Chloroplast DNA reveals genetic population structure in Sinomenium acutum in subtropical China / 中草药·英文版

OBJECTIVE@#The population density and diversity of Sinomenium acutum (Menispermaceae) have been greatly reduced recently by overharvesting for medicinal purposes in China. Therefore, it is urgent that the remaining populations are investigated, and that strategies for the utilization and conservation of this species are developed. This study aimed to find the possible glacial refugia and define the genetic diversity of S. acutum for its proper utilization and conservation.@*METHODS@#A total of 77 S. acutum samples were collected from four locations, Qinling Mountains, Daba Mountains, Dalou Mountains, and Xuefeng Mountains, in subtropical China. Genetic diversity among and between these populations were phylogenetically analyzed using four chloroplast DNA molecular markers (atpI-atpH, trnQ-5'rps16, trnH-psbA and trnL-trnF).@*RESULTS@#A total of 14 haplotypes (C1 to C14) were found in collected samples. Haplotypes C1 and C3 were shared among all populations, with C3 as the ancestral haplotype. Haplotypes C11 and C12 diverged the most from C3 and other haplotypes. No obvious phylogeographic structure was found in four locations using the GST/NST test. There is no evidence of rapid demographic expansion in S. acutum based on the mismatch distribution, and the results of Tajima's D test, and Fu's FS test. Our analyses of molecular variance revealed a high level of genetic variation within populations. In contrast, the genetic differentiation among S. acutum populations was low, indicating frequent gene flow.@*CONCLUSION@#Xuefeng, Dalou, and Daba Mountains were possible glacial refugia for the populations of S. acutum. C1, C3, C11 and C12 haplotypes of S. acutum should be carefully preserved and managed for their genetic value.

Identification and Genetic Variation Analysis of Wild and Cultivated Germplasm of Angelica sinensis Based on cp DNA / 中国实验方剂学杂志

ObjectiveTo conduct genetic variation analysis of 11 cultivars and 7 wild populations of Angelica sinensis in Gansu province based on the chloroplast gene （cp DNA）， and provide references for germplasm identification and breeding of new cultivars of A. sinensis. MethodThree pairs of cp DNA primers were used for polymerase chain reaction （PCR） amplification and sequencing of A. sinensis samples. MegaX was used to perform statistics on sequence characteristics and calculate mean genetic distances among A. sinensis populations. Unweighted pair-group method with arithmetic means （UPGMA） clustering tree based on genetic distance was constructed by NTSYS 2.10e. DanSP v6 was used to calculate sequence polymorphism and Tajima's D of A. sinensis. PERMUT was used to calculate the population structure of A. sinensis. Arlequin v3.5 was used to perform molecular variation analysis， and PopART1.7 was used to construct TCS haplotype network. ResultThree pairs of cp DNA primers were amplified， sequenced， compared， and combined to give a sequence length of 1 759 bp. One variable site was detected in the wild A. sinensis and 480 variable sites were detected in the cultivated A. sinensis， including 97 singleton variable sites， 383 parsimony informative sites， and 152 insertion-deletion sites. In the three regions of matK， psbA-trnH， and rbcL of cp DNA in the wild and cultivated A. sinensis， matK was the region with the highest polymorphism. Tajima’s D of all the combined sequences of A. sinensis were not significantly negative， but psbA-trnH and rbcL genes of the cultivated A. sinensis were significantly negative， indicating that the A. sinensis followed neutral evolution on a whole， while psbA-trnH and rbcL genes had undergone selection. The degree of genetic differentiation （Fst=0） among wild populations was lower than that among cultivated populations （Fst=0.114 19， P<0.05）. The degree of genetic differentiation between wild and cultivated A. sinensis was relatively high （Fst=0.942 55， P<0.01）. Genetic variation in the cultivated A. sinensis was mainly found within the populations （89%）. UPGMA cluster tree based on genetic distance showed that the wild A. sinensis and the cultivated A. sinensis were clustered into one branch， respectively， with a distant genetic relationship， and the population 3 in the cultivated A. sinensis was far from other cultivated populations. The TCS haplotype network consisted of 15 haplotypes and 4 unknown haplotypes， which was divided into 3 parts， with a large number of variations among each part. Shared haplotypes were only found in the wild or cultivated groups， and there were no shared haplotypes between groups. ConclusionThe genetic diversity of A. sinensis was low at species level， and the population diversity of the wild was lower than that of the cultivated. The degree of genetic differentiation between the wild and the cultivated A. sinensis was high， but that in the wild and the cultivated populations were low. Genetic variation in the cultivated A. sinensis was mainly found within populations.

