With the activity track ranking the TE copies according to the most identical pair of copies between the two genomes which can be seen as the last putative horizontally transferred copy in the case of an HT, we were able to balance the direction of the transfers, which is crucial to understand the horizontally transferred TE history and dynamics.
Phylogenetic relationships of these six angiosperms are strongly supported by numerous studies from multiple single copy (or effectively single copy in the case of 18S rDNA) loci [ 41- 43], and in some cases from nuclear gene family data in which ortholog groups have been extracted [ 44].
To help in the synthetic interpretation of the recent history of each TE in our results, we start by defining the most identical pair of copies between the two genomes, as the last putative horizontally transferred copy in the case of an HT.
Groups with radiate capitula are represented in the major clades and subclades of DpcCYC, while the discoid groups Bassecoia, Pseudoscabiosa, and Dipsacus appear to have only one copy of DpcCYC1 (or no copy in the case of Pseudoscabiosa), 2Ba, and 2Bb.
Because we deal with a single chromosomal copy in the case of the mec operon and a few in the case of the plasmid-borne bla operon, one needs to consider populations of bacteria in this analysis and not a single microorganism.
All tetrapod species examined in this study possess a single copy of the Cygb gene, and all teleost fish possess either two duplicated copies or, in the case of zebra fish, three copies (fig. 1).
In the case of an increase of copy numbers in specific genes or chromosomal regions, log2 values should be higher than 0 (1, 2, etc. depending on the number of copies), but in the case of loss of S. cerevisiae gene copies in the hybrid, a ratio of 0 (lof2 of – ∞) should be observed.
Numbers in brackets denote the number of intronless gene copies, which in the case of multi-exon genes may indicate putative retrocopy genes.
These parasites express only one VSG gene at a time, from a repertoire of silent copies that in the case of T. b. brucei contains more than 1500 different genes [ 5].
