Anti-inflammatory effect of Trichospira verticillata via suppression of the NLRP3 inflammasome in neutrophilic asthma.

Trichospira verticillata is an annual herb that belongs to the family Asteraceae. Trichospira verticillata extract (TVE) elicits anti-plasmodial activity; however, there has been no detailed report about its anti-inflammatory effects and molecular mechanisms. In addition, herbal plants exhibit anti-inflammatory effects by suppressing the NLRP3 inflammasome. Therefore, the primary goal of this study was to examine the effects of TVE on NLRP3 inflammasome activation by measuring interleukin-1ß (IL-1ß) secretion. We treated lipopolysaccharides (LPS)-primed J774A.1 and THP-1 cells with TVE, which attenuated NLRP3 inflammasome activation. Notably, TVE did not affect nuclear factor-kappa B (NF-κB) signalling or intracellular reactive oxygen species (ROS) production and potassium efflux, suggesting that it inactivates the NLRP3 inflammasome via other mechanisms. Moreover, TVE suppressed the formation of apoptosis-associated speck-like protein (ASC) speck and oligomerization. Immunoprecipitation data revealed that TVE reduced the binding of NLRP3 to NIMA-related kinase 7 (NEK7), resulting in reduced ASC oligomerization and speck formation. Moreover, TVE alleviated neutrophilic asthma (NA) symptoms in mice. This study demonstrates that TVE modulates the binding of NLPR3 to NEK7, thereby reporting novel insights into the mechanism by which TVE inhibits NLRP3 inflammasome. These findings suggest TVE as a potential therapeutic of NLRP3 inflammasome-mediated diseases, particularly NA.

Aiouea padiformis extract exhibits anti-inflammatory effects by inhibiting the ATPase activity of NLRP3.

Inflammation is implicated as a cause in many diseases. Most of the anti-inflammatory agents in use are synthetic and there is an unmet need for natural substance-derived anti-inflammatory agents with minimal side effects. Aiouea padiformis belongs to the Lauraceae family and is primarily found in tropical regions. While some members of the Aiouea genus are known to possess anti-inflammatory properties, the anti-inflammatory properties of Aiouea padiformis extract (AP) have not been investigated. In this study, we aimed to examine the anti-inflammatory function of AP through the NOD-, LRR- and pyrin domain-containing protein 3 (NLRP3) inflammasome and elucidate the underlying mechanisms. Treatment with AP inhibited the secretion of interleukin-1 beta (IL-1ß) mediated by NLRP3 inflammasome in J774A.1 and THP-1 cells without affecting the viability. In addition, AP treatment did not influence NF-κB signaling, potassium efflux, or intracellular reactive oxygen species (ROS) production-all of which are associated with NLRP3 inflammasome activation. However, intriguingly, AP treatment significantly reduced the ATPase activity of NLRP3, leading to the inhibition of ASC oligomerization and speck formation. Consistent with cellular experiments, the anti-inflammatory property of AP in vivo was also evaluated using an LPS-induced inflammation model in zebrafish, demonstrating that AP hinders NLRP3 inflammasome activation.

Guarea microcarpa C. DC. extract inhibits NLRP3 inflammasome by suppressing its ATPase activity.

