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15. Additional file 5 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

Author

Zhou, Yanli, Zhang, Chengjun, Zhang, Li, Ye, Qiannan, Liu, Ningyawen, Wang, Muhua, Long, Guangqiang, Fan, Wei, Long, Manyuan, and Wing, Rod A.

Subjects
fungi, food and beverages
Abstract

Additional file 5: Supplemental figures. Figure S1. Expression profiles of fusion genes and their parent genes in O. sativa v.g. japonica and other sibling species like O. barthii, O. glaberrima, O. punctata, O. brchyantha and O. Leersia; Figure S2. Statistics of expression levels between long homolog and short homolog; Figure S3. Expression heat map of two selected fusion genes in response to abiotic stress; Figure S4. Spatial expression pattern of 69 expressed fusion genes; Figure S5. Generation of transgenic rice plants. (A) Embryogenic callus derived from the scutella of mature seeds. (B) Subculture elite callus for proliferation. (C) Inoculation of callus with Agrobacterium carrying CRISPR/Cas9 vector by co-culture. (D) Screen hygromycin-resistant callus by transferring to selective medium. (E) Regeneration of hygromycin-resistant callus on MS medium for 1 month. (F) Rooting and growth of transgenic rice plants.

Published
2022
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21. Genome and GWAS analysis identified genes significantly related to phenotypic state of Rhododendronbark

Author

Ye, Qiannan, Zhang, Lu, Li, Qing, Ji, Yaliang, Zhou, Yanli, Wu, Zhenzhen, Hu, Yanting, Ma, Yongpeng, Wang, Jihua, and Zhang, Chengjun

Abstract

As an important horticultural plant, Rhododendronis often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and make the breeding of new varieties require a longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi(30 samples), R. irroratum(30 samples) and their F1generation R. agastum(200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5 328 800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600and Rhdel08G0220700in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.

Published
2024
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22. Occurrence of dark septate endophytes in Phragmites australisin Baiyang Lake and their resistance to Cd stress

Author

XU, Minghui, LI, Xia, YE, Qiannan, GONG, Feng, and HE, Xueli

Abstract

Heavy metal pollution poses a serious hazard to human health, and microbial remediation of heavy metals in soil has been widely studied. A group of ascomycetes classified as dark septate endophytes (DSEs) colonize plant roots and benefit host plants under abiotic stress conditions. In this study, Phragmites australis, a common remediation plant in Baiyang Lake, was investigated. The root system and soil of P. australiswere collected in typical heavy metal-contaminated sites, and the species diversity and community structure of DSEs in P. australisroots were studied. In addition, DSE strains were isolated, cultured, and tested for their tolerance to Cd stress. The results showed that DSEs occur extensively in P. australisroots, forming typical dark septate hyphae, with a total colonization rate of 19.7–83.1%. Morphological and ITS sequencing analyses were used to identify 10 DSE fungi in 9 genera. Among these fungi, 6 strains with considerable resistance to Cd stress were identified. The biomass values of Poaceascoma helicoides, Alternaria doliconidium, and Acrocalymma vagumstrains increased as the Cd concentration increased. These results can not only help to understand plant-DSE interactions in wetland environments, but also provide a theoretical basis for making full use of DSE fungi to alleviate heavy metals in soil.

Published
2024
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24. Salidroside Inhibits CCl4-Induced Liver Fibrosis in Mice by Reducing Activation and Migration of HSC Induced by Liver Sinusoidal Endothelial Cell-Derived Exosomal SphK1.

