Fig. 3

Intein-containing proteins are distinct between nDNA, cpDNA, and vDNA and fall into functional categories. Modified phylogenetic trees of intein-positive species in a fungi, choanoflagellates, amoebozoa, and apusozoa, b algae and seaweeds, and c eukaryotic viruses are presented. The heat maps correspond to the tree and show inteins present in nDNA (red), cpDNA (green), and vDNA (blue). The nDNA inteins are mostly in fungi, overwhelmingly in Prp8, VMA1 and DdRP. One Prp8 intein is found in green algae in nDNA. The cpDNA inteins are in DnaB and ClpP, but are also found in DdRP. The vDNA inteins are present in DdDP, DdRP, HEL, and RIR proteins, but no intein overlap is observed between virus and virus host. Black bars show the number of intein positive genomes relative to the number of sequenced genomes in the phylogenetic category. Extein abbreviations are as follows: Prp8 – pre-mRNA processing factor 8; VMA1 – vacuolar membrane ATPase; DdRP –DNA-directed RNA polymerase; ThrRS – threonyl tRNA synthetase; CHS – chitin synthase; GLT – glutamate synthase; ClpP – ATP-dependent Clp protease, proteolytic subunit; DnaB – DNA helicase; DdDP – DNA-directed DNA polymerase; RIR – ribonucleotide reductase; HEL – helicase. d Orthologous group analysis for nDNA, cpDNA, and vDNA classifies intein-containing exteins to functional categories (Additional file 1: Tables S8-S10). nDNA inteins are biased towards category A, RNA processing, from insertions in Prp8. cpDNA and vDNA inteins have bias towards catergory L, or proteins with replication, recombination and repair functions. Functional categories are as follows: A – RNA processing and modification; C – energy production and conversion; F – nucleotide transport and metabolism; K – transcription; L – replication, recombination, and repair