TY - JOUR T1 - Field-based species identification in eukaryotes using single molecule, real-time sequencing JF - bioRxiv DO - 10.1101/107656 SP - 107656 AU - Joe Parker AU - Andrew J. Helmstetter AU - Dion Devey AU - Alexander S.T. Papadopulos Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/02/10/107656.abstract N2 - Advances in DNA sequencing and informatics have revolutionised biology over the past four decades, but technological limitations have left many applications unexplored1,2. Recently, portable single molecule, real-time (SMRT) technologies have become available. These offer opportunities to rapidly collect and analyse genomic data anywhere3–5. However, the generation of datasets from large, complex genomes has been constrained to laboratories6,7. The portability and long DNA sequences of SMRT offer great potential for field-based species identification, but the feasibility and accuracy of these technologies for this purpose have not been assessed. Here, we show that a field-based SMRT analysis of closely-related plant species (Arabidopsis spp.)8 has many advantages over laboratory-based high-throughput sequencing (HTS) methods for species level identification-by-sequencing and de novo phylogenomics. Samples were collected and sequenced in a single day by SMRT using a portable, “al fresco” laboratory. Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with SMRT reads enables rapid and confident species identification. Individually annotated SMRT reads can be used to infer the evolutionary relationships of A. thaliana. Furthermore, hybrid genome assembly with SMRT and HTS reads substantially improved upon a genome assembled from HTS reads alone. Field-based SMRT makes real-time, rapid specimen identification and genome wide analyses possible. These technological advances are set to revolutionise research in the biological sciences9 and have broad implications for conservation, taxonomy, border agencies and citizen science. ER -