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Li Z, Liu J, Liang M, Guo Y, Chen X, Wu H, Jin S. De novo assembly of the complete mitochondrial genome of pepino (Solanum muricatum) using PacBio HiFi sequencing: insights into structure, phylogenetic implications, and RNA editing. BMC PLANT BIOLOGY 2024; 24:361. [PMID: 38702620 PMCID: PMC11069145 DOI: 10.1186/s12870-024-04978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/02/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND Solanum muricatum is an emerging horticultural fruit crop with rich nutritional and antioxidant properties. Although the chromosome-scale genome of this species has been sequenced, its mitochondrial genome sequence has not been reported to date. RESULTS PacBio HiFi sequencing was used to assemble the circular mitogenome of S. muricatum, which was 433,466 bp in length. In total, 38 protein-coding, 19 tRNA, and 3 rRNA genes were annotated. The reticulate mitochondrial conformations with multiple junctions were verified by polymerase chain reaction, and codon usage, sequence repeats, and gene migration from chloroplast to mitochondrial genome were determined. A collinearity analysis of eight Solanum mitogenomes revealed high structural variability. Overall, 585 RNA editing sites in protein coding genes were identified based on RNA-seq data. Among them, mttB was the most frequently edited (52 times), followed by ccmB (46 times). A phylogenetic analysis based on the S. muricatum mitogenome and those of 39 other taxa (including 25 Solanaceae species) revealed the evolutionary and taxonomic status of S. muricatum. CONCLUSIONS We provide the first report of the assembled and annotated S. muricatum mitogenome. This information will help to lay the groundwork for future research on the evolutionary biology of Solanaceae species. Furthermore, the results will assist the development of molecular breeding strategies for S. muricatum based on the most beneficial agronomic traits of this species.
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Affiliation(s)
- Ziwei Li
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jiaxun Liu
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Mingtai Liang
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Yanbing Guo
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xia Chen
- Horticultural Research Institute Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, 650205, China
| | - Hongzhi Wu
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shoulin Jin
- Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Lin HH, Hsu JY, Tseng CY, Huang XY, Tseng HC, Chen JH. Hepatoprotective Activity of Nelumbo nucifera Gaertn. Seedpod Extract Attenuated Acetaminophen-Induced Hepatotoxicity. Molecules 2022; 27:molecules27134030. [PMID: 35807275 PMCID: PMC9268144 DOI: 10.3390/molecules27134030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 01/27/2023] Open
Abstract
The aim is to investigate the effect of lotus (Nelumbo nucifera Gaertn.) seedpod extract (LSE) on acetaminophen (APAP)-induced hepatotoxicity. LSE is rich in polyphenols and has potent antioxidant capacity. APAP is a commonly used analgesic, while APAP overdose is the main reason for drug toxicity in the liver. Until now, there has been no in vitro test of LSE in drug-induced hepatotoxicity responses. LSEs were used to evaluate the effect on APAP-induced cytotoxicity, ROS level, apoptotic rate, and molecule mechanisms. The co-treatment of APAP and LSEs elevated the survival rate and decreased intracellular ROS levels on HepG2 cells. LSEs treatment could significantly reduce APAP-induced HepG2 apoptosis assessed by DAPI and Annexin V/PI. The further molecule mechanisms indicated that LSEs decreased Fas/FasL binding and reduced Bax and tBid to restore mitochondrial structure and subsequently suppress downstream apoptosis cascade activation. These declines in COX-2, NF-κB, and iNOS levels were observed in co-treatment APAP and LSEs, which indicated that LSEs could ameliorate APAP-induced inflammation. LSE protected APAP-induced apoptosis by preventing extrinsic, intrinsic, and JNK-mediated pathways. In addition, the restoration of mitochondria and inflammatory suppression in LSEs treatments indicated that LSEs could decrease oxidative stress induced by toxic APAP. Therefore, LSE could be a novel therapeutic option for an antidote against overdose of APAP.
