Informativeness of SSR loci following amplification from 18 geographically diverse <i>Callosobruchus chinensis</i> populations in China.

<p>Notes: Number of alleles (<i>Na</i>), expected heterozygosity (<i>He</i>), observed heterozygosity (<i>Ho</i>) and Shannon’s information index (<i>I</i>).</p

Final assembly of adzuki bean weevil genome.

<p>Final assembly of adzuki bean weevil genome.</p

Summary of adzuki bean weevil sequencing data output.

<p>Notes: Effective rate (%) = clear reads/raw reads×100, Q20 and Q30 refer to the values of quality of sequencing data.</p

Distribution between GC content and sequencing depth.

<p>Distribution between GC content and sequencing depth.</p

The base content in adzuki bean weevil genome.

<p>The base content in adzuki bean weevil genome.</p

Characteristics of 20 polymorphic SSR markers used in genetic diversity analysis (F = forward primer, R = reverse primer, Size = size of cloned allele, Ta = annealing temperature).

<p>Characteristics of 20 polymorphic SSR markers used in genetic diversity analysis (F = forward primer, R = reverse primer, Size = size of cloned allele, Ta = annealing temperature).</p

Rapid Development of Microsatellite Markers for <i>Callosobruchus chinensis</i> Using Illumina Paired-End Sequencing

<div><p>Background</p><p>The adzuki bean weevil, <i>Callosobruchus chinensis</i> L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from <i>C. chinensis</i> via high-throughput sequencing.</p><p>Principal Findings</p><p>In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with <i>de novo</i> assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 <i>C. chinensis</i> genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 <i>C. chinensis</i> populations. The results showed the twenty SSR loci were highly polymorphic among these populations.</p><p>Conclusions</p><p>This study presents a first report of genome sequencing and <i>de novo</i> assembly for <i>C. chinensis</i> and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for <i>C. chinensis</i> research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among <i>C. chinensis</i>.</p></div

SSR PCR amplification patterns of 20 <i>Callosobruchus chinensis</i> individuals from RD population using primer CCM46.

<p>(M is the 100 bp DNA ladder marker).</p

Dendrogram for 18 populations of <i>Callosobruchus chinensis</i> in China based on 20 SSR loci (Population code see table 2).

<p>Dendrogram for 18 populations of <i>Callosobruchus chinensis</i> in China based on 20 SSR loci (Population code see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095458#pone-0095458-t002" target="_blank">table 2</a>).</p

Re-assembly of adzuki bean weevil genome after decontamination.

<p>Re-assembly of adzuki bean weevil genome after decontamination.</p