998, Journal of molecular biology.

[37]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[38]  Gregory D Schuler,et al.  Sequence mapping by electronic PCR , 1997, Genome research.

[39]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[40]  Sumit G. Gandhi,et al.  Development of chemical and EST-SSR markers for Ocimum genus , 2015 .

[41]  T. Sharma,et al.  Informative genomic microsatellite markers for efficient genotyping applications in sugarcane , 2008, Theoretical and Applied Genetics.

[42]  BIOINFORMATICS APPLICATIONS NOTE , 2005 .