Genetic Diversity Analysis of Isatis indigotica Germplasm Materials by Chloroplast DNA Variation and ISSR Molecular Marker / 中国实验方剂学杂志

ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.

Genetic Diversity Analysis of Isatis indigotica Germplasm Materials by Chloroplast DNA Variation and ISSR Molecular Marker / 中国实验方剂学杂志

ObjectiveTo analyze the sequence variation and genetic diversity of 47 Isatis indigotica germplasm materials， and carry out the study on the genetic differentiation and structure. MethodGenomic DNA of 47 I. indigotica germplasm materials were extracted by kit extraction method. Two chloroplast DNA （cp DNA） sequences and five inter-simple sequence repeat （ISSR） primers were used for amplification and sequencing. Chromas， Mega 7.0， DanSP5， and GenALEx were used to calibrate， splice， and analyze the sequence characteristics. PERMUT and PopGen 1.31 were used to analyze the genetic diversity parameters and genetic structure， and NTSYS was used to obtain the unweighted pair-group method with arithmetic means（UPGMA） clustering tree plot of 47 I. indigotica germplasm materials. ResultA total of 129 samples from 47 I. indigotica germplasm materials were successfully amplified and sequenced. The length of 2 cp DNA sequences after spliced was 1 412 bp， and there were 377 polymorphic variation loci， and 36 haplotypes. Fu and Li's D* test was significant （P<0.01）. The values of Pi， HS， and HT based on cp DNA were 0.119 89， 0.787， and 0.891， respectively. The genetic differentiation coefficients of gene differentiation coefficient（Gst）， nucleotide differentiation coefficient（Nst）， and fixation index（Fst） were 0.117， 0.468， and 0.488， respectively， and the gene flow （Nm） was 0.615. The mean values of PPB， Shannon information diversity index（I）， Nei's genetic diversity index（H）， and Gst based on ISSR were 78.85%， 0.334 8， 0.218 6， and 0.754 4， respectively， and the Nm value was 0.162 8. ConclusionI. indigotica has high genetic diversity and abundant haplotypes at the species level， with abundant haplotypes. Genetic differentiation among different germplasm materials is obvious， and gene exchange is not frequent. Genetic variation mainly exists among populations. The population has accumulated various low-frequency gene mutations recently， suggesting that it has experienced significant regional expansion in the history.

Identification of Uygur Herb Capparis spinose Based on Sequences of the Plastid psbA-trnH Intergenic Regions / 中国药学杂志

OBJECTIVE: To provide a reference for molecular biology identification of C. spinosa by comparing and analyzing the sequence of psbA-trnH gene intergenic regions between Capparis spinosa L. and others 8 medicinal plants. METHODS: Total DNA were extracted, psbA-trnH intergenic regions sequences were isolated using PCR amplification, and sequence analysis, evaluation of intraspecific and interspecific genetic distance used the Kimura 2 parameter(K2P)model as well as construction of phylogenetic tree based on UPGMA were conducted by the MEGA7. RESULTS: Compared with C. spinosa, the interspecific genetic distance is 0.045-0.474. The average is 0.238. The interspecific minimum was larger than the intraspecific maximum. The results of UPGMA tree indicated every species was sorted out and C. spinosa was distinguished from the others effectively. CONCLUSION: The sequences of chloroplast psbA-trnH gene intergenic regions is valuable for the identification and study of C. spinosa.

DNA barcoding construction of medicinal plants in genus Lycium L. based on multiple genomic segments / 中草药

Objective: To construct the DNA barcoding of medicinal plants in genus Lycium L. from China based on sequences of ITS, nine chloroplast DNA segments, and two mitochondrial DNA segments. Methods: Specimens and samples of Lycium ruthenicum, L. barbarum var. auranticarpum, L. barbarum, L. chinense, and L. dasystemum were collected and nuclear DNA ITS, chloroplast DNA matK, rbcL, rpoC1, trnL (UAA) intron, psbA-trnH, atpB-rbcL, trnS (GCU)-trnG (UCC), rpl20-rps12, trnL (UAA)-trnF (GAA), and mitochondrial DNA nad1/b-c and nad5/d-e were sequenced from these samples. Gentiana lhassica was used as the external group to make statistical analysis. Results: One hundred and eight sequences were obtained. The mutation site of ITS region was the most abundant; The six chloroplast DNA fragments were selected; Two mitochondrial DNA fragments could be used as the bar code recommendation sequences of the three species from the genus, and the multiple genomic and multi fragment combination DNA bar code of each species was constructed. Conclusion: ITS region and the screening of six chloroplast DNA fragments have the significance of species identification; The two mitochondrial DNA fragments have a certain significance. The study may provide the reference for the species identification and genetic background of the plants in Lycium L. from China.