Ure 2 Identification and analysis of insertions and deletions specific to nematode
Ure 2 Identification and analysis of insertions and deletions specific to nematode proteins Identification and analysis of insertions and deletions specific to nematode proteins. The results obtained from each step of the workflow are shown.Page 5 of(page number not for citation purposes)BMC Evolutionary Biology 2009, 9:http://www.biomedcentral.com/1471-2148/9/Figure 3 Frequency distribution of sizes of insertions and deletions Frequency distribution of sizes of insertions and deletions. Fifty percent of deletions are longer than 10 residues, whereas only 17 of insertions are of a comparable length.respectively) (Additional file 3). The differences in frequency and size of indels within proteins involved in single pathways versus proteins involved in multiple pathways were also investigated. This analysis included > 300 families homologous to multi-pathway proteins and > 600 families homologous to other proteins, and revealed that the average frequencies of both insertions and deletions of the multi-pathway families were 30 higher than those of others (insertions: 3.01 versus 2.42; deletions: 8.79 versus 6.29) (Additional file 4) and the differences were highly significant (P < 0.0001; T-test).that similar mutational mechanisms might apply to the protein-coding sequences. However, the observed larger size of deletions cannot be explained by mutational bias, since deletion and insertion mutations have similar sizes [45]. So, the role that natural selection and adaptation have played here is unclear. From the structural perspective, proteins are more flexible with insertions than deletions [46], although single-residue deletions can be tolerated [47]. Therefore, deletions, particularly larger ones, are not expected to be maintained, which contrasts current observations. It is likely that function-related selection has played a role. Such selection has been identified in a primate sperm ion channel protein [48]. Both the increased number of deletions at the terminal nodes (Figure 4) and the increased common deletions (Table 1) among parasitic nematodes further suggest that the function-related selection is associated with recent species adaptation. Nonetheless, the observed, larger number of deletions and their larger sizes (compared with insertions) indicate a size decrease in nematode transcriptomes during evolution. This size reduction in nematode transcriptomes seems to be consistent with a tendency for their genomes to be smaller than some other metazoa, such flatworms [49] and birds [50]. The biased distributions of indels on different functional pathways (Table 3) further demonstrate the selective forces on them, and suggest the association between increased indels and functional adaptation. Proteins PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27362935 involved in genetic information processing are believed to have stringent selective constraints, and are under strong “purifying selection” [51,52]. Accordingly, these proteins have the least number of insertions and deletions per protein (Additional file 4). Depending on the function, some proteins are under positive selections and accumulate more insertions and deletions [53]. The present study showed that nematode proteins involved in cellular processes (Table 3, Additional file 2) BAY1217389 web including endocrine signaling pathways and immune system (such PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28212752 as Toll-like receptors and antigen processing) had 50 more deletions and insertion than those involved in genetic information processing. This information agrees with the findings of previo.
