Fig 1.
Hierarchical levels of the classification of TEs and the equivalent population genetics terminology used in this work.
Shapes represent lineages, and colors represent the genetic information of a TE insertion. Elements with the same color belong to the same population (cluster). Elements with only one color are 100% membership, and elements with more than one color are admixed.
Table 1.
Summary of the S. italica full-length LTR retrotransposon prediction and classification.
Fig 2.
Evolutionary relationships of the Maximus/Sire lineage elements.
(A) Bayesian phylogenetic tree based on RT amino acid sequences. Posterior probabilities values below 0.7 are not shown. (B) STRUCTURE plot (colored bars, bottom axis) based on RT sequences, showing the percentage of membership of the elements in the clusters and the time of insertion (dotted bars, upper axis) based on the LTR sequences. In both the tree branches and plots, each color represents a cluster. The numbers at the end of the name of the elements indicate the family. The tree and STRUCTURE plot were based on an amino acid alignment with 248 positions. n/a: not analyzed–nested element with no LTRs identified. mya: millions of years ago; my: millions of years.
Table 2.
Means and standard deviations of the times of insertion of the LTR-RT elements.
Mean values were separately calculated for admixed and 100% membership elements. The columns ‘Cluster 1’ to ‘Cluster 13’ show the values of the 100% membership elements, and the column ‘Admixed elements’ shows the values for elements assigned to more than one cluster.
Fig 3.
Evolutionary relationships of the TAR/Tork lineage elements.
(A) Bayesian phylogenetic tree based on RT amino acid sequences. Posterior probability values below 0.7 are not shown. (B) STRUCTURE plot (colored bars, bottom axis) based on RT sequences, showing the percentage of membership of the elements in the clusters and time of insertion (dotted bars, upper axis) based on the LTR sequences. In both the tree branches and plots, each color represents a cluster. The numbers at the end of the name of the elements indicate the family. The tree and STRUCTURE plot were based on an amino acid alignment with 251 positions. mya: millions of years ago; my: millions of years.
Fig 4.
Evolutionary relationships of the Reina lineage elements.
(A) Bayesian phylogenetic tree based on RT amino acid sequences. Posterior probability values below 0.7 are not shown. (B) STRUCTURE plot (colored bars, bottom axis) based on RT sequences, showing the percentage of membership of the elements in the clusters and time of insertion (dotted bars, upper axis) based on the LTR sequences (mya). In both the tree branches and plots, each color represents a cluster. The numbers at the end of the name of the elements indicate the family. The tree and STRUCTURE plot were based on an amino acid alignment with 176 positions. mya: millions of years ago; my: millions of years.
Fig 5.
Pairwise distances (mean ± SD) between copies of the S. italica LTR-RT lineages.
Each texture represents a different pattern of clusterization obtained via the population genetic structure analyses.
Fig 6.
Distribution of LTR-RT lineages in S. italica chromosomes.
The nine chromosomes are represented by vertical bars. Black arrows indicate centromeric regions, as previously described [24].