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For both species, the LIM1 proteins have undergone a probable duplication event, and it is difficult to class them into either the αLIM1 or the βLIM1 subgroup (Fig. 3).
The similarity within these BrLIM protein sequences ranged from 23 to 99% and 8 BrLIMs showed above 90% similarity within the species indicating their probable duplication.> -wrap-foot>> -wrap-foot> a Brassica database (http://brassicadb.org/brad/index.php), bGenbank accession number, c Brassica database accession number, dAdditional 2 UIM domain and eAdditional 4 UIM domain.
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However, it must also be acknowledged that other equally probable duplications increase the frequencies of other subgraphs.
In our analysis, the ABCB1-ABCB2 showed a relatively recent duplication (with low Ks), and more important, the ancestral state may have shown both expression patterns of the descendants prior to duplication (Table 4), therefore, this pair is the most probable duplicates for subfunctionalization.
Therefore, of the four instances of two "bacterial-like" iPGMs in one bacterial genome, one is explained by a pseudogene, one represents probable gene duplication while two appear to be the result of LGT.
These paralog groups reflect probable recent duplication [ 30].
In order to explore possible functional redundancy in plant serine protease-like proteins, we investigated chromosomal locations of serine protease-like proteins from the two plant species and inferred probable gene duplication events that may have facilitated this distribution.
There was also evidence of probable gene duplication in this copy: an allele with a 57-bp intron gap was present in most individuals, but as the gene dynamics were unclear, these alleles were excluded.
The alignment of two or more D. aromatica protein sequences in a clade such that they displayed higher % identity to each other than to orthologs present in other species was interpreted as an indication of a probable recent duplication event, either in the D. aromatica genome itself or in a progenitor species.
The three groups could not be displayed simultaneously on the bedside monitor making duplication more probable.
The most probable explanation is such duplications occurred recently and take place frequently.
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