The complete chloroplast genome of Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen. 1834 (Lamiaceae) and its phylogenetic analysis.

Lagochilus ilicifolius Bunge ex Bentham, Labiat. Gen is a perennial herb with much-branched stems native to Nei Mongol, Ningxia, Gansu, N Shaanxi. It can be used clinically as a hemostatic agent. The chloroplast genome length is 151,466 bp. It contained two inverted repeat regions of 25,660 bp each, a large single-copy region of length 82,504 bp, and a small single-copy region of length 17,642 bp. Also, the GC content is 38.6%. There were 133 genes annotated, including 88 known protein-coding genes, 37 tRNAs, and eight rRNAs. The phylogenetic tree was constructed using Bayesian method for plastome data of 29 species. The entire chloroplast genome of L. ilicifolius within the Lamiaceae is the first to reveal genetic taxonomy at the molecular level, and the new phylogenetic tree data can be used for future evolutionary studies.

The complete chloroplast genome of Pulsatilla chinensis f. alba D. K. Zang (Ranunculaceae, Pulsatilla Miller).

Pulsatilla chinensis f. alba D. K. Zang 1993 is a forma of Pulsatilla chinensis (Bge.) Regel, the root of P. chinensis is traditional Chinese medicine called Pulsatillae radix. The biggest difference between P. chinensis f. alba and P. chinensis is that P. chinensis f. alba sepals is white. The complete chloroplast genome of P. chinensis f. alba was sequenced using the Illumina NovaSeq platform for the first time. The lengths of the genome, large single-copy (LSC), small single-copy (SSC), two inverted repeats (IRs), and GC content were 163,654 bp, 82,355 bp, 19,069 bp, 31,115 bp, and 37.2%, respectively. It had 134 genes, including 90 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The maximum-likelihood tree indicated that P. chinensis f. alba had a closer relationship with P. chinensis. This study would provide a theoretical basis for the further study of Pulsatilla plants genetics phylogenetic research.

The complete chloroplast genome sequence of Syringa oblata Lindl. var. alba Hort. ex Rehd. 1763 (Oleaceae).

Syringa oblata var. alba is a shrub or a small tree from China with high ornamental, medicinal, and edible value. Here, we present its first complete chloroplast genome. The entire circular genome is 155,648 bp in length, with large single-copy (LSC) length of 86,247, small single-copy (SSC) length of 17,937, inverted repeat (IR) length of 25,732, and GC content of 37.9%. One hundred and thirty-two genes, including 88 protein-coding, 36 tRNA, and eight rRNA genes were predicted. A phylogenetic tree of 25 plant species was constructed based on the maximum-likelihood method, indicating that S. oblata var. alba, S. vulgaris, and S. oblata form a sister group. This study will provide valuable basic information for phylogeny, species identification, and varieties breeding of this species.

The complete chloroplast genome of Dictamnus dasycarpus Turcz. (Rutaceae).

Dictamnus dasycarpus Turcz. 1842 is a medicinal plant of China. Its dry root bark is called BAIXIANPI, which is a common traditional Chinese medicine. Here, we report the complete chloroplast genome of D. dasycarpus. The length of the genome, large single-copy (LSC), small single-copy (SSC), inverted repeat (IR), and GC content was 157,056 bp, 84,497 bp, 18,487 bp, 27,036 bp, and 38.5%, respectively. A total of 132 genes were annotated, including 87 protein coding, eight rRNA, and 37 tRNA genes. Interestingly, 15 genes contained single intron while two others contained two introns. The phylogenetic tree showed the two D. dasycarpus (D. albus) clustered in a clade, which was sister to clade formed by the species of Melicope, Tetradium, Phellodendron, and Zanthoxylum.

[Comparison of chloroplast genomes of medicinal plants in Aristolochiaceae].