ETHNOPHARMACOLOGICAL RELEVANCE: Guarea genus comprises tropical and subtropical terrestrial herbs inhabiting Central and South America. These plants, including Guarea guidonia (L.) Sleumer, have anti-inflammatory, analgesic, antibacterial, antiviral, and immune-enhancing properties. AIM OF THE STUDY: Although various species of the Guarea genus are known for their medicinal properties, comprehensive data on their anti-inflammatory effects remain limited. Therefore, we investigated the NLRP3 inflammasome-inhibiting effects of the Guarea genus in this study. MATERIALS AND METHODS: To evaluate the anti-inflammatory activities of 18 members of the Guarea genus, we treated NLRP3 inflammasome activators with their extracts in LPS-primed J774A.1 and THP-1 cells. Cell viability was determined by water soluble tetrazolium salt (WST) and cytokine production, protein expression, and nuclear fractionation were determined by western blotting. Reactive oxygen species (ROS) production and apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) oligomerization were measured using confocal microscopic analysis. Inflammation-induced zebrafish was used in the in vivo experiments. RESULTS: Among the 18 Guarea members tested, Guarea microcarpa C. DC. extract (GM) exhibited no cytotoxicity and specifically suppressed the activation of the NLRP3 inflammasome, but not of the AIM2 or NLRC4 inflammasomes, by inhibiting the ATPase activity of NLRP3. This was achieved without affecting NF-κB signaling, potassium efflux, or intracellular ROS production, all of which are involved in NLRP3 activation. The reduced ATPase activity of NLRP3 led to decreased ASC oligomerization. Furthermore, GM exhibited anti-inflammatory effects in vivo. Additionally, GM treatment alleviated inflammation at the organismal level in an LPS-induced inflammation model using zebrafish embryos. CONCLUSION: Our results demonstrate the anti-inflammatory effects of GM via suppressing the NLRP3 inflammasome. Therefore, GM can be a potential therapeutic candidate for various inflammatory diseases caused by aberrant NLRP3 inflammasome activation.

Anti-Inflammatory Effect of Meriania hexamera Sprague by Targeting Syk Kinase in NF-κB Signaling.

Inflammation is a protective mechanism against harmful stimuli. There are two types of inflammation, acute and chronic, and severe diseases such as cardiovascular disease and cancer can be caused by chronic inflammation. Therefore, this research was conducted to discover new anti-inflammatory drugs. Meriania hexamera Sprague is a common herb in the Amazon region in South America. It is used as a traditional medical herb by natives, but no studies to date have investigated its anti-inflammatory activity. Using lipopolysaccharide (LPS), pam3CSK4 (Pam3), and poly(I:C), we studied the M. hexamera Sprague-Methanol Extract's (Mh-ME) in vitro anti-inflammatory functions. Using RAW264.7 cells, we detected the released nitric oxide (NO) and mRNA expression extent of inducible nitric oxide synthase (iNOS) with pro-inflammatory proteins like tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and iterleukin-1 beta (IL-1ß). It was found that Mh-ME suppressed the inflammatory activities in a dose-dependent manner. In the luciferase assay, the nuclear factor kappa light chain enhancer of the activated B cells (NF-κB) pathway was inhibited by Mh-ME. Mh-ME especially acted as an inhibitor of Syk kinase according to the results from CETSA. We also confirmed that Mh-ME mitigates acute gastritis derived from HCl/EtOH in ICR mice, ameliorating the expression of IL-1ß and tumor necrosis factor-alpha (TNF-α). In conclusion, Mh-ME is an herb with anti-inflammatory effects that targets Syk in the NF-κB pathway, suggesting that Mh-ME could be used as an anti-inflammatory herbal medicine.

Guettarda crispiflora Vahl Methanol Extract Ameliorates Acute Lung Injury and Gastritis by Suppressing Src Phosphorylation.

Many species in the genus Guettarda are known to exert anti-inflammatory effects and are used as traditional medicinal plants to treat various inflammatory symptoms. However, no studies on the inflammatory activities of Guettarda crispiflora Vahl have been reported. The aim of the study was to investigate in vitro and in vivo the anti-inflammatory effects of a methanol extract of Guettarda crispiflora Vahl (Gc-ME). To determine the anti-inflammatory activity of Gc-ME, lipopolysaccharide (LPS)-, poly(I:C)-, or Pam3CSK4-treated RAW264.7 cells, HCl/EtOH- and LPS-treated mice were employed for in vitro and in vivo tests. LPS-induced nitric oxide production in RAW264.7 cells was determined by Griess assays and cytokine gene expression in LPS-activated RAW264.7 cells, confirmed by RT- and real-time PCR. Transcriptional activation was evaluated by luciferase reporter gene assay. Target protein validation was assessed by Western blot analysis and cellular thermal shift assays (CETSA) with LPS-treated RAW264.7 and gene-transfected HEK293 cells. Using both a HCl/EtOH-induced gastritis model and an LPS-induced lung injury model, inflammatory states were checked by scoring or evaluating gastric lesions, lung edema, and lung histology. Phytochemical fingerprinting of Gc-ME was observed by using liquid chromatography-mass spectrometry. Nitric oxide production induced by LPS and Pam3CSK4 in RAW264.7 cells was revealed to be reduced by Gc-ME. The LPS-induced upregulation of iNOS, COX-2, IL-6, and IL-1ß was also suppressed by Gc-ME treatment. Gc-ME downregulated the promotor activities of AP-1 and NF-κB triggered by MyD88- and TRIF induction. Upstream signaling proteins for NF-κB activation, namely, p-p50, p-p65, p-IκBα, and p-Src were all downregulated by Ch-EE. Moreover, Src was revealed to be directly targeted by Gc-ME. This extract, orally treated strongly, attenuated the inflammatory symptoms in HCl/EtOH-treated stomachs and LPS-treated lungs. Therefore, these results strongly imply that Guettarda crispiflora can be developed as a promising anti-inflammatory remedy with Src-suppressive properties.

