Singh J et al. (2015), Biocomputational characterization and evolution...

ECB-ART-43964

Asian-Australas J Anim Sci 2015 Jun 01;286:876-87. doi: 10.5713/ajas.14.0767.

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Biocomputational characterization and evolutionary analysis of bubaline dicer1 enzyme.

Singh J , Mukhopadhyay CS , Arora JS , Kaur S .

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Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-à-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.

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Species referenced: Echinodermata
Genes referenced: dicer1 LOC100887844 LOC575231 rnasek

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References [+] :

Altschul, Basic local alignment search tool. 1990, Pubmed

	Figure 1. Confirmation of clones by EcoRI RE digestion for release of insert, run on 1.5% agarose gel. (A) Lane 1: Insert release of ~913 bp (DR2); (B) Lane 1: Insert release of ~518 bp (RN5); (C) Lane 1: Insert release of ~928 bp (DR3), Lane 2: Insert release of ~910 bp (DR5), Lane 3: Insert release of ~927 bp (DR6); (D) Lane 1: Insert release of ~789 bp (RSE2); (E) Lane 1: Insert release of ~1,009 bp (RN6). EcoRI restriction endonuclease (RE) enzyme isolated form strain of E. coli. M: 1 Kb plus DNA ladder.
	Figure 2. Coding amino acid sequence of the Bubaline Dicer1 enzyme.
	Figure 3. Phylogenetic tree of Dicer1 enzyme among the animal species, constructed using maximum likelihood method (500 bootstrap resampling). The species belonging to same family that were forming a cluster have been merged as a single operational taxonomic unit (OTU). The bootstrap value (>50) have been indicated along the nodes.
	Figure 4. Phylogenetic tree constructed from 17 divergent Dicer amino acid sequences, using maximum likelihood method (500 bootstrap resampling). The tree is drawn to the scale and branch length (number of substitutions per site) as well as bootstrap value (>50) have been indicated in the tree.
	Figure 5. Evolutionary divergence heat map: realtive distance among seventeen divergent animal species based on Dicer sequence.
	Figure 6. Evolutionary divergence heat map:realtive distance among ruminants species based on Dicer1 sequence.
	Figure 7. Graphical representation of the dN-dS test statistic versus the codon positions obtained from SLAC (A) and REL (B) analyses. SLAC, single likelihood ancestor counting; REL, random effects likelihood.
	Figure 8. Phylogenetic tree of seventeen divergent animal species based on Branch site REL result depicting the episodic diversifying selection. REL, random effects likelihood.
	Figure 9. Comparative representation of domains of Dicer enzyme of divergent animal species.
	Figure 10. Heatmap of amino acid percentage of Dicer (ribonuclease type III) belonging to divergent species.