Transfer RNA (tRNA) is a small RNA that transfers a specific amino acid to synthesize a polypeptide chain at the ribosomal site during translat\
ion. In the Archaea, some tRNA precursors have been reported to contain intron(s) in diverse sites of the gene. Moreover, recent studies reveal\
ed unique type of archaeal tRNA that made of two separate genes; one encoding the 5'-half and the other the 3'-half of tRNA sequence. The disco\
very of these disrupted tRNA genes raised questions why tRNA genes are in pieces and whether the disruption is reflecting the ancient form of t\
RNA origin or later products. Although the analysis of archaeal tRNA genes is becoming more important to evaluate the origin and evolution of t\
RNA, several tRNA genes are still missing in certain archaeal species due to the difficulty of the computational prediction of the disrupted tR\
NA genes. In order to present an entire picture of the archaeal tRNA diversity and its evolution, we initially developed SPLITS, which is aimed\
at searching for the split and intron-containing tRNA genes at the genome level. Then we conducted a comprehensive prediction of tRNA genes fr\
om the complete genomes of approximately 50 archaeal species and extracted a total of 2,187 reliable tRNA gene candidates, which covered more t\
han 99.9% of the codon tables in Archaea. Lastly, sequence analysis on the basis of the comprehensive tRNA gene dataset revealed that the disru\
ption of tRNA genes could have been occurred at a later stage of archaeal tRNA evolution. Here we propose a new model explaining the emergence \
of disrupted tRNA genes in archaeal genomes from evolutional point of view.