title: De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis.
abstract: Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work.
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. plm013@lynu.edu.cn.|School of Life Sciences, Luoyang Normal University, 71 Longmen Road, Luoyang 471022, China. plm013@lynu.edu.cn.
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Zhou
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. wyynwu@163.com.
authors.forename: Yue-Yue
authors.initials: YY
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. xbdxxuyn@163.com.
authors.forename: Ya-Nan
authors.initials: YN
authors.lastname: Xu
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. yanrongshan@126.com.
authors.forename: Rong-Shan
authors.initials: RS
authors.lastname: Yan
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. pengzhao@nwu.edu.cn.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhao
authors.affiliation: School of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China. lwenzhe@nwu.edu.cn.
authors.forename: Wen-Zhe
authors.initials: WZ
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D056727:Endangered Species; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics* / Q000378:metabolism; D005819:Genetic Markers; D018745:Genome, Plant; D019684:Magnoliopsida / Q000235:genetics* / Q000378:metabolism; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: EST-SSRs (Expressed sequence tag simple sequence repeats); Illumina sequencing; Tapiscia sinensis; transcriptome