Ameliorative Effects of Daphnopsis costaricensis Extract against Oxazolone-Induced Atopic Dermatitis-like Lesions in BALB/c Mice.

The genus Daphnopsis has been traditionally used as a purgative, diuretic, stimulant, and psoriasis treatment. In this study, the anti-AD (atopic dermatitis) activities of the Daphnopsis costaricensis EtOH extract (DCE) were investigated in an oxazolone (OX)-induced mouse model of AD, and the anti-inflammatory effects of its active compounds were confirmed in PI-sensitized or IgE/DNP-BSA-sensitized RBL-2H3 cells. DCE improved the symptoms of OX-induced inflammatory dermatitis (swelling, erythema, and increased ear thickening) in OX-induced BALB/c mice ears and reduced epidermal thickness and mast cell infiltration. Eleven flavonoid compounds were isolated from DCE, and two compounds (7,8-dimethoxyflavone and 7,2'-dimethoxyflavone) significantly inhibited IL-4 overexpression in PI-induced RBL-2H3 cells and mast cell degranulation in IgE + DNP-BSA-induced RBL-2H3 cells. Our study indicates that DCE and two compounds (7,8-dimethoxyflavone and 7,2'-dimethoxyflavone) might effectively improve inflammatory and atopic skin symptoms.

Antinociceptive activity of the Caesalpinia eriostachys Benth. ethanolic extract, fractions, and isolated compounds in mice.

Caesalpinia eriostachys Benth. (CE) is native to the Mexico and multiple effects have been observed from several plants belonging to the same family. CE was subjected to extraction with 95% ethanol, and the components were isolated through column chromatography. The structure of the compound was elucidated based on nuclear magnetic resonance (NMR) spectral data, electron ionization-mass (EI-MS) spectroscopy, and liquid chromatography-mass (LC-MS) spectroscopy. In vivo antinociceptive studies were conducted using writhing, 5% formalin, tail-flick, hot-plate, and von Frey filament tests. The ethanolic extract showed a significant effect in the acetic acid-induced pain model and nociceptive behavior in the formalin model (second phase). In hot-plate test and tail-flick test, the results showed no difference compared to the control group. The results suggest that the ethanolic extract may act peripherally to reduce pain. In the streptozotocin (STZ)-induced pain model, the ethanolic extract showed significant effect in the von Frey test model. The n-Hex (Hexane) and MC (Methylene chloride) fractions and isolated compounds, ellagic acid and agathisflavone, showed increased effect. Based on these results, we confirmed that the CE ethanolic extract and their compounds, ellagic acid and agathisflavone, have antinociceptive effect on diabetes mellitus-induced pain. Furthermore, the results of this study might be valuable for identifying compounds with antinociceptive activity from natural products.

Anti-Inflammatory Effects of Huberia peruviana Cogn. Methanol Extract by Inhibiting Src Activity in the NF-κB Pathway.

