Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiaegene duplicates

Objective: Toll-like receptors are the pattern recognition receptors that recognize a diverse set of conserved pathogens. The receptors are also constantly under selection pressure because of the host antigen modifications. The present study focuses on how selection and mutation have modified the TLRs throughout the evolution in selected groups.Methods: We have selected the sequences of TLR2, 4 and 9 among Hominid group, Homo sapiens, Bubalus bubalis and Danio rerio in our analysis and analyzed different parameters like relative synonymous codon usage (RSCU), sequence divergence, amino acid composition and estimated evolutionary selection forces using Tajima’s test.Results: The phylogenetic assessment proved that positive selection influences TLR2 and TLR4, but neutral selection/balancing selection occurred in TLR9 which concluded from the Tajima's test. Synonymous codon usage described the selection of leucine and arginine in all the sequences which describe the structural similarities of TLRs. Values of nucleotide pairs and disparity index proved the close relationship of Hominid and Human between TLR2 and TLR4 and TLR9 where the distant relationship was found with Danio. It can be hypothesized that some of the codons may be best selected for binding with the antigens and it was selected in the genome and some were eliminated due to selection pressure.Conclusion: The present study aimed to substantiate the closeness of TLR2 and TLR4 due to their functional similarity but distant with TLR9 because of the different antigens they recognized in the endosome.

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The Complete Chloroplast Genomes of Two Lespedeza Species: Insights into Codon Usage Bias, RNA Editing Sites, and Phylogenetic Relationships in Desmodieae (Fabaceae: Papilionoideae)

Plants ◽

10.3390/plants9010051 ◽

2019 ◽

Vol 9 (1) ◽

pp. 51 ◽

Cited By ~ 3

Author(s):

Yamuna Somaratne ◽

De-Long Guan ◽

Wen-Qiang Wang ◽

Liang Zhao ◽

Sheng-Quan Xu

Keyword(s):

Codon Usage ◽

Rna Editing ◽

Economic Value ◽

Gc Content ◽

Sequence Divergence ◽

Morphological Characters ◽

Lespedeza Cuneata ◽

Genome Sequences ◽

Molecular Features ◽

Chloroplast Genomes

The genus Lespedeza (tribe: Desmodieae) consists of about 40 species that have high medicinal and economic value. However, in this genus, using morphological characters, the species identification is quite complicated, which can be solved by the analysis of the complete chloroplast genomes. As primary organelle genomes, the complete genome sequences of chloroplasts (cp) provide unique molecular information to study the divergence of species, RNA editing, and phylogeny. Therefore, to the best of our knowledge, for the first time, we sequenced the complete cp genomes of two representative Lespedeza species: Lespedeza davurica and Lespedeza cuneata. The cp genomes of both the species were found to be 149,010 bp in length, exhibiting the typical angiosperm chloroplast structure containing four regions. The Lespedeza cp genomes showed similar conserved gene contents, order, and orientations with a total GC content of 35.0%. A total of 128 genes, including 83 protein-coding genes, 37 tRNAs, and eight rRNAs, were identified from each genome. Unique molecular features of the two Lespedeza cp genome sequences were obtained by performing the analysis of repeats, sequence divergence, codon usage, and predicting the RNA editing sites in addition to phylogenetic analysis with other key genera in tribe Desmodieae. Using the two datasets, the phylogenetic relationship of Lespedeza species among Deasmodieae was discovered, suggesting that whole cp genomes provided useful information for phylogenetic studies of these species.

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