Analysis of Codon Usage Between Different Poplar Species

Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.

Cloning and sequence analysis of the partial sequence of the rbcL from Bryopsis hypnoides

The partial sequence of the rbcL from Bryopsis hypnoides, including the sequences of the upstream, extron and partial intron, was amplified by PCR and their sequences were determined. With Spinacia oleracea as the outgroup, neighbor-joining method and maximum parsimony method were used respectively to build phylogenetic trees according to the rbcL exon sequence among 13 species that were the typical species of six phyla. Two kinds of trees showed clearly that there were two groups among those species, the green lineage and the non-green lineage. And the relationships of algae in the green lineage were similar in the two trees but those in the non-green lineage were not consistent. Analysis of codon preference indicated that the codon preference of the rbcL exon of Bryopsis hypnoides distinctly differed from that of the relevant sequence of photosynthetic bacteria.

A Synonymous Polymorphism of APCDD1 Affects Translation Efficacy and is Associated with Androgenic Alopecia

The APCDDI （adenomatosis polyposis coli down-regulated 1） gene is an inhibitor of the Wnt signaling pathway, and a rare mutation of this gene has been associated with hereditary hypotrichosis simplex. In this study, the authors aimed to investigate whether common APCDD1 gene polymorphisms contribute to the development of androgenic alopecia. Patients （n = 210） with androgenic alopecia and 98 controls were investigated. SNPs （Single nucleotide polymorphisms） in the coding region of the gene were sequenced. A significant difference in genotype distribution was found for the c. 1781C/T, p.L476L SNP （rs3185480） of the APCDD1 gene. This SNP is located in exon 5 and is associated with a 3.5- and a 2.8-fold increase in risk for the development of androgenic alopecia for homozygote （CI 0.933-13.125; nominal regression P = 0.063） and heterozygote （CI 1.086-7.217; nominal regression P = 0.033） carriers, respectively. These data suggest that the rs3185480 polymorphism contributes to the development of androgenic alopecia. Protein expression experiments revealed that the polymorphism is associated with reduced APCDDI protein abundance. This reduction is likely due to altered codon usage for leucine from a preferred codon （CTC） to a rare codon （CTT）, which might influence translation efficiency and, thus, APCDDI protein level.

Codon usage and evolutionary dynamics of genetic diversity of novel imported porcine reproductive and respiratory syndrome virus in China

Porcine reproductive and respiratory syndrome(PRRS)is a problem that has significant economic impact on the global pig industry.In recent years,there has been an increased importation of pork into China,contributing to the emergence of novely imported porcine reproductive and respiratory syndrome virus(PRRSV)sub-types.Nevertheless,codon usage patterns and their effects on the evolution and adaptation of these new input PRRSV sub-types in hosts remain elusive.To investigate this,we employed a Bayesian approach to analyze two novel imported PRRSV sub-types,namely,NADC30-like and NADC34-like viruses.These sub-types have different codon preferences.Besides,the Effective Number of Codon(ENC)analysis revealed that both NADC30-like and NADC34-like fall within the expected curve distribution,describing a balanced codon usage for both NADC30-like and NADC34-like virus.Based on the Codon Adaptation Index(CAI),NADC30-like showed the highest similarity to the host,aligning with the main prevalence trend of the host.In contrast,NADC34-like exhibited the highest frequency of optimal codon usage;this analysis is based on Frequency of Optimal Codons(FOP).Moreover,the Relative Codon Deoptimization Index(RCDI)indicates that NADC30-like sub-types have a greater degree of inverse optimization sub-type.These findings suggest that mutational pressure affects codon usage preferences of genes in newly imported PRRSV,and that natural selection plays a vital role in determining PRRSV gene codon preferences.Our study provides new insights into the disease,origin,evolutionary patterns,and host adaptation of these newly imported PRRSV sub-types in China.It also contributes to the development of theoretical frameworks for studying genetics and the evolution of PRRSV.