There is a growing need to develop anti-inflammatory drugs to regulate inflammatory responses. An extract of Huberia peruviana Cogn. had the best inhibitory effect on nitric oxide (NO) production in screening process undertaken in our laboratory. However, the anti-inflammatory effect of Huberia peruviana Cogn. methanol extract (Hp-ME) has not been studied. In this study, the anti-inflammatory effect of Hp-ME was assessed by using an NO assay, RT-PCR, luciferase reporter gene activity assay, western blotting assay, HCl/EtOH-induced acute gastritis model, and LPS-induced acute lung injury model. The phytochemical components of Hp-ME were determined through LC-MS/MS analysis. When RAW264.7 and HEK293T cells were treated with Hp-ME, NO production was decreased dose-dependently without cytotoxicity and the mRNA levels of iNOS, COX-2, and TNF-α were decreased. In a luciferase assay, the activity of transcription factors, NF-κB in TRIF or MyD88-overexpressing HEK293T cells was extremely reduced by Hp-ME. The western blotting analysis indicated that Hp-ME has anti-inflammatory effects by inhibiting the phosphorylation of Src. Hp-ME showed anti-inflammatory effects on in vivo models of HCl/EtOH-induced gastritis and LPS-induced acute lung injury. LC-MS/MS revealed that Hp-ME contains several anti-inflammatory flavonoids. The final findings of this study imply that Hp-ME could be used as an anti-inflammatory drug in several inflammatory diseases.

Plastome comparison and evolution within the tribes of Plantaginaceae: Insights from an Asian gypsyweed.

In spite of availability of several plastomes representing different tribes of Plantaginaceae, sparse attempts have been made to understand the plastome structure, evolution, and phylogenomics. In the present study, we have made an effort to understand the gene content and plastome evolution in the family Plantaginaceae using the newly generated plastome sequence of Veronica ovata subsp. kiusiana, a taxon native to SE Asia. In the first-ever attempt, plastomes of seven out of 10 tribes of Plantaginaceae have been compared to understand the evolution across the tribes of Plantaginaceae. The size of the plastome of V. ovata subsp. kiusiana is 152,249 bp, showing a typical quadripartite structure containing LSC, SSC, and two IRs with the sizes of 83,187, 17,704, and 25,679 respectively. The plastome comparison revealed the unique deletions in ycf2 and ndhF genes of members of different tribes, and also revealed high nucleotide variable hotspots. The study also revealed six highly variable genes and intergenic spacer viz. rps16, rps15-ycf1, ccsA-ndhD, ndhC-trnV, petN-psbM, and ycf1-trnN as potential DNA barcodes for the genus Veronica. The phylogenomic study revealed the sister relationship between V. ovata subsp. kiusiana and V. persica and also suggested the tentative placement of seven tribes in the family Plantaginaceae.

Quadrella incana (Capparaceae) Leaf Extract Enhances Proliferation and Maintenance of Neural Stem/Progenitor Cells through Upregulating Glycolytic Flux and Redox Potential.

Neural stem/progenitor cells (NSPCs) are self-renewing, multipotent cells located in the embryonic and adult central nervous system (CNS). Extensive preclinical and clinical studies have shed light on the potential of stem cell replacement therapy for various neurodegenerative diseases. The key prerequisite for the success of these clinical applications is the procurement of a sufficient number of high-quality NSPCs. In this study, we explored the biological activity of Quadrella incana leaf in NSPC homeostasis. We showed that the leaf extract of Quadrella incana upregulated NSPC marker and proliferative potential. On the other hand, Quadrella incana leaf suppressed spontaneous unintended NSPC differentiation. Mechanistically, Quadrella incana leaf contributed to the maintenance of NSPCs by upregulating glycolytic flux and redox potential.

Viburnum pichinchense methanol extract exerts anti-inflammatory effects via targeting the NF-κB and caspase-11 non-canonical inflammasome pathways in macrophages.

