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Moreover, D. simulans is thought to have transferred sequences of both elements to D. melanogaster.
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Lateral gene transfer of SMR sequences to evolutionarily unrelated hosts would act as its own codon bias keeping Sd values high and has been shown in studies of other horizontally transferred sequences (for an example refer to [ 38]).
Most horizontally transferred genes go through the process of amelioration, the adjustment of the transferred sequence to the base composition and codon usage of the resident genome.
Since only portions of these genomes have been scanned, further studies are needed to determine the full insert length for many of the known Wolbachia homologs and to reveal more transferred sequences, some of which may encode full-length gene products.
Due to possible miss-assignments caused either by the representativeness of the database or to the amelioration of the transferred sequences [ 93], only broad categories of donors are presented.
Horizontal genetic transfers (HGTs) have been reported in several Wolbachia-infected filarial and arthropod species [6], [7], [8], [9], and evidence for transcription of transferred sequences has been reported in Drosophila ananassae that have been cured of Wolbachia by antibiotic treatment [7].
Future studies should aim to determine if a native copy of atp1 still exists in these parasites and characterize the genomic location and flanking sequence of putatively transferred sequences.
However, alien genes tend to be purified by selection and to be transient residents in the host genome due to the natural barriers to oppose the invasiveness of transferred sequences [36], [39].
Genes from low G+C regions not containing phage gene BLAST hits were then compared against the NCBI non-redundant database to confirm the absence of horizontally transferred sequences.
In eukaryotes, the study of horizontally transferred sequences is confined to CDSs and often focuses on specific TEs.
This represents only a small part of most eukaryote genomes and introduces an important detection bias for the analysis of horizontally transferred sequences.
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