Pellionia scabra belongs to the genus Pellionia in the family of Urticaceae, and is a high-quality wild vegetables with high nutritional value. In this study, high-throughput techniques were used to sequence, assemble and annotate the chloroplast genome. We also analyzed its structure, and construct the phylogenetic trees from the P. scabra to further study the chloroplast genome characteristics. The results showed that the chloroplast genome size was 153 220 bp, and the GC content was 36.4%, which belonged to the typical tetrad structure in P. scabra. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes in P. scabra. Among them, 15 genes contained 1 intron, 2 genes contained 2 introns, and rps12 had trans-splicing, respectively. In P. scabra, chloroplast genomes could be divided into four categories, including 43 photosynthesis, 64 self-replication, other 7 coding proteins, and 4 unknown functions. A total of 51 073 codons were detected in the chloroplast genome, among which the codon encoding leucine (Leu) accounted for the largest proportion, and the codon preferred to use A and U bases. There were 72 simple sequence repeats (SSRs) in the chloroplast genome of P. scabra, containing 58 single nucleotides, 12 dinucleotides, 1 trinucleotide, and 1 tetranucleotide. The ycf1 gene expansion was present at the IRb/SSC boundary. The phylogenetic trees showed that P. scabra (OL800583) was most closely related to Elatostema stewardii (MZ292972), Elatostema dissectum (MK227819) and Elatostema laevissimum var. laevissimum (MN189961). Taken together, our results provide worthwhile information for understanding the identification, genetic evolution, and genomics research of P. scabra species.
Phylogeny ; Genome, Chloroplast/genetics* ; Genomics ; Chloroplasts/genetics* ; Codon ; Urticaceae/genetics*

The genomic DNA of Rubus rosaefolius was extracted and sequenced by Illumina NovaSeq platform to obtain the complete chloroplast genome sequence, and the sequence characteristics and phylogenetic analysis of chloroplast genes were carried out. The results showed that the complete chloroplast genome of the R. rosaefolius was 155 650 bp in length and had a typical tetrad structure, including two reverse repeats (25 748 bp each), a large copy region (85 443 bp) and a small copy region (18 711 bp). A total of 131 genes were identified in the whole genome of R. rosaefolius chloroplast, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The GC content of the whole genome was 36.9%. The genome of R. rosaefolius chloroplast contains 47 scattered repeats and 72 simple sequence repeating (SSR) loci. The codon preference is leucine codon, and the codon at the end of A/U is preferred. Phylogenetic analysis showed that R. rosaefolius had the closest relationship with R. taiwanicola, followed by R. rubraangustifolius and R. glandulosopunctatus. The chloroplast genome characteristics and phylogenetic analysis of R. rosaefolius provide a theoretical basis for its genetic diversity research and chloroplast development and utilization.
Phylogeny ; Rubus/genetics* ; Genome, Chloroplast ; Fruit/genetics* ; Codon/genetics*

With the widespread application of genomics and transcriptomics in the genetics and cell biology of different species, synonymous codon usage bias has been gradually accepted and used to study the deep connection between biological evolution and biological phenotypes. It is an important part of the life activities that mRNA is expressed into proteins with normal biological activities. The synonymous codon usage patterns, which were named as 'the second genetic codon', can express genetic information carried by themselves at the levels of transcriptional regulations, translational regulations and metabolic activities through molecular mechanisms such as fine-tune translation selection. Some studies have shown that the length of mRNA half-life has significant impacts on mRNA activity and the process of transcription and translation. This review summarized the roles of synonymous codon usage patterns in transcription, translational regulation and post-translational modification, with the aim to better understand how organisms skillfully utilize the genetic effects caused by codon usage patterns to accurately synthesize different types of proteins, so as to ensure the growth or differentiation of the specific gene expression procedures to carry out smoothly and maintain the normal life cycle.
Codon/genetics* ; Codon Usage ; Half-Life ; Protein Processing, Post-Translational ; RNA, Messenger/genetics*

TIR (Translation Initiation Region) efficiency is very important in prokaryotic expression. The TIR's efficiency is highly dependent on SD (Shine-Dalgarno) sequence, distance between SD sequence and start codon, DB (Downstream Box) sequence, TIR's second structure, codon adaptation and so on. In this paper, we designed and implemented the software to optimize DB sequence and 5' rare codons. It generated some optimization sequences by analyzing the target sequence and comparing it with 16S RNA. And the optimization sequences is sorting by number of base pairing, location of base pairing and codon adaptation. We drew up the algorithm and the core of code in this paper.
Base Sequence ; Codon ; genetics ; Programming Languages ; Protein Biosynthesis ; genetics ; Software

Codon, Nonsense ; Epilepsy ; genetics ; Humans ; KCNQ2 Potassium Channel ; genetics

In order to characterize the chloroplast genome and phylogenetic relationships of Isopyrum anemonoides, we performed Illumina Hiseq high-throughput sequencing to sequence the complete chloroplast genome of this plant and constructed a whole-genome map based on contig assembly and annotation. The chloroplast genome of I. anemonoides is 161 034 bp in length and has a typical tetrad structure, comprising 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The genome also contains a total of 44 dispersed repeat sequences and 47 simple sequence repeats. Among the genome's 53 678 codons, the largest proportion are leucine-encoding codons (5 251), whereas the smallest proportion encode tryptophan (712). Colinear analysis revealed an absence of inversions and rearrangements between I. anemonoides and related species at the chloroplast genome level. Whereas phylogenetic analysis indicated that I. anemonoides did not cluster in a clade with I. manshuricum, it did show a very close phylogenetic relationship with Paraquilegia microphylla. The findings of this study provide basic data that will contribute to further species identification and phylogenetic study of the genus Isopyrum.
Codon ; Genome, Chloroplast/genetics* ; Microsatellite Repeats ; Phylogeny ; Ranunculaceae/genetics*