ETHNOPHARMACOLOGICAL RELEVANCE: Viburnum pichinchense Benth. Mainly found in Ecuador and Colombia has been ethnopharmacologically utilized as a remedy for various female disorders with kidney inflammation and uterine relaxant. AIM OF THE STUDY: The pharmacological activity of Viburnum pichinchense has never been studied, therefore, this study explored anti-inflammatory activity of Viburnum pichinchense methanol extract (Vp-ME). MATERIALS AND METHODS: Anti-inflammatory activities of Vp-ME were evaluated in lipopolysaccharide (LPS)-stimulated RAW264.7 cells and HCl/EtOH-induced gastritis mice by MTT assay, nitric oxide (NO) production assay, semi-quantitative reverse-transcriptase-polymerase chain reaction (RT-PCR), luciferase reporter assay, Western blotting, and enzyme-linked immunosorbent assays (ELISA). Anti-inflammatory compounds in Vp-ME were identified by high performance liquid chromatography (HPLC). RESULTS: Vp-ME inhibited NO production in RAW264.7 cells stimulated with pam3CSK4, poly I:C or LPS and in LPS-stimulated peritoneal macrophages without cytotoxicity and downregulated mRNA expression of inflammatory enzymes, inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) and pro-inflammatory cytokines, tumor necrosis factor-α (TNF-α), interleukin-1ß (IL-1ß), and IL-6. The anti-inflammatory activity was accomplished by inhibiting nuclear factor-kappa B (NF-κB) transcriptional activation, upstream signaling molecules in the NF-κB pathway, and caspase-11 non-canonical inflammasome in RAW264.7 cells. Moreover, Vp-ME exhibited in vivo anti-inflammatory activity by ameliorating gastritis symptoms, inhibiting iNOS and IL-6 mRNA expression and IκBα activation in mice. HPLC analysis identified resveratrol, quercetin, luteolin, and kaempferol as the anti-inflammatory components in Vp-ME. CONCLUSION: This study demonstrated Vp-ME has the anti-inflammatory activity via targeting NF-κB and caspase-11 non-canonical inflammasome pathways in macrophage-mediated inflammatory responses, suggesting Vp-ME could be developed as anti-inflammatory ethnopharmacological remedies to prevent and treat inflammatory diseases.

A comparative analysis of complete plastid genomes from Prangos fedtschenkoi and Prangos lipskyi (Apiaceae).

Prangos fedtschenkoi (Regel & Schmalh.) Korovin and P. lipskyi Korovin (Apiaceae) are rare plant species endemic to mountainous regions of Middle Asia. Both are edificators of biotic communities and valuable resource plants. The results of recent phylogenetic analyses place them in Prangos subgen. Koelzella (M. Hiroe) Lyskov & Pimenov and suggest they may possibly represent sister species. To aid in development of molecular markers useful for intraspecific phylogeographic and population-level genetic studies of these ecologically and economically important plants, we determined their complete plastid genome sequences and compared the results obtained to several previously published plastomes of Apiaceae. The plastomes of P. fedtschenkoi and P. lipskyi are typical of Apiaceae and most other higher plant plastid DNAs in their sizes (153,626 and 154,143 bp, respectively), structural organization, gene arrangement, and gene content (with 113 unique genes). A total of 49 and 48 short sequence repeat (SSR) loci of 10 bp or longer were detected in P. fedtschenkoi and P. lipskyi plastomes, respectively, representing 42-43 mononucleotides and 6 AT dinucleotides. Seven tandem repeats of 30 bp or longer with a sequence identity ≥90% were identified in each plastome. Further comparisons revealed 319 polymorphic sites between the plastomes (IR, 21; LSC, 234; SSC, 64), representing 43.8% transitions (Ts), 56.1% transversions (Tv), and a Ts/Tv ratio of 0.78. Within genic regions, two indel events were observed in rpoA (6 and 51 bp) and ycf1 (3 and 12 bp), and one in ndhF (6 bp). The most variable intergenic spacer region was that of accD/psaI, with 21.1% nucleotide divergence. Each Prangos species possessed one of two separate inversions (either 5 bp in ndhB intron or 9 bp in petB intron), and these were predicted to form hairpin structures with flanking repeat sequences of 18 and 19 bp, respectively. Both species have also incorporated novel DNA in the LSC region adjacent to the LSC/IRa junction, and BLAST searches revealed it had a 100 bp match (86% sequence identity) to noncoding mitochondrial DNA. Prangos-specific primers were developed for the variable accD/psaI intergenic spacer and preliminary PCR-surveys suggest that this region will be useful for future phylogeographic and population-level studies.

