TBlastN search for reverse-transcriptases suggests “extinction, or at least strong copy number reduction, of major clades of non-LTR retrotransposons”. “About 80 Odin reverse transcriptase sequences were detected by TBlastN analysis in the 41 Mb genome assembly of O. dioica using a 335 amino acid reverse transcriptase sequence as a query (we can not exclude that some nonoverlapping short hits might belong to a same partially sequenced element). About 30% of Odin endonuclease and reverse transcriptase-encoding sequences were corrupted by stop or frameshift mutations, suggesting that an important proportion of Odin elements is not functional. The degree of nucleotide sequence identity between Odin elements ranged from less than 60% up to 90%.”

“About 180 Tor reverse transcriptase sequences were detected in the 41 Mb genome assembly (about 50 sequences for Tor2, Tor3, and Tor4, but only two for Tor1; the remaining sequences were too short to be classified unambiguously). The degree of nucleotide identity inside of the Tor2, Tor3, and Tor4 families ranged from less than 60% up to 98–99% (the two Tor1 elements showed 70% nucleotide identity). On average, open reading frame–corrupting mutations were observed each 7.5 kb, 2.8 kb, and 16 kb for Tor2, Tor3, and Tor4, respectively.” “The Tor4b family might have acquired its env-like gene from a paramyxovirus.”

“Among other groups of LTR retrotransposons, only DIRS1-like elements were found in Oikopleura.” “About 70 reverse transcriptase sequences from DIRS1-related elements were detected in the 41 Mb genome assembly, with degrees of nucleotide identity ranging from less than 60% up to 90%. DIRS1-related elements were apparently absent from the sea squirt genome and would therefore represent the only type of autonomous retroelement lost in C. intestinalis but present in O. dioica.”