title: Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery.
abstract: BACKGROUND
  Simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low.
  
  
  RESULTS
  Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity.
  
  
  CONCLUSIONS
  SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wang
authors.forename: Jiafu
authors.initials: J
authors.lastname: Jiang
authors.forename: Sumei
authors.initials: S
authors.lastname: Chen
authors.forename: Xiangyu
authors.initials: X
authors.lastname: Qi
authors.forename: Hui
authors.initials: H
authors.lastname: Peng
authors.forename: Pirui
authors.initials: P
authors.lastname: Li
authors.forename: Aiping
authors.initials: A
authors.lastname: Song
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Guan
authors.forename: Weimin
authors.initials: W
authors.lastname: Fang
authors.forename: Yuan
authors.initials: Y
authors.lastname: Liao
authors.forename: Fadi
authors.initials: F
authors.lastname: Chen
mesh_terms: D019659:Asteraceae / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D020224:Expressed Sequence Tags; D059014:High-Throughput Nucleotide Sequencing; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary