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10. Plastid phylogenomic insights into relationships of all flowering plant families

Author

Li, Hong-Tao, Luo, Yang, Gan, Lu, Ma, Peng-Fei, Gao, Lian-Ming, Yang, Jun-Bo, Cai, Jie, Gitzendanner, Matthew A., Fritsch, Peter W., Zhang, Ting, Jin, Jian-Jun, Zeng, Chun-Xia, Wang, Hong, Yu, Wen-Bin, Zhang, Rong, van der Bank, Michelle, Olmstead, Richard G., Hollingsworth, Peter M., Chase, Mark W., Soltis, Douglas E., Soltis, Pamela S., Yi, Ting-Shuang, and Li, De-Zhu

Published
2021
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12. Plastid phylogenomic insights into the evolution of Caryophyllales

Author

Yao, Gang, Jin, Jian-Jun, Li, Hong-Tao, Yang, Jun-Bo, Mandala, Venkata Shiva, Croley, Matthew, Mostow, Rebecca, Douglas, Norman A., Chase, Mark W., Christenhusz, Maarten J.M., Soltis, Douglas E., Soltis, Pamela S., Smith, Stephen A., Brockington, Samuel F., Moore, Michael J., Yi, Ting-Shuang, and Li, De-Zhu

Published
2019
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14. Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species.

Author

Zhao, Ying, Kipkoech, Amos, Li, Zhi-Peng, Xu, Ling, and Yang, Jun-Bo

Subjects
PLANT identification, PRODUCT counterfeiting, GENETIC barcoding, PLANT species, RESOURCE exploitation
Abstract

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Origin of angiosperms and the puzzle of the Jurassic gap

Author

Li, Hong-Tao, Yi, Ting-Shuang, Gao, Lian-Ming, Ma, Peng-Fei, Zhang, Ting, Yang, Jun-Bo, Gitzendanner, Matthew A., Fritsch, Peter W., Cai, Jie, Luo, Yang, Wang, Hong, van der Bank, Michelle, Zhang, Shu-Dong, Wang, Qing-Feng, Wang, Jian, Zhang, Zhi-Rong, Fu, Chao-Nan, Yang, Jing, Hollingsworth, Peter M., Chase, Mark W., Soltis, Douglas E., Soltis, Pamela S., and Li, De-Zhu

Published
2019
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28. Fungal diversity notes 491–602: taxonomic and phylogenetic contributions to fungal taxa

Author

Tibpromma, Saowaluck, Hyde, Kevin D., Jeewon, Rajesh, Maharachchikumbura, Sajeewa S. N., Liu, Jian-Kui, Bhat, D. Jayarama, Jones, E. B. Gareth, McKenzie, Eric H. C., Camporesi, Erio, Bulgakov, Timur S., Doilom, Mingkwan, de Azevedo Santiago, André Luiz Cabral Monteiro, Das, Kanad, Manimohan, Patinjareveettil, Gibertoni, Tatiana B., Lim, Young Woon, Ekanayaka, Anusha Hasini, Thongbai, Benjarong, Lee, Hyang Burm, Yang, Jun-Bo, Kirk, Paul M., Sysouphanthong, Phongeun, Singh, Sanjay K., Boonmee, Saranyaphat, Dong, Wei, Raj, K. N. Anil, Latha, K. P. Deepna, Phookamsak, Rungtiwa, Phukhamsakda, Chayanard, Konta, Sirinapa, Jayasiri, Subashini C., Norphanphoun, Chada, Tennakoon, Danushka S., Li, Junfu, Dayarathne, Monika C., Perera, Rekhani H., Xiao, Yuanpin, Wanasinghe, Dhanushka N., Senanayake, Indunil C., Goonasekara, Ishani D., de Silva, N. I., Mapook, Ausana, Jayawardena, Ruvishika S., Dissanayake, Asha J., Manawasinghe, Ishara S., Chethana, K. W. Thilini, Luo, Zong-Long, Hapuarachchi, Kalani Kanchana, Baghela, Abhishek, Soares, Adriene Mayra, Vizzini, Alfredo, Meiras-Ottoni, Angelina, Mešić, Armin, Dutta, Arun Kumar, de Souza, Carlos Alberto Fragoso, Richter, Christian, Lin, Chuan-Gen, Chakrabarty, Debasis, Daranagama, Dinushani A., Lima, Diogo Xavier, Chakraborty, Dyutiparna, Ercole, Enrico, Wu, Fang, Simonini, Giampaolo, Vasquez, Gianrico, da Silva, Gladstone Alves, Plautz, Jr., Helio Longoni, Ariyawansa, Hiran A., Lee, Hyun, Kušan, Ivana, Song, Jie, Sun, Jingzu, Karmakar, Joydeep, Hu, Kaifeng, Semwal, Kamal C., Thambugala, Kasun M., Voigt, Kerstin, Acharya, Krishnendu, Rajeshkumar, Kunhiraman C., Ryvarden, Leif, Jadan, Margita, Hosen, Md. Iqbal, Mikšík, Michal, Samarakoon, Milan C., Wijayawardene, Nalin N., Kim, Nam Kyu, Matočec, Neven, Singh, Paras Nath, Tian, Qing, Bhatt, R. P., de Oliveira, Rafael José Vilela, Tulloss, Rodham E., Aamir, S., Kaewchai, Saithong, Marathe, Sayali D., Khan, Sehroon, Hongsanan, Sinang, Adhikari, Sinchan, Mehmood, Tahir, Bandyopadhyay, Tapas Kumar, Svetasheva, Tatyana Yu., Nguyen, Thi Thuong Thuong, Antonín, Vladimír, Li, Wen-Jing, Wang, Yong, Indoliya, Yuvraj, Tkalčec, Zdenko, Elgorban, Abdallah M., Bahkali, Ali H., Tang, Alvin M. C., Su, Hong-Yan, Zhang, Huang, Promputtha, Itthayakorn, Luangsa-ard, Jennifer, Xu, Jianchu, Yan, Jiye, Ji-Chuan, Kang, Stadler, Marc, Mortimer, Peter E., Chomnunti, Putarak, Zhao, Qi, Phillips, Alan J. L., Nontachaiyapoom, Sureeporn, Wen, Ting-Chi, and Karunarathna, Samantha C.

Published
2017
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37. Blood Lead and High-Density Lipoprotein Concentrations in Relation to Human Blood Pressure: A Cross Sectional Study

Author

Hu, Biao, He, Pei-yao, Zhong, Nan-nan, Gao, Zi-min, Guo, Jiang-long, Feng, Jun-tao, Huang, Chu-qin, Yang, Jun-bo, and Sun, Dong-lin

Subjects
Nutrition and Dietetics, Endocrinology, Diabetes and Metabolism, Food Science
Abstract

BackgroundWhile the relationship between blood pressure and blood lead has been studied more extensively, the effect of high-density lipoprotein (HDL) concentration on this relationship remains uncertain. Therefore, this study aimed to determine the effect of HDL concentration on the relationship between blood lead and blood pressure.MethodsThe research used cross-sectional data from the 2005 to 2014 National Health and Nutrition Examination Survey (NHANES), which included 16,451 participants aged 20–60 years. Multivariable linear regression was used to evaluate the correlation among blood lead, systolic blood pressure (SBP), and diastolic blood pressure (DBP). HDL concentration was determined by low HDL concentration (≤ 49 mg/dl) and high HDL concentration (>49 mg/dl) stratified. The effect of HDL concentration was assessed by an interaction test between blood lead and SBP in multivariable linear regression.ResultsIn this cross-sectional research, we identified a positive correlation between blood lead and SBP, but not DBP. The relationship between blood lead and SBP was different in the group with low and high HDL concentrations (β: 0.21 95% Cl:−0.05-0.46 vs. β:0.47 95% Cl: 0.15-0.79). In addition, high HDL significantly altered the positive correlation between blood lead and SBP (P-value of interaction < 0.001).ConclusionThe study suggests an interaction between HDL and blood lead in elevating SBP, which may have important clinical implications.

Published
2022
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40. Hetero-Diels-Alder Reaction Coupled with Semipinacol Rearrangement for the Biosynthesis of Structurally Diversified Notoamides

Author

Liu, Shuai, primary, Xu, Wenqiang, additional, Cao, Ming-Ming, additional, Tang, Man-Cheng, additional, Chang, Yao-Wen, additional, Lei, Xin-Xiang, additional, Tang, Hong-Yu, additional, Yuan, Chunmao, additional, Yang, Jun-Bo, additional, Zuo, Zhili, additional, Zeng, Ying, additional, Shen, Yuemao, additional, Di, Ying-Tong, additional, Wu, Yun-dong, additional, and Hao, Xiaojiang, additional

Published
2022
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44. Genome Skimming Contributes to Clarifying Species Limits in Paris Section Axiparis (Melanthiaceae)

Author

Ji, Yunheng, Yang, Jin, Landis, Jacob B., Wang, Shuying, Jin, Lei, Xie, Pingxuan, Liu, Haiyang, Yang, Jun-Bo, and Yi, Ting-Shuang

Subjects
Plant Science
Abstract

Paris L. section Axiparis H. Li (Melanthiaceae) is a taxonomically perplexing taxon with considerable confusion regarding species delimitation. Based on the analyses of morphology and geographic distribution of each species currently recognized in the taxon, we propose a revision scheme that reduces the number of species in P. sect. Axiparis from nine to two. To verify this taxonomic proposal, we employed a genome skimming approach to recover the plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) regions of 51 individual plants across the nine described species of P. sect. Axiparis by sampling multiple accessions per species. The species boundaries within P. sect. Axiparis were explored using phylogenetic inference and three different sequence-based species delimitation methods (ABGD, mPTP, and SDP). The mutually reinforcing results indicate that there are two species-level taxonomic units in P. sect. Axiparis (Paris forrestii s.l. and P. vaniotii s.l.) that exhibit morphological uniqueness, non-overlapping distribution, genetic distinctiveness, and potential reproductive isolation, providing strong support to the proposed species delimitation scheme. This study confirms that previous morphology-based taxonomy overemphasized intraspecific and minor morphological differences to delineate species boundaries, therefore resulting in an overestimation of the true species diversity of P. sect. Axiparis. The findings clarify species limits and will facilitate robust taxonomic revision in P. sect. Axiparis.

Published
2022
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48. Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae)

Author

Qin, Ming, Zhu, Cheng‐jie, Yang, Jun‐bo, Vatanparast, Mohammad, Schley, Rowan, Lai, Qiang, Zhang, Dan‐yan, Tu, Tie‐yao, Klitgård, Bente B., Li, Shi‐jin, Zhang, Dian‐xiang, Qin, Ming, Zhu, Cheng‐jie, Yang, Jun‐bo, Vatanparast, Mohammad, Schley, Rowan, Lai, Qiang, Zhang, Dan‐yan, Tu, Tie‐yao, Klitgård, Bente B., Li, Shi‐jin, and Zhang, Dian‐xiang

Published
2022

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