Chloroplast genomes for 3Bidensplants endemic to China (Bidens bipinnataLinn.,Bidens pilosaLinn., andBidens albavar.radiata) have been sequenced, assembled and annotated in this study to distinguish their molecular characterization and phylogenetic relationships. The chloroplast genomes are in typical quadripartite structure with two inverted repeat regions separating a large single copy region and a small single copy region, and ranged from 151,599 to 154,478 bp in length. Similar number of SSRs and long repeats were found inBidens, wherein mononucleotide repeats (A/T), forward and palindromic repeats were the most in abundance. Gene loss ofclpPandpsbD, IR expansion and contraction were detected in theseBidensplants. It seems thatndhE,ndhF,ndhG, andrpl32from theBidensplants were under positive selection while the majority of chloroplast genes were under purifying selection. Phylogenetic analysis revealed that 3Bidensplants clustered together and further formed molophyletic clade with otherBidensspecies, indicatingBidensplants might be under radiation adaptive selection to the changing environment world-widely. Moreover, mutation hotspot analysis and in silico PCR analysis indicated that inter-genic regions ofndhD-ccsA,ndhI-ndhG, ndhF-rpl32, trnL_UAG-rpl32, ndhE-psaC, matK-rps16, rps2-atpI, cemA-petA,petN-psbMwere candidate markers of molecular identification forBidensplants. This study may provide useful information for genetic diversity analysis and molecular identification forBidensspecies.

Background: Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. Results: Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. Conclusion: The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.

Background: This study aimed to investigate the role of ROS/MAPK signaling pathways and the effects of baicalin in LPS-induced inflammatory responses in mice and porcine intestinal epithelial cells (IPEC-J2). Methods: In vivo, 18 male C57BL/6J mice were randomly divided into three groups (n = 6): control, LPS (3.5 mg/kg LPS administered intraperitoneally [ip] on day 7), and baicalin (200 mg/kg orally for 7 days, with LPS ip on day 7). On day 8, mice were sacrificed, and jejunal tissues were collected for H&E staining. ROS levels in serum and cytokine protein expressions (TNF-α and IL-6) in the jejunum were measured via ELISA, while intestinal MAPK proteins were analyzed using Western blotting. In vitro, the study involved two experimental setups: NAC (a ROS scavenger) and baicalin. For the NAC experiment, IPEC-J2 cells were divided into three groups: control, LPS, and NAC. In the LPS group, cells were treated with LPS (40 μg/mL) for 1 h. In the NAC group, cells were pretreated with NAC prior to LPS exposure. For the baicalin experiment, IPEC-J2 cells were divided into five groups: control, LPS, and baicalin at low (10 μM), medium (20 μM), and high (40 μM) doses. Cells were pretreated with baicalin for 24 h before LPS exposure. ROS/LDH levels and cytokine expressions in the supernatant were determined via ELISA, and MAPK protein expressions were assessed using Western blotting. Results: In vivo, LPS-induced oxidative stress and inflammatory responses in the intestine, reduced the villus height-to-crypt ratio, and significantly increased protein expressions of p-ERK, p-P38, JNK, and p-JNK (p < 0.05). Baicalin treatment significantly inhibited serum ROS levels (p < 0.01), reduced jejunal cytokine expressions (TNF-α and IL-6, p < 0.05), improved intestinal structural damage, and decreased p-ERK, p-P38, and p-JNK protein expressions (p < 0.05). In vitro, NAC significantly reduced ROS levels (p < 0.01), cytokine expressions (TNF-α and IL-6), and MAPK activation (ERK, JNK, P38, and their phosphorylated forms, p < 0.05). Baicalin also significantly decreased ROS (p < 0.05), TNF-α (p < 0.05), IL-6 (p < 0.05), and MAPK protein expressions (ERK, p-ERK, and p-P38, p < 0.05). Molecular docking demonstrated that baicalin effectively bound to ERK and P38 proteins. Conclusions: Baicalin mitigated LPS-induced inflammatory responses via the ROS/p-ERK/p-P38 signaling pathway in vivo and in vitro.

Patrinia monandra C. B. Clarke is traditionally used for the treatment of inflammation, typhoid fever, injuries due to falls, abdominal pain, malaria, and acute appendicitis ulcers in China and Korea. In this study, the complete chloroplast genome of P. monandra was sequenced using the Illumina HiSeq X-Ten platform. It had a circular shape and a length of 158,940 bp, with 38.51% GC content. It contained a large single-copy region of 87,641 bp, a small single-copy region of 12,807 bp, and two inverted repeat regions of 29,246 bp. In total, 128 different genes, including 83 protein-coding genes, 37 distinct tRNA genes, and eight rRNA genes, were identified. Maximum-likelihood phylogenomic analysis showed that P. monandra is closely related to Patrinia scabiosifolia and Patrinia villosa in the Valerianaceae family. There were 4535 variable sites, 157,354 conserved sites, and 3085 singleton sites in the six Patrinia chloroplast genomes.