Complete mitochondrial genome of Callipogon relictus Semenov (Coleoptera: Cerambycidae): a natural monument and endangered species in Korea.

In the present study, we report the first complete mitochondrial DNA genome of the genus Callipogon based on C. relictus, a natural monument and endangered species in South Korea. The mitogenome is 15,742 base pairs with 13 protein coding genes (PCGs), two rRNAs, 22 tRNAs, and a 1033 bp long AT-rich region. The overall base composition was 67.3% AT and 32.7 GC. Among 13 PCGs, seven genes (Nad2, Atp8, Atp6, Nad4L, Nad6, Cob, Nad1) harbour the typical stop codon TAA or TAG, whereas remaining five genes terminate with T. Interestingly, Cox3 employs AGA as the termination codon.

The complete chloroplast genome sequences of Pogostemon stellatus and Pogostemon yatabeanus (Lamiaceae).

The nucleotide sequences of the two chloroplast (cp) genomes from Pogostemon stellatus and Pogostemon yatabeanus are the first to be completed in genus Pogostemon of family Lamiaceae. The structure of two Pogostemon cp genomes shows similar characteristic to the typical cp genome of angiosperms. The lengths of two cp genomes are 151,825bp and 152,707 bp, respectively. Two cp genomes are divided into LSC region (83,012 bp and 83,791 bp) and SSC region (17,524 bp and 17,568 bp) by two IR regions (25,644 bp and 25,674 bp). Both of two cp genomes contain 114 genes (80 protein-coding genes, 30 tRNA genes and 4 rRNA genes), 10 protein-coding genes and 7 tRNA genes duplicated in the IR regions. Similar to the typical cp genome of angiosperms, 18 of the genes in the Pogostemon cp genome have one or two introns. The overall A-T contents of two genomes are 61.8% which is also similar to general angiosperms. The A-T content in the non-coding (64.4%) is higher than in the coding (59.9%) regions. Sixty-seven and seventy-three simple sequence repeat (SSR) loci were identified in the P. stellatus and P. yatabeanus cp genomes, respectively. In phylogenetic analysis, genus Pogostemon shows closed relationship with Scutellaria baicalensis of Scutellarioideae.

Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa.

The nucleotide sequence of the two chloroplast (cp) genomes from Paulownia coreana and P. tomentosa are the first to be completed in genus Paulownia of family Paulowniaceae. The structure of two Paulownia cp genomes shows similar characteristic with general cp genome of angiosperms. The lengths of two cp genomes are 154,545 bp and 154,540 bp, respectively. The cp genomes are divided into LSC region (85,241 bp and 85,236 bp) and SSC region (17,736 bp and 17,736 bp) by two IR regions (25,784 bp and 25,784 bp). Both of two cp genomes contain 113 genes (79 protein coding genes, 30 tRNA genes and 4 rRNA genes), eight protein-coding genes, seven tRNA genes and four rRNA genes duplicated in the IR regions. Similar to the general cp genome of angiosperms, 18 of the genes in the two cp genomes have one or two introns. The overall A-T contents of two genomes are 62.0% which is similar with general angiosperms. The A-T content in the non-coding (64.6%) is higher than in the coding (60.1%) regions. Seventy-one and seventy simple sequence repeat (SSR) loci were identified in the P. coreana and P. tomentosa cp genomes, respectively. In phylogenetic analysis, genus Paulownia shows closed relationship with Lindenbergia philippensis of Orobanchaceae.

The two complete plastomes from Scrophularia (Scrophulariaceae): Scrophularia buergeriana and S. takesimensis.

