Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

Comparative analysis of nuclear tRNA genes of Nasonia vitripennis and other arthropods, and relationships to codon usage bias

Using bioinformatics methods, we identified a total of 221 and 199 tRNA genes in the nuclear genomes of Nasonia vitripennis and honey bee (Apis mellifera), respectively. We performed comparative analyses of Nasonia tRNA genes with honey bee and other selected insects to understand genomic distribution, sequence evolution and relationship of tRNA copy number with codon usage patterns. Many tRNA genes are located physically close to each other in the form of small clusters in the Nasonia genome. However, the number of clusters and the tRNA genes that form such clusters vary from species to species. In particular, the Ala-, Pro-, Tyr- and His-tRNA genes tend to accumulate in clusters in Nasonia but not in honey bee, whereas the bee contains a long cluster of 15 tRNA genes (of which 13 are Gln-tRNAs) that is absent in Nasonia. Though tRNA genes are highly conserved, contrasting patterns of nucleotide diversity are observed among the arm and loop regions of tRNAs between Nasonia and honey bee. Also, the sequence convergence between the reconstructed ancestral tRNAs and the present day tRNAs suggests a common ancestral origin of Nasonia and honey bee tRNAs. Furthermore, we also present evidence that the copy number of isoacceptor tRNAs (those having a different anticodon but charge the same amino acid) is correlated with codon usage patterns of highly expressed genes in Nasonia.