In this study, the chloroplast genome of Asarum sieboldii f. seoulense was sequenced, analyzed, and compared with chloroplast genomes of other medicinal plants in Aristolochiaceae downloaded from GenBank, aiming to clarify the characteristics of the chloroplast genome of A. sieboldii f. seoulense and the differences in chloroplast genome among medicinal plants of Aristolochiaceae. To be specific, the chloroplast genome of A. sieboldii f. seoulense was sequenced and assembled by high-throughput sequencing, and the general characteristics, repeats, inverted repeat(IR) boundary, and phylogenetic relationship of the chloroplast genomes of 11 medicinal species in Aristolochiaceae were analyzed with REPuter. The result showed that the genome of A. sieboldii f. seoulense was 167 293 bp, with large single-copy(LSC) region of 89 840 bp, small single-copy(SSC) region of 21 415 bp, IR region of 28 019 bp, and GC content of 37.9%. A total of 133 genes were annotated, including 89 protein-coding genes, 36 tRNA genes and 8 rRNA genes. The chloroplast genomes of the 11 medicinal species were 159 308-167 293 bp, with 130-134 genes annotated. Forward(F), reverse(R), complement(C), and palindromic(P) long repeats and simple sequence repeat(SSR) were found in the chloroplast genomes of five species. Among them, A. sieboldii f. seoulense had six types of SSR. In the phylogenetic tree, A. sieboldii f. seoulense and A. heterotropoides were in the same clade. The result is expected to lay a basis for the classification, identification, and phylogeny of medicinal plants in Aristolochiaceae.

The complete chloroplast genome sequence of Convallaria majalis L.

The complete chloroplast genome of an important medicinal plant, Convallaria majalis Linnaeus, was sequenced for the first time. The entire circular genome is 162,218 bp in length, with 37.9% GC contents. The genome has consisted of a large single-copy region (LSC) with a length of 85,417 bp, a small single-copy region (SSC) with a length of 18,495 bp, and two inverted repeat regions (IRs) with a length of 29,153 bp each. The genome harbored 133 genes, including 87 protein coding genes, 38 tRNA genes, and eight rRNA genes. The phylogenetic tree of 24 plant species was constructed based on the maximum-likelihood method. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

The complete chloroplast genome sequence of Veratrum nigrum L.

The complete chloroplast genome of an important medicinal plant, Veratrum nigrum Linnaeus, was sequenced. The entire circular genome is 151,580 bp in length, with 37.7% GC contents. The genome has a large single-copy (LSC) region with a length of 81,806 bp, a small single-copy (SSC) region with a length of 17,472 bp, and two inverted repeat regions (IRs) with a length of 26,151 bp. It harbored 131 genes, including 85 protein coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analysis suggested V. nigrum formed a monophyletic clade with relatively short genetic distance to Veratrum oxysepalum and Veratrum taliense. This study will provide theoretical basis for further study on plant genetics phylogenetic research.

The complete mitochondrial genome of Dryopteris crassirhizoma Nakai (Dryopteridaceae, Dryopteris Adanson).

The complete mitochondrial genome of Dryopteris crassirhizoma was sequenced for the first time. The mitochondrial genome length was 313,346 bp, with 48.58% GC contents. There were 94 genes annotated, including 27 known protein-coding genes, 49 tRNAs, and 18 rRNAs. The maximum likelihood method was used to establish the phylogenetic tree of six species. The phylogenetic results showed that D. crassirhizoma was sister to Ophioglossum californicum. It reveals the genetic relationship between different species and provides a theoretical basis for the establishment of a classification system.

The complete mitochondrial genome of Aucklandia lappa Decne. (Asteraceae, Aucklandia Falc.).

The complete mitochondrial genome of Aucklandia lappa was sequenced for the first time. The mitochondrial genome length was 320,439 bp, with 45.05% GC contents. There were 67 genes annotated, including 31 known protein-coding genes, 25 tRNAs, and six rRNAs. The maximum likelihood method was used to establish the phylogenetic tree of 37 species. Results have shown that A. lappa and Arctium lappa were sister groups. It reveals the genetic relationship between different species and provides a theoretical basis for the establishment of a classification system.