The plastome sequences of Scrophularia buergeriana and S. takesimensis are completed in family Scrophulariaceae. The structure of two Scrophularia plastomes shows similar characteristic with the typical plastome of angiosperm. The lengths of two plastomes are 153,631bp and 152,436bp, respectively. They are divided into LSC region (84,454bp and 83,542bp) and SSC region (17,929bp and 17,938bp) by two IR regions (25,624bp and 25,478bp). Both plastomes contain 113 genes including 79 protein coding genes, 30 tRNA genes and 4 rRNA genes. Eight protein-coding, seven tRNA and four rRNA genes are duplicated in the IR regions. Eighteen genes have one or two intron(s). The overall A-T contents of two genomes are 62.0% and 61.9%, respectively. The A-T content in the non-coding (both 64.5%) is higher than in the coding (60.2% and 60.1%) region. Forty-four and forty-one simple sequence repeat (SSR) loci are identified in the S. buergeriana and S. takesimensis plastomes, respectively. In phylogenetic analysis, the genus Scrophularia shows closed relationship with Plantaginaceae.

The complete plastid genome sequence of Abies koreana (Pinaceae: Abietoideae).

The nucleotide sequence of the chloroplast genome from Abies koreana is the first to have complete genome sequence from genus Abies of family Pinaceae. The circular double-stranded DNA, which consists of 121,373 base pairs (bp), contains a pair of very short inverted repeat regions (IRa and IRb) of 264 bp each, which are separated by a small and large single-copy regions (SSC and LSC) of 54,197 and 66,648 bp, respectively. The genome contents of 114 genes (68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames and one pseudogene) are similar to the chloroplast DNA of other species of Abietoideae. Loss of ndh genes was also identified in the genome of A. koreana like other genomes in the family Pinaceae. Thirteen genes contain one (11 genes) or two (rps12 and ycf3 genes) introns. In phylogenetic analysis, the tree confirms that Abies, Keteleeria and Cedrus are strongly supported as monophyletic. Other inverted repeat sequences located in 42-kb inversion points (1186 bp) include trnS-psaM-ycf12- ψtrnG genes.

The complete plastid genome sequence of Picea jezoensis (Pinaceae: Piceoideae).

The nucleotide sequence of the complete chloroplast genome of P. jezoensis was completed. The total genome size was 124 146 bp, containing a pair of very short inverted repeats (IRa and IRb) of 422 bp, which were separated by large single copy (LSC) and small single copy (SSC) with 66 956 bp and 56 346 bp, respectively. The overall GC contents of the plastid genome were determined as 38.8%. One hundred fifteen genes including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open-reading frames, and two pseudogenes were annotated. In these genes, 15 genes contained only one or two introns. Phylogenetic analyses using maximum likelihood (ML) methods were performed from fully sequenced Gymnosperms and other species of dataset composed of 69 protein-coding genes.

Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L.

Sesamum indicum is an important crop plant species for yielding oil. The complete chloroplast (cp) genome of S. indicum (GenBank acc no. JN637766) is 153,324 bp in length, and has a pair of inverted repeat (IR) regions consisting of 25,141 bp each. The lengths of the large single copy (LSC) and the small single copy (SSC) regions are 85,170 bp and 17,872 bp, respectively. Comparative cp DNA sequence analyses of S. indicum with other cp genomes reveal that the genome structure, gene order, gene and intron contents, AT contents, codon usage, and transcription units are similar to the typical angiosperm cp genomes. Nucleotide diversity of the IR region between Sesamum and three other cp genomes is much lower than that of the LSC and SSC regions in both the coding region and noncoding region. As a summary, the regional constraints strongly affect the sequence evolution of the cp genomes, while the functional constraints weakly affect the sequence evolution of cp genomes. Five short inversions associated with short palindromic sequences that form step-loop structures were observed in the chloroplast genome of S. indicum. Twenty-eight different simple sequence repeat loci have been detected in the chloroplast genome of S. indicum. Almost all of the SSR loci were composed of A or T, so this may also contribute to the A-T richness of the cp genome of S. indicum. Seven large repeated loci in the chloroplast genome of S. indicum were also identified and these loci are useful to developing S. indicum-specific cp genome vectors. The complete cp DNA sequences of S. indicum reported in this paper are prerequisite to modifying this important oilseed crop by cp genetic engineering techniques.

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.