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Efficiency of Corynebacterium pseudotuberculosis Cp31 Genome Assembly with the Hi-Q Enzyme on an Ion Torrent PGM Sequencing Platform

Adonney AO Veras, Pablo HCG de Sa, Kenny C Pinheiro, Diego Assis das Gracas, Rafael Azevedo Barauna, Maria Paula Cruz Schneider, Vasco Azevedo, Rommel TJ Ramos and Artur Silva

Despite the high accuracy obtained through high throughput sequencing (HTS) platforms, including sequencing methods such as pyrosequencing (Roche 454), ligase (SOLiD System), and recently post-light sequencing using the Ion Torrent PGM that is able to detect ions released during sequencing, there are still many errors inherent in the chemistry used by these platforms, for example, INDEL (Insertion/Deletion) that are very common on platforms 454 of Roche and Ion Torrent PGM; Substitution abound in Illumina platforms and SOLiD. Thus, efforts to address these problems have been undertaken by the sequencing companies. To improve the accuracy of the Ion Torrent PGM reads, Life Technologies has developed an enzyme called Hi-Q.

This work aims to demonstrate the performance of the genome assembly of Corynebacterium pseudotuberculosis Cp31 using the enzyme Hi-Q. To evaluate the results, we used an Ion Torrent dataset obtained without the enzyme for the same strain.

The sequencing using the Hi-Q enzyme affected the accuracy of the reads, improving the assembly quality. As a result, a high number of complete genes related to the reference genome were obtained compared to the previous data (without Hi-Q). Furthermore, the use of Hi-Q reduced the number of contigs. After evaluated the GC bias in the genome produced through the Hi-Q, we identified a reduction of GC-Bias, what can reduce the amount and size of gaps generated in the genome assembly process. Furthermore, the comparison of the amount of pseudogenes observed in the genome annotation of C. pseudotuberculosis 31 available at NCBI and the genome sequenced by Ion Torrent PGM with a Hi-Q enzyme, show 3-fold less pseudogenes in the genome obtained through Hi-Q enzyme.

Thus, the high efficiency of Hi-Q was validated, which will be useful to whole-genome sequencing and RNASeq projects, due to its high accuracy, compared to the previous chemistry.