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Huang J, Chen J, Shi M, Zheng J, Chen M, Wu L, Zhu H, Zheng Y, Wu Q, Wu F. Genome assembly provides insights into the genome evolution of Baccaurea ramiflora Lour. Sci Rep 2024; 14:4867. [PMID: 38418841 PMCID: PMC10901894 DOI: 10.1038/s41598-024-55498-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 03/02/2024] Open
Abstract
Baccaurea ramiflora Lour., an evergreen tree of the Baccaurea genus of the Phyllanthaceae family, is primarily distributed in South Asia, Southeast Asia, and southern China, including southern Yunnan Province. It is a wild or semi-cultivated tree species with ornamental, edible, and medicinal value, exhibiting significant development potential. In this study, we present the whole-genome sequencing of B. ramiflora, employing a combination of PacBio SMRT and Illumina HiSeq 2500 sequencing techniques. The assembled genome size was 975.8 Mb, with a contig N50 of 509.33 kb and the longest contig measuring 7.74 Mb. The genome comprises approximately 73.47% highly repetitive sequences, of which 52.1% are long terminal repeat-retrotransposon sequences. A total of 29,172 protein-coding genes were predicted, of which 25,980 (89.06%) have been annotated, Additionally, 3452 non-coding RNAs were identified. Comparative genomic analysis revealed a close relationship between B. ramiflora and the Euphorbiaceae family, with both being sister groups that diverged approximately 59.9 million years ago. During the evolutionary process, B. ramiflora exhibited positive selection in 278 candidate genes. Synonymous substitution rate and collinearity analysis demonstrated that B. ramiflora underwent a single ancient genome-wide triploidization event, without recent genome-wide duplication events. This high-quality B. ramiflora genome provides a valuable resource for basic research and tree improvement programs focusing on the Phyllanthaceae family.
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Affiliation(s)
- Jianjian Huang
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Jie Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Min Shi
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Jiaqi Zheng
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Ming Chen
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Linjun Wu
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Hui Zhu
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Yuzhong Zheng
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Qinghan Wu
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China
| | - Fengnian Wu
- School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, 521041, Guangdong, China.
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Wang Y, Wang J, Li H, Lao J, Jia D, Liu J, Wang J, Luo J, Guan G, Yin H, Li Y. Antioxidant effects of Bifidobacterium longum T37a in mice weight loss and aging model induced by D-galactose. BMC Microbiol 2023; 23:103. [PMID: 37061697 PMCID: PMC10105457 DOI: 10.1186/s12866-023-02846-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Probiotics can reduce free radical scavenging rate and oxidative damage, and improve activity of crucial antioxidative enzymes in host cells. This study aimed to isolate Bifidobacterium spp. from faeces of babies, and investigate the antioxidant effects of the Bif. longum T37a in mice weight loss and aging model induced by D-galactose. RESULTS T37a have good antioxidant properties in the DPPH assay and anti-lipid peroxidation test. Compared with the model group, T37a low group significantly increased the thymus index and the levels of T-AOC and GSH-Px of mice. T37a high group significantly decreased the spleen and liver index of mice and the levels of MDA in liver, significantly increased in liver HDL-C levels, and decreased LDL-C in liver. CONCLUSIONS T37a may be an anti-aging and weight-loss probiotics for its antioxidant capacity, and it is necessary to study further the molecular mechanism of T37a as antioxidant.
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Affiliation(s)
- Ya Wang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
- College of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Jiahui Wang
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
- College of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Hehai Li
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Jianlong Lao
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Dan Jia
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