The structure and size of the chloroplast genome of Castanopsis hystrix was determined by Illumina HiSeq 2500 sequencing platform to understand the difference between C. hystrix and the chloroplast genome of the same genus, and the evolutionary position of C. hystrix in the genus, so as to facilitate species identification, genetic diversity analysis and resource conservation of the genus. Bioinformatics analysis was used to perform sequence assembly, annotation and characteristic analysis. R, Python, MISA, CodonW and MEGA 6 bioinformatics software were used to analyze the genome structure and number, codon bias, sequence repeats, simple sequence repeat (SSR) loci and phylogeny. The genome size of C. hystrix chloroplast was 153 754 bp, showing tetrad structure. A total of 130 genes were identified, including 85 coding genes, 37 tRNA genes and 8 rRNA genes. According to codon bias analysis, the average number of effective codons was 55.5, indicating that the codons were highly random and low in bias. Forty-five repeats and 111 SSR loci were detected by SSR and long repeat fragment analysis. Compared with the related species, chloroplast genome sequences were highly conserved, especially the protein coding sequences. Phylogenetic analysis showed that C. hystrix is closely related to the Hainanese cone. In summary, we obtained the basic information and phylogenetic position of the chloroplast genome of red cone, which will provide a preliminary basis for species identification, genetic diversity of natural populations and functional genomics research of C. hystrix.
Phylogeny ; Genome, Chloroplast ; Codon/genetics* ; Genomics ; Chloroplasts/genetics*

Objective: To analyze the phenotype and genotype of two pedigrees with inherited fibrinogen (Fg) deficiency caused by two heterozygous mutations. We also preliminarily probed the molecular pathogenesis. Methods: The prothrombin time (PT), activated partial thromboplastin time (APTT), thrombin time (TT) and plasma fibrinogen activity (Fg∶C) of all family members (nine people across three generations and three people across two generations) were measured by the clotting method. Fibrinogen antigen (Fg:Ag) was measured by immunoturbidimetry. Direct DNA sequencing was performed to analyze all exons, flanking sequences, and mutated sites of FGA, FGB, and FGG for all members. Thrombin-catalyzed fibrinogen polymerization was performed. ClustalX 2.1 software was used to analyze the conservatism of the mutated sites. MutationTaster, PolyPhen-2, PROVEAN, SIFT, and LRT online bioinformatics software were applied to predict pathogenicity. Swiss PDB Viewer 4.0.1 was used to analyze the changes in protein spatial structure and molecular forces before and after mutation. Results: The Fg∶C of two probands decreased (1.28 g/L and 0.98 g/L, respectively). The Fg∶Ag of proband 1 was in the normal range of 2.20 g/L, while it was decreased to 1.01 g/L in proband 2. Through genetic analysis, we identified a heterozygous missense mutation (c.293C>A; p.BβAla98Asp) in exon 2 of proband 1 and a heterozygous nonsense mutation (c.1418C>G; p.BβSer473*) in exon 8 of proband 2. The conservatism analysis revealed that Ala98 and Ser473 presented different conservative states among homologous species. Online bioinformatics software predicted that p.BβAla98Asp and p.BβSer473* were pathogenic. Protein models demonstrated that the p.BβAla98Asp mutation influenced hydrogen bonds between amino acids, and the p.BβSer473* mutation resulted in protein truncation. Conclusion: The dysfibrinogenemia of proband 1 and the hypofibrinogenemia of proband 2 appeared to be related to the p.BβAla98Asp heterozygous missense mutation and the p.BβSer473* heterozygous nonsense mutation, respectively. This is the first ever report of these mutations.
Humans ; Afibrinogenemia/genetics* ; Codon, Nonsense ; Pedigree ; Phenotype ; Fibrinogen/genetics* ; Genotype

OBJECTIVETo analyze the codon usage of chloroplast genome and the influencing factor in Eleutherococcus senticosus.

METHODCodon of 52 genes, which were selected from the chloroplast genome sequence of E. senticosus, was multivariate statistical and correspondence analyzed using CodonW and SPSS software.

RESULTGC content at the three position of codons by turns was 46.46%, 38.26%, 29.88%, whereas GC1 and GC2 had a significant correlation coefficient (P < 0.01). The correlation coefficient with GC12, and GC3 was 0.205 and was not significant correlated. There were 30 codons which relative synonymous codon usage was greater than 1 and 29 codons end with A and T. In the corresponding analysis, the first axis shows 10.35% variation. And there was significant correlation coefficient between ENC and GC3. The correlation coefficients with GC3 and ENC were -0.288 and 0.353, respectively. We defined 16 codons from 16 amino acids as the major preference codons in chloroplast genome of E. senticosus.

CONCLUSIONThe third positions for all codon are preferred to ending with A and T. The codon usage bias is formed under effect of mutation and selection, as well as other factors. But the selection will have a far greater impact than others.

Amino Acids ; genetics ; Chloroplasts ; genetics ; Codon ; genetics ; Eleutherococcus ; genetics ; Genome, Plant ; genetics ; Genomics ; Multivariate Analysis ; Mutation

Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain.
Codon ; Escherichia coli ; Genome, Fungal ; Reishi ; genetics ; Saccharomyces cerevisiae ; Transcriptome