Data from: Parallel tagged amplicon sequencing of relatively long PCR products using the Illumina HiSeq platform and transcriptome assembly

In the field of phylogenetics and population genetics, large number of loci are often needed to accurately resolve relationships of related species. In most cases, targeted DNA regions are enriched by PCR and sequenced by Sanger sequencing, which is rather expensive when the number of PCR products are large. Recently, next-generation sequencing (NGS) technique is increasingly used for parallel amplicon sequencing. However, for all current NGS methods, amplicons are required to be purified and quantified before sequencing and their lengths are also restricted (normally < 700 bp). Here, we describe an approach to sequence pooled amplicons of any lengths from multilocus and multitaxa using Illumina HiSeq platform. Using this method, all PCR products are pooled at equal volume rather than equal concentration, thus eliminating the laborious purification and quantification steps. We demonstrated the utility of our approach by recovering 93.5% of the target amplicons in full length for a 16 taxa × 101 loci project, using ~2.0 G HiSeq paired-end 90 bp read data. The obtained amplicon sequences was highly accurate (>99.8%) and suitable for phylogenetic and population genetic analyses. Overall, we validate a rapid, cost-effective and scalable approach to sequence large numbers of targeted gene regions from a large number of samples and it is particularly suitable for both phylogenetics and population genetics studies that require a modest scale of data.