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Fig. 2 | Mobile DNA

Fig. 2

From: Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

Fig. 2

Phylogenetic trees and classification of Ty3/gypsy elements. a Unrooted phylogenetic tree inferred from concatenated RT-RH-INT sequences from both Viridiplantae and non-Viridiplantae elements. Branches of elements from non-Viridiplantae species are in gray. Circles, triangles and diamonds mark elements possessing CHD, CHDCR and aRH domain, respectively. Note the different position of aRH domain in the polyprotein of Tat elements. b Collapsed rectangular phylogram inferred from concatenated RT-RH-INT sequences from the Viridiplantae elements. Phylogenetic trees were calculated using maximum likelihood. Trees inferred from the concatenated RT-RH-INT domains were consistent with trees inferred from individual domains (Additional file 6 and data not shown). The only exception included a few chromovirus elements from Selaginella moellendorffii which occurred at discordant positions in the trees. Branches containing these elements are marked with numbers 1, 2, and 3 and were labeled as unclassified chromoviruses. c Proposed classification of Ty3/gypsy elements in plants

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ISSN: 1759-8753