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Affiliation(s)
- Hui-Hsuan Lin
- Department of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung City 40201, Taiwan;
| | - Jen-Ying Hsu
- Department of Nutrition, Chung Shan Medical University, Taichung City 40201, Taiwan; (J.-Y.H.); (C.-Y.T.); (X.-Y.H.)
| | - Chiao-Yun Tseng
- Department of Nutrition, Chung Shan Medical University, Taichung City 40201, Taiwan; (J.-Y.H.); (C.-Y.T.); (X.-Y.H.)
| | - Xiao-Yin Huang
- Department of Nutrition, Chung Shan Medical University, Taichung City 40201, Taiwan; (J.-Y.H.); (C.-Y.T.); (X.-Y.H.)
| | - Hsien-Chun Tseng
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung City 40201, Taiwan
- Department of Radiation Oncology, School of Medicine, Chung Shan Medical University, Taichung City 40201, Taiwan
- Correspondence: (H.-C.T.); (J.-H.C.); Tel.: +886-4-24730022 (ext. 12195) (J.-H.C.); Fax: +886-4-23248175 (J.-H.C.)
| | - Jing-Hsien Chen
- Department of Nutrition, Chung Shan Medical University, Taichung City 40201, Taiwan; (J.-Y.H.); (C.-Y.T.); (X.-Y.H.)
- Department of Radiation Oncology, Chung Shan Medical University Hospital, Taichung City 40201, Taiwan
- Correspondence: (H.-C.T.); (J.-H.C.); Tel.: +886-4-24730022 (ext. 12195) (J.-H.C.); Fax: +886-4-23248175 (J.-H.C.)
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Song X, Liu H, Shen S, Huang Z, Yu T, Liu Z, Yang Q, Wu T, Feng S, Zhang Y, Wang Z, Duan W. Chromosome-level pepino genome provides insights into genome evolution and anthocyanin biosynthesis in Solanaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1128-1143. [PMID: 35293644 DOI: 10.1111/tpj.15728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high-quality, chromosome-level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequences. In addition to the shared ancient whole-genome triplication (WGT) event in eudicots, an additional new WGT event was present in the pepino. Our findings suggest that pepinos experienced chromosome rearrangements, fusions, and gene loss after a WGT event. The large number of gene removals indicated the instability of Solanaceae genomes, providing opportunities for species divergence and natural selection. The paucity of disease-resistance genes (NBS) in pepino and eggplant has been explained by extensive loss and limited generation of genes after WGT events in Solanaceae. The outbreak of NBS genes was not synchronized in Solanaceae species, which occurred before the Solanaceae WGT event in pepino, tomato, and tobacco, whereas it was almost synchronized with WGT events in the other four Solanaceae species. Transcriptome and comparative genomic analyses revealed several key genes involved in anthocyanin biosynthesis. Although an extra WGT event occurred in Solanaceae, CHS genes related to anthocyanin biosynthesis in grapes were still significantly expanded compared with those in Solanaceae species. Proximal and tandem duplications contributed to the expansion of CHS genes. In conclusion, the pepino genome and annotation facilitate further research into important gene functions and comparative genomic analysis in Solanaceae.
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Affiliation(s)
- Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Haibin Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shaoqin Shen
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhinan Huang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - Tong Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhuo Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Qihang Yang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Tong Wu
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shuyan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yu Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Zhiyuan Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Weike Duan
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
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Aqueous Extract of Pepino Leaves Ameliorates Palmitic Acid-Induced Hepatocellular Lipotoxicity via Inhibition of Endoplasmic Reticulum Stress and Apoptosis. Antioxidants (Basel) 2021; 10:antiox10060903. [PMID: 34204987 PMCID: PMC8227507 DOI: 10.3390/antiox10060903] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/17/2022] Open
Abstract
Saturated fatty acid is one of the important nutrients, but contributes to lipotoxicity in the liver, causing hepatic steatosis. Aqueous pepino leaf extract (AEPL) in the previous study revealed alleviated liver lipid accumulation in metabolic syndrome mice. The study aimed to investigate the mechanism of AEPL on saturated long-chain fatty acid-induced lipotoxicity in HepG2 cells. Moreover, the phytochemical composition of AEPL was identified in the present study. HepG2 cells treated with palmitic acid (PA) were used for exploring the effect of AEPL on lipid accumulation, apoptosis, ER stress, and antioxidant response. The chemical composition of AEPL was analyzed by HPLC-ESI-MS/MS. AEPL treatment reduced PA-induced ROS production and lipid accumulation. Further molecular results revealed that AEPL restored cytochrome c in mitochondria and decreased caspase 3 activity to cease apoptosis. In addition, AEPL in PA-stressed HepG2 cells significantly reduced the ER stress and suppressed SREBP-1 activation for decreasing lipogenesis. For defending PA-induced oxidative stress, AEPL promoted Nrf2 expression and its target genes, SOD1 and GPX3, expressions. The present study suggested that AEPL protected from PA-induced lipotoxicity through reducing ER stress, increasing antioxidant ability, and inhibiting apoptosis. The efficacy of AEPL on lipotoxicity was probably concerned with kaempferol and isorhamnetin derived compounds.
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