The complete mitochondrial genome of Aconitum kusnezoffii Rchb. (Ranales, Ranunculaceae).

Aconitum kusnezoffii Rchb. is a medicinal plant in the Ranunculaceae family. In this study, we report the first complete mitochondrial genome of A. kusnezoffii. The total length of the mitochondrial genome of A. kusnezoffii is 440,720 bp and the GC content of 46.85%. The mitochondrial genome contained 37 protein-coding genes, 29 tRNAs, and three rRNAs. These data will provide the basis for the systematic evolutionary analysis of Ranunculaceae.

The complete mitochondrial genome of Euonymus alatus (celastraceae, Euonymus L.).

The complete mitochondrial genome of medicinal plant, Euonymus alatus, was sequenced for the first time. The genome sequence is 1,045,106 bp in length (GenBank accession number MW009108), with 44.98% GC contents. There are 72 genes in the genome, including 41 known protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). The phylogenetic trees of 28 species are constructed using the maximum-likelihood method. The information will provide references for phylogenetic research.

The complete mitochondrial genome of Glycyrrhiza uralensis Fisch. (Fabales, Leguminosae).

The complete mitochondrial genome of an important medicinal plant Glycyrrhiza uralensis Fisch. is reported for the first time. The mitochondrial genome sequence of G. uralensis was 463,869 bp in length and had a GC content of 45.19%. The genome contained 40 protein-coding genes (PCGs), 30 transfer RNAs (tRNAs), and three ribosomal RNAs (rRNAs). The phylogenetic tree was built based on 25 plants, using the maximum-likelihood method. These data will provide certain help to determine the taxonomic status of G. uralensis.

Pathways involved in pony body size development.

BACKGROUND: The mechanism of body growth in mammals is poorly understood. Here, we investigated the regulatory networks involved in body growth through transcriptomic analysis of pituitary and epiphyseal tissues of smaller sized Debao ponies and Mongolian horses at the juvenile and adult stages. RESULTS: We found that growth hormone receptor (GHR) was expressed at low levels in long bones, although growth hormone (GH) was highly expressed in Debao ponies compared with Mongolian horses. Moreover, significant downregulated of the GHR pathway components m-RAS and ATF3 was found in juvenile ponies, which slowed the proliferation of bone osteocytes. However, WNT2 and PLCß2 were obviously upregulated in juvenile Debao ponies, which led to premature mineralization of the bone extracellular matrix. Furthermore, we found that the WNT/Ca2+ pathway may be responsible for regulating body growth. GHR was demonstrated by q-PCR and Western blot analyses to be expressed at low levels in long bones of Debao ponies. Treatment with WNT antagonistI decreased the expression of WNT pathway components (P < 0.05) in vitro. Transduction of ATDC5 cells with a GHR-RNAi lentiviral vector decreased the expression of the GHR pathway components (P < 0.05). Additionally, the expression of the IGF-1 gene in the liver was lower in Debao ponies than in Mongolian horses at the juvenile and adult stages. Detection of plasma hormone concentrations showed that Debao ponies expressed higher levels of IGF-1 as juveniles and higher levels of GH as adults than Mongolian horses, indicating that the hormone regulation in Debao ponies differs from that in Mongolian horses. CONCLUSION: Our work provides insights into the genetic regulation of short stature growth in mammals and can provide useful information for the development of therapeutic strategies for small size.

Development of a Modified Score System as Prediction Model for Successful Vaginal Birth After Cesarean Delivery.

