Research note

Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing

Yawen Wu , Ruhua Zhang, Margaret Staton, Scott E. Schlarbaum, Mark V. Coggeshall, Jeanne Romero-Severson, John E. Carlson, Haiying Liang, Yi Xu, Daniela I. Drautz-Moses, Stephan C. Schuster, Oliver Gailing

Yawen Wu
Michigan Technological University, School of Forest Resources and Environmental Science, 1400 Townsend Drive, Houghton, MI 49931. Email: na@yw.com
Ruhua Zhang
Michigan Technological University, School of Forest Resources and Environmental Science, 1400 Townsend Drive, Houghton, MI 49931, USA
Margaret Staton
Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN 37996, USA
Scott E. Schlarbaum
Department of Forestry, Wildlife and Fisheries, The University of Tennessee, Knoxville, TN 37996-4563, USA
Mark V. Coggeshall
USDA Forest Service, Northern Research Station, Purdue University, West Lafayette, IN 47907, USA
Jeanne Romero-Severson
Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
John E. Carlson
The Department of Ecosystem Science and Management and Department of Plant Science, Pennsylvania State University, University Park, PA 16802, SUA
Haiying Liang
Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
Yi Xu
Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
Daniela I. Drautz-Moses
The Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
Stephan C. Schuster
The Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
Oliver Gailing
University of Göttingen, Forest Genetics and Forest Tree Breeding, Büsgenweg 2, 37077 Göttingen, Germany

Online First: June 29, 2017
Wu, Y., Zhang, R., Staton, M., Schlarbaum, S., Coggeshall, M., Romero-Severson, J., Carlson, J., Liang, H., Xu, Y., Drautz-Moses, D., Schuster, S., Gailing, O. 2017. Development of genic and genomic microsatellites in Gleditsia triacanthos L. (Fabaceae) using Illumina sequencing. Annals of Forest Research DOI:10.15287/afr.2017.819


Twenty new polymorphic genic SSRs (EST-SSRs) and 13 genomic SSRs were developed in honeylocust (Gleditsia triacanthos) using Illumina transcriptome and low-coverage genome sequencing. A diversity panel of 40 honeylocust samples covering large parts of the species distribution range was characterized. As expected the level of genetic variation was lower in EST-SSRs than for non-genic genomic SSRs. This is the first report of EST-SSRs for honeylocust. All markers are polymorphic and produce clear single locus amplification products and can be used for genetic diversity and gene flow analyses. The transcriptome sequencing data provide a rich resource for new marker development.


Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L., 2009. BLAST plus: architecture and applications. BMC Bioinformatics 10:421. DOI: 10.1186/1471-2105-10-421

Gailing O., Staton M.E., Lane T., Schlarbaum S.E., Nipper R., Owusu S.A., Carlson J.E., 2017. Construction of a framework genetic linkage map in Gleditsia triacanthos L. Plant Molecular Biology Reporter 35:177-187. DOI: 10.1007/s11105-016-1012-0

Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., Leduc R.D., Friedman N., Regev A., 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols 8:1494-1512. DOI: 10.1038/nprot.2013.084

Kubisiak T.L., Nelson C.D., Staton M.E., Zhebentyayeva T., Smith C., Olukolu B.A., Fang G.C., Hebard F.V., Anagnostakis S., Wheeler N., Sisco P.H., Abbott A.G., Sederoff R.R., 2013. A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica). Tree Genetics & Genomes 9:557-571. DOI: 10.1007/s11295-012-0579-3

La Malfa S., Curro S., Douglas A.B., Brugaletta M., Caruso M., Gentile A., 2014. Genetic diversity revealed by EST-SSR markers in carob tree (Ceratonia siliqua L.). Biochemical Systematics and Ecology 55:205-211. DOI: 10.1016/j.bse.2014.03.022

Lane T., Best T., Zembower N., Davitt J., Henry N., Xu Y., Koch J., Liang H., McGraw J., Schuster S., Shim D., Coggeshall M.V., Carlson J.E., Staton M.E., 2016. The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC genomics 17:702. DOI: 10.1186/s12864-016-3052-0

Magrane M., UniProt C., 2011. UniProt Knowledgebase: a hub of integrated protein data. Database-the Journal of Biological Databases and Curation. 10.1093/database/bar009 DOI.

Owusu S.A., Schlarbaum S., Carlson J.E., Gailing O., 2016. Gene flow analyses and identification of full-sib families in isolated populations of Gleditsia triacanthos L. Botany-Botanique 94:523-532. DOI: 10.1139/cjb-2015-0244

Owusu S.A., Staton M., Jennings T.N., Schlarbaum S., Coggeshall M.V., Romero-Severson J., Carlson J.E., Gailing O., 2013. Development of genomic microsatellites in Gleditsia triacanthos (Fabaceae) using Illumina Sequencing. Applications in Plant Sciences 1:1300050. DOI: 10.3732/apps.1300050

Peakall R., Smouse P.E., 2006. GENEALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6:288-295. DOI: 10.1111/j.1471-8286.2005.01155.x

Peakall R., Smouse P.E., 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537-2539. DOI: 10.1093/bioinformatics/bts460

Preston Jr. R.J., Braham R.R. 2002. North American trees. Iowa State Press, Ames, Iowa, USA.

Raymond M., Rousset F., 1995. GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248-249. DOI: 10.1093/oxfordjournals.jhered.a111573

Rousset F., 2008. GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103-106. DOI: 10.1111/j.1471-8286.2007.01931.x

Schnabel A., Wendel J.F., 1998. Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. American Journal of Botany 85:1753-1765. DOI: 10.2307/2446510

Schuelke M., 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18:233-234. DOI: 10.1038/72708

Simao F.A., Waterhouse R.M., Ioannidis P., Kriventseva E.V., Zdobnov E.M., 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210-3212. DOI: 10.1093/bioinformatics/btv351

Staton M., Best T., Khodwekar S., Owusu S., Xu T., Xu Y., Jennings T., Cronn R., Arumuganathan A.K., Coggeshall M., Gailing O., Liang H., Romero-Severson J., Schlarbaum S., Carlson J.E., 2015. Preliminary genomic characterization of ten hardwood tree species from multiplexed low coverage whole genome sequencing. Plos One 10:e0145031. DOI: 10.1371/journal.pone.0145031

Untergasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B.C., Remm M., Rozen S.G., 2012. Primer3-new capabilities and interfaces. Nucleic Acids Research 40: e115. DOI: 10.1093/nar/gks596


Supp. Info. 1. EST-SSRs, dinucleotide and trinucleotiderepeats for honeylocust (unigene version 082614)
| DOWNLOAD 12KB
Supp. Info. 2. Genomic SSRs
| DOWNLOAD 11KB
Supp. Info. 3. Geographic coordinates of Gleditsia triacanthos provenances
| DOWNLOAD 17KB
No metrics available for this article.