Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery

Haibin Wang; Jiafu Jiang; Sumei Chen; Xiangyu Qi; Hui Peng; Pirui Li; Aiping Song; Zhiyong Guan; Weimin Fang; Yuan Liao; Fadi Chen

doi:10.1371/journal.pone.0062293

Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery

PLoS One. 2013 Apr 23;8(4):e62293. doi: 10.1371/journal.pone.0062293. Print 2013.

Authors

Haibin Wang¹, Jiafu Jiang, Sumei Chen, Xiangyu Qi, Hui Peng, Pirui Li, Aiping Song, Zhiyong Guan, Weimin Fang, Yuan Liao, Fadi Chen

Affiliation

¹ College of Horticulture, Nanjing Agricultural University, Nanjing, China.

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.

Methodology/principal findings: 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/significance: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Asteraceae / classification
Asteraceae / genetics*
Computational Biology* / methods
DNA, Complementary / chemistry
DNA, Complementary / genetics
Expressed Sequence Tags
High-Throughput Nucleotide Sequencing*
Microsatellite Repeats*
Molecular Sequence Annotation
Phylogeny
Polymorphism, Genetic
Transcriptome*

Substances

DNA, Complementary

Grants and funding

This work was supported by funding from the Program for New Century Excellent Talents in University of Chinese Ministry of Education (Grant No. NCET-10-0492); 863 Project (2011AA100208), the Fundamental Research Funds for the Central Universities (KYZ201147, KYZ201112); a Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), and the Youth Science and Technology Innovation Fund from Nanjing Agricultural University (KJ2011009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.