Author

Ye, Qiannan, Zhou, Yang, Zhao, Changqing, Xu, Lieming, and Ping, Jian

Subjects
ASPARTATE aminotransferase, LIVER cells, SPHINGOSINE kinase, LIVER, ALANINE aminotransferase, FIBROSIS
Abstract

Sphingosine kinase 1 (SphK1)/Sphingosine-1-phosphate (S1P)/S1PRs signaling pathway is known to involve the advancement of liver fibrosis. Exosomal SphK1 promotes hepatic stellate cells (HSC) migration. Salidroside (Sal) inhibits liver fibrosis, but its mechanism is yet to be elucidated. This study was to explore the influences of Sal on the SphK/S1P/S1PRs signaling pathway in liver fibrosis induced by carbon tetrachloride (CCl4) in vivo , and investigated the mechanism of Sal affecting the migration and activation of HSC triggered by exosomal SphK1 in vitro. Our data showed that Sal reduced the activities of alanine transaminase (ALT), aspartate aminotransferase (AST) in serum, and hydroxyproline (Hyp) content in the liver tissue. Sal subdued the expression of α-smooth muscle actin (α-SMA), fibronectin (FN) and type I collagen (Col I) of the liver. Sal also reduced mitochondria-induced hepatocyte apoptosis and to inhibit JNK activation. Furthermore, Sal remarkably eradicated the influence of SphK1, SphK2, S1P, and S1PRs triggered by CCl4, whether stimulating or hindering. Compared with serum-derived exosomes from model group mice, serum-derived exosomes from Sal group mice expressed lower SphK1 and reduced JS 1 (mouse HSC cell line) migration. In addition, Sal was also observed to subdue Col I expression, AKT activation, and LX-2 migration induced by exosomal SphK1 from SK-HEP-1 (a kind of liver sinusoidal endothelial cells (LSEC) cell line). In conclusion, Sal could effectively alleviate liver injury, hepatocyte apoptosis, and liver fibrosis in vivo , providing supports that the protective effects of Sal might be realized by suppressing JNK activation and modulating the SphK/S1P/S1PRs axis. In vitro , it was observed that Sal might alleviate LX-2 migration and activation induced by exosomal SphK1 by inhibiting the AKT activation. [ABSTRACT FROM AUTHOR]

Published
2021
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25. Salidroside Inhibits CCl 4 -Induced Liver Fibrosis in Mice by Reducing Activation and Migration of HSC Induced by Liver Sinusoidal Endothelial Cell-Derived Exosomal SphK1.

Author

Ye Q, Zhou Y, Zhao C, Xu L, and Ping J

Abstract

Sphingosine kinase 1 (SphK1)/Sphingosine-1-phosphate (S1P)/S1PRs signaling pathway is known to involve the advancement of liver fibrosis. Exosomal SphK1 promotes hepatic stellate cells (HSC) migration. Salidroside (Sal) inhibits liver fibrosis, but its mechanism is yet to be elucidated. This study was to explore the influences of Sal on the SphK/S1P/S1PRs signaling pathway in liver fibrosis induced by carbon tetrachloride (CCl 4 ) in vivo , and investigated the mechanism of Sal affecting the migration and activation of HSC triggered by exosomal SphK1 in vitro . Our data showed that Sal reduced the activities of alanine transaminase (ALT), aspartate aminotransferase (AST) in serum, and hydroxyproline (Hyp) content in the liver tissue. Sal subdued the expression of α-smooth muscle actin (α-SMA), fibronectin (FN) and type I collagen (Col I) of the liver. Sal also reduced mitochondria-induced hepatocyte apoptosis and to inhibit JNK activation. Furthermore, Sal remarkably eradicated the influence of SphK1, SphK2, S1P, and S1PRs triggered by CCl 4 , whether stimulating or hindering. Compared with serum-derived exosomes from model group mice, serum-derived exosomes from Sal group mice expressed lower SphK1 and reduced JS 1 (mouse HSC cell line) migration. In addition, Sal was also observed to subdue Col I expression, AKT activation, and LX-2 migration induced by exosomal SphK1 from SK-HEP-1 (a kind of liver sinusoidal endothelial cells (LSEC) cell line). In conclusion, Sal could effectively alleviate liver injury, hepatocyte apoptosis, and liver fibrosis in vivo , providing supports that the protective effects of Sal might be realized by suppressing JNK activation and modulating the SphK/S1P/S1PRs axis. In vitro , it was observed that Sal might alleviate LX-2 migration and activation induced by exosomal SphK1 by inhibiting the AKT activation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ye, Zhou, Zhao, Xu and Ping.)

Published
2021
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