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*

In this study, the chloroplast genome of Camellia insularis Orel & Curry was sequenced using high-throughput sequencing technology. The results showed that the chloroplast genome of C. insularis was 156 882 bp in length with a typical tetrad structure, encoding 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Codon preference analysis revealed that the highest number of codons coded for leucine, with a high A/U preference in the third codon position. Additionally, 67 simple sequence repeats (SSR) loci were identified, with a preference for A and T bases. The inverted repeat (IR) boundary regions of the chloroplast genome of C. insularis were relatively conserved, except for a few variable regions. Phylogenetic analysis indicated that C. insularis was most closely related to C. fascicularis. Yellow camellia is a valuable material for genetic engineering breeding. This study provides fundamental genetic information on chloroplast engineering and offers valuable resources for conducting in-depth research on the evolution, species identification, and genomic breeding of yellow Camellia.
Genome, Chloroplast/genetics* ; Phylogeny ; Plant Breeding ; Camellia/genetics* ; Chloroplasts/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*

To explore the different chloroplast genome characteristics of Sinopodophyllum hexandrum, five chloroplast genome sequences of S. hexandrum were compared. Its genome map, repeat sequence, codon preference, inverted repeat (IR)/single-copy (SC) boundary, alignment of chloroplast genome sequences and phylogenetic were analyzed using bioinformatics tools. The results showed that: the total length of five chloroplast genomes of S. hexandrum, with a typical tetrad structure, were 157 203-157 940 bp, and a total of 133-137 genes were annotated, reflecting the diversity of chloroplast genomes of S. hexandrum. Different chloroplast genomes of S. hexandrum has different simple sequence repeat (SSR), where simple repeat of single nucleotide of A/T were the majority among the SSR detected. The interspersed repetitive sequences included direct, palindromic and inverted repeats. The value of effective number of codon (ENc) which was analyzed by using codon bias was 51.14~51.17, the proportion of GC and GC3s was less than 50%, the codon usage pattern tended towards frequently use of A/U-ending bases. Genome sequences and the IR/SC boundaries of five chloroplast genomes of S. hexandrum were relatively conservative. Phylogenetic analysis showed that S. hexandrum and Podophyllum pettatum had the closest genetic relationship. In summary, the chloroplast genome characteristics and evolutionary relationship of different chloroplast genomes of S. hexandrum were obtained, which may facilitate the utilization, protection, variety identification and genetic evolution of S. hexandrum resources.
Phylogeny ; Genome, Chloroplast ; Chloroplasts/genetics* ; Genomics ; Evolution, Molecular

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

To optimize indices of molecular identification for authentication of Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix, four indices, including sequence similarity, specific positions, genetic distance and phylogenetic tree, were compared based on trnL-trnF sequences. Total DNA was extracted from Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix, and trL-trnF sequences were amplified and sequenced. Sequence similarity was calculated by BLAST analysis. Specific positions were compared by DNAman software. Genetic distance and phylogenetic tree were analyzed by Mega software. The results showed that the inter-specific and intra-specific similarity of P. ginseng and P. quinquefolius respectively was 100% and 99. 6%. There were four specific positions at G153A, T463A, C732G and T818C. The inter-specific genetic distance (0) of trL-trnF sequences was lower than intra-specific genetic distance (0. 004). P. ginseng can be distinguished from P. quinquefolius based on the phylogenetic tree. It is concluded that Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix can be authenticated by identification indices of sequence similarity, specific positions, genetic distance and phylogenetic tree. Index of specific positions based on trnL-trnF sequences is the most efficient index to authenticate Ginseng Radix et Rhizoma and Panacis Quinquefolii Radix.
Chloroplasts ; genetics ; DNA Barcoding, Taxonomic ; methods ; Panax ; classification ; genetics ; Phylogeny ; Plant Proteins ; genetics ; Rhizome ; classification ; genetics

The paper introduces the current situation and the characteristics of the medicinal plant core collection. It expounds the significance and research methods for the medicinal plant core collection based on molecular phylogeography. Guided by molecular phylogeography, the essay explores the feasibility and methods of medicinal plant core collection for the medicinal plants with rich wild resources and without wild resources. It further forecasts the application of medicinal plant core collection methods on the basis of molecular phylogegraphy.
Chloroplasts ; genetics ; Drugs, Chinese Herbal ; Haplotypes ; Phylogeography ; Plants, Medicinal ; genetics ; Scutellaria baicalensis ; genetics

