biostudies-literatureWright DANIGMS NIH HHS122-31https://www.ebi.ac.uk/biostudies/studies/S-EPMC155253biostudies-literatureUnknown12(1)The Athila retroelements of Arabidopsis thaliana encode a putative envelope gene, suggesting that they are infectious retroviruses. Because most insertions are highly degenerate, we undertook a comprehensive analysis of the A. thaliana genome sequence to discern their conserved features. One family (Athila4) was identified whose members are largely intact and share >94% nucleotide identity. As a basis for comparison, related elements (the Calypso elements) were characterized from soybean. Consensus Calypso and Athila4 elements are 12-14 kb in length and have long terminal repeats of 1.3-1.8 kb. Gag and Pol are encoded on a single open reading frame (ORF) of 1801 (Calypso) and 1911 (Athila4) amino acids. Following the Gag-Pol ORF are noncoding regions of ~0.7 and 2 kb, which, respectively, Genome researchAthila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses.PMC155253R41 GM61420Voytas DFWright DAfalseAthila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses.The Athila retroelements of Arabidopsis thaliana encode a putative envelope gene, suggesting that they are infectious retroviruses. Because most insertions are highly degenerate, we undertook a comprehensive analysis of the A. thaliana genome sequence to discern their conserved features. One family (Athila4) was identified whose members are largely intact and share >94% nucleotide identity. As a basis for comparison, related elements (the Calypso elements) were characterized from soybean. Consensus Calypso and Athila4 elements are 12-14 kb in length and have long terminal repeats of 1.3-1.8 kb. Gag and Pol are encoded on a single open reading frame (ORF) of 1801 (Calypso) and 1911 (Athila4) amino acids. Following the Gag-Pol ORF are noncoding regions of ~0.7 and 2 kb, which, respectively, 2002-01-01T00:00:00Z2002 Jan2025-04-05T15:32:20.025Z2019-03-27T00:35:15ZS-EPMC1552531177983710.1101/gr.196001