tRNADB-CE: tRNA gene database well-timed in the era of big sequence data

Abstract

The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data.

Keywords: BLSOM; big data; database; metagenome; phylogenic maker; tRNA.

FIGURE 1

Basic functions of tRNADB-CE. (A) Statistics information for frequency of nucleotide in each position on tRNA cloverleaf secondary structure, (B) List of Phylum/Class/Species and anticodon table, (C) tRNA gene list, (D) Detailed information, (E) Search of neighboring tRNA genes, and (F) Advanced keyword and pattern search.

FIGURE 2

List and search for (A) Identical sequence groups (ISGs) found in environmental samples, (B) Table of microbial population in all samples, (C) List of microbial population in a sample, and (D) Detailed information for samples assignable to phylum.

FIGURE 3

Examples of non-standard-type tRNAs. (A) The anticodon occurrence table of bacterial tRNAs. It is clear that A-starting anticodons are very rare in bacterial tRNAs. (B) Cloverleaf secondary structure of M. mobile tRNA^Ile2.