Chloroplast genetic engineering, offers several advantages over nuclear transformation, including high level of gene expression, increased biosafety, remedying some limitations associated with nuclear genetic transformation, such as gene silencing and the stability of transformed genes. It is now regarded as an attractive new transgenic technique and further development of biotechnology in agriculture. In this article we reviewed the characteristics, applications of chloroplast genetic engineering and its promising prospects were discussed.
Biotechnology ; methods ; Chloroplasts ; genetics ; Genetic Engineering ; methods ; Plants, Genetically Modified ; genetics ; Transformation, Genetic

OBJECTIVEThe genetic diversity and genetic relationship of Jatropha curcas resources in Sichuan and Yunnan were studied in order to provide a theoretical basis for breeding fine varieties and protecting germplasm resources.

METHODTen J. curcas populations were studied by 12 cpSSR primers in this paper. On the base of amplified bands, genetic diversity parameters were analyzed by POPGENE version 1.32. Furthermore, UPGMA tree of 10 J. curcas populations established from pairwise population distance by NTSYSpc version 2.10.

RESULTTwenty-two polymorphic bands were detected, and the percentage of polymorphic loci (P) was 76.28%. Among of the 10 J. curcas populations, the average percentage of polymorphic loci of YNSB was higher than that of the other populations, and it reached 95.45%; On the other hand, that of YNLS was the lowest in all populations, and it was 45.45%. Nei's gene diversity index(H(e)), Shannon information index(I), Effective Num of alleles(A(e)) were respectively 0.4020, 0.576 7, 1.713 6. The total gene diversity (H(T)), the gene differentiation coefficient (G(st)), the gene flow (N(m)) and the gene diversity within populations (H(s)) were 0.443 3, 0.080 2, 3.058 5, 0.405 1, 0.035 7, respectively. The highest gene diversity ratio was showed within populations and the lowest among populations. The results by AMOVA analysis showed that 91.02% of genetic variation existed within populations while 8.98% of genetic variation existed among populations. On the base of the results, the conclusion was extracted that variation existed mainly within populations, and the variation within populations was bigger than that among populations. The result was consistent with that of the gene differentiation coefficient. The order of the genetic diversity was YNLS population < XSBN population < SCHPZ population < SCHD population < SCJH population < YNPR population < SCLB population < YNSB population < YNFY population < SCHL population. The range of Nei's genetic identity and genetic distance of 10 respectively populations were respectively 0.812 7-0.979 8, 0.020 4-0.207 3. All these showed the similarity was higher and there was a close relationship among the 10 respectively populations; Results based on the cluster analysis showed that 10 respectively populations were divided into 2 groups: one was SCJH population and CHPZ population, the other was SCHL population, SCHD population, SCLB population, YNSB population, YNFY population, YNPR population, XSBN population and YNLS population.

CONCLUSIONSignificant genetic diversity was observed among respectively resources in Sichuan and Yunnan. On the other hand, genetic relationship was close between populations.

China ; Chloroplasts ; genetics ; Genetic Markers ; Genetic Variation ; Jatropha ; classification ; genetics ; Microsatellite Repeats ; Phylogeny

HSP21 gene is a key gene to respond high temperature stress in plant and plays an important role in preventing protein denaturation, protecting cell structure and maintaining normal growth and development. Therefore, cloning HSP21 gene is the basis for revealing the molecular mechanism of resistance to high temperature stress in cassava. To obtain cassava HSP21 homologous gene and analyze the properties of predicted protein, electronic cloning technology was used to assemble and derivate new gene in this study, and bioinformatics analysis method was used to analyze the primary to highest structure, hydrophilicity/hydrophobicity, signal peptide, protein homology and phylogenetic evolution of expressed protein. HSP21 gene was 969 bp, its open reading frame was 705 bp, and the predicted protein contains 234 amino acids. The predicted protein is a non-transmembrane protein that is alkaline and hydrophilic, and is mainly localized in the chloroplast. Through multiple sequence alignment and phylogenetic analysis, it was found that the cassava HSP21 protein has high homology with other plants such as Hevea brasiliensis, Ricinus communis, and Jatropha curcas. The results could provide reference for the study of cloning and transformation of this gene.
Chloroplasts ; Cloning, Molecular ; Computational Biology ; Computer Simulation ; Evolution, Molecular ; Heat-Shock Proteins ; genetics ; Manihot ; genetics ; Phylogeny