This study was designed to establish a modified prediction score system to improve the safety and success rate of vaginal birth after cesarean delivery (VBAC). We recruited 406 patients (between January 2012 and December 2016) and generated a modified score system in predicting the success rate of VBAC. All patients were required to sign informed consent forms. There were 87.2% of patients who had successful VBAC deliveries and 12.8% patients who had repeated cesarean sections. We conducted multivariable logistic regression and found seven variables that were associated with VBAC success, including previous primary indication of cesarean delivery (odds ratio (OR), 2.1; 95% confidence interval (CI), 1.4-3.0), previous vaginal birth history (OR, 2.5; 95% CI, 1.8-3.8), < 40 years of age (OR, 2.1; 95% CI, 1.2-3.3), < 20 kg weight gain (OR, 1.5; 95% CI, 1.2-2.3), no labor induction (OR, 1.9; 95% CI, 1.5-2.9), high score of pelvic/birth weight (OR, 1.4; 95% CI, 1.1-2.1), and Bishop score (OR, 1.3; 95% CI, 1.2-1.4). After adjustment for optimism, the area under the receiver operating characteristic curve (AUC-ROC) was 0.849 (95% CI, 0.78-0.89), and the modified VBAC score was positively correlated with the success rate of trial of labor after cesarean delivery (TOLAC). A valid and useful score system was established to predict VBAC success rate.

[Study on high throughput sequencing identification of Fructus Arctii and five counterfeit species mix power].

Fructus Arctii is a traditional Chinese medicine. The main counterfeit species are the seeds of Arctium tomentosum, Onopordum acanthium, Silybum marianum, Saussurea costus, Amorpha fruticosa. Traditional identification methods or molecular barcoding techniques can identify Fructus Arctii and its counterfeit species. However, the identification of the mixture of it and its spurious species is rarely reported. In this paper, we sequenced the ITS2 sequences of Fructus Arctii and 5 kinds of spurious species mix powder by high-throughput sequencing to identify the mixed powder species and providing new ideas for the identification of Fructus Arctii mix powder. The total DNA in mixed powder was extracted, and the ITS2 sequences in total DNA was amplified. Paired-end sequencing was performed on the DNA fragment of the community using the Illumina MiSeq platform. The sequence was analyzed by the software FLASH, QIIME and GraPhlAn etc. The results showed that the high quality ITS2 sequences of 39910 mix samples were obtained from the mixed samples, of which the total ITS2 sequence of the samples genus was 34 935. Phylogenetic analysis showed that the samples contained Fructus Arctii, A. tomentosum, O. acanthium, S. marianum, S. costus and A. fruticosa. Using ITS2 sequences as DNA barcodes, high-throughput sequencing technology can be used to detect the Fructus Arctii and its spurious specie in mixed powder, which can provide reference for the quality control, safe use of medicinal materials of Fructus Arctii and the identification of mixed powder of traditional Chinese medicine.

Examination of the association of physical activity during pregnancy after cesarean delivery and vaginal birth among Chinese women.

BACKGROUND: The goal was to study whether higher physical activity can increase the success rate of Vaginal Birth after Cesarean Delivery (VBAC). METHODS: We enrolled 823 patients with previous cesarean section delivery history (between January 2015 and December 2017) and measured their physical activity during pregnancy. A final number of 519 patients were included for the trial of labor after cesarean delivery (TOLAC). All patients signed informed consent forms. RESULTS: We conducted bivariate analyses and identified that several variables were associated with successful VBAC: Prior history of vaginal birth (odds ratio [OR] 2.4, 95% CI 1.8-3.9); previous indication for primary cesarean delivery (OR 2.2, 95% CI 1.5-3.0); age younger than 40 years (OR 2.1, 95% CI 1.3-3.4); Weight gain less than 20 kg (OR 1.5, 95% CI 1.3-2.4); high pelvic/birth weight score (OR 1.4, 95% CI 1.1-2.0); no induction of labor (OR 1.9, 95% CI 1.4-2.8); and estimated prenatal fetal weight (OR 1.4, 95% CI 1.2-1.5). We also found that the bivariate association between physical activity and VBAC was significant (p = 0.002). In addition, there was higher odds of VBAC in women who had active physical activity of more than 150 min/week (adjusted OR 1.86, 95% CI 1.69-2.07). Lower odds of VBAC was associated with older age, weight gain during pregnancy, induction of labor, and having estimated prenatal fetal weight more than 3500 g. CONCLUSION: Physical activity during pregnancy may influence the success rate of VBAC in Chinese women. Future studies will be needed to prove the robustness of this association using more detailed exposure and outcome definitions.

Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species.

[Single nucleotide polymorphisms in cell cycle regulator p21 and p27 genes are associated with susceptibility to epithelial ovarian cancer].

OBJECTIVE: To investigate the association of single nucleotide polymorphisms (SNP) in p21 and p27 genes with the risk of epithelial ovarian cancer (EOC). METHODS: Genotypes were analyzed by polymerase chain reaction-restrictive fragment length polymorphism (PCR-RFLP) method in 234 patients with EOC and 284 control women in China. RESULTS: (1) The frequencies of the p21 in healthy controls were 34.2%, 49.6% and 16.2%, while the distribution of the C and T allele was 59.0% and 41.0%, respectively. The p21 C/C (28.2%), C/T (53.0%), T/T (18.8%) distribution in ovarian cancer patients was not significantly different from that in healthy controls (P > 0.05). There was no statistic difference in allele distribution between ovarian cancer patients and healthy controls (P > 0.05) either. The stratification analysis by tumor histological type did show that the genotype distribution in four types of ovarian cancer patients was significantly different from that in healthy controls (P = 0.02) . The C/C genotype was likely to reduce the risk of epithelial endometrial cancer, and the adjusted odds ratio was 0.56 (95% CI:0.32-0.98). (2) The genotype frequencies of the p27 in healthy controls were 88.4%, 10.9% and 0.7%, while the distribution of the V and G allele was 93.8% and 6.2%, respectively. The V/V (93.6%), V/G (5.1%) and G/G (1.3%) distribution in ovarian cancer patients was significantly different from that in healthy controls (P = 0. 04). There was no statistic difference in allele distribution between ovarian cancer patients and healthy controls (P > 0.05). Compared with the V/G and G/G genotypes, the V/V genotype increased the risk of EOC, the adjusted odds ratio was 1.92 (95% CI: 1.02-3.63). CONCLUSION: The C/C genotype of p21 may reduce the risk of epithelial endometrial cancer, and the genotype of p27 V/V may be a potential risk factor for susceptibility to EOC.

Expression pattern and activity of six glutelin gene promoters in transgenic rice.

The shortage of strong endosperm-specific expression promoters for driving the expression of recombinant protein genes in cereal endosperm is a major limitation in obtaining the required level and pattern of expression. Six promoters of seed storage glutelin genes (GluA-1, GluA-2, GluA-3, GluB-3, GluB-5, and GluC) were isolated from rice (Oryza sativa L.) genomic DNA by PCR. Their spatial and temporal expression patterns and expression potential in stable transgenic rice plants were examined with beta-glucuronidase (GUS) used as a reporter gene. All the promoters showed the expected spatial expression within the endosperm. The GluA-1, GluA-2, and GluA-3 promoters directed GUS expression mainly in the outer portion (peripheral region) of the endosperm. The GluB-5 and GluC promoters directed GUS expression in the whole endosperm, with the latter expressed almost evenly throughout the whole endosperm, a feature different from that of other rice glutelin gene promoters. The GluB-3 promoter directed GUS expression solely in aleurone and subaleurone layers. Promoter activities examined during seed maturation showed that the GluC promoter had much higher activity than the other promoters. These promoters are ideal candidates for achieving gene expression for multiple purposes in monocot endosperm but avoid promoter homology-based gene silencing. The GluC promoter did not contain the endosperm specificity-determining motifs GCN4, AACA, and the prolamin-box, which suggests the existence of additional regulatory mechanism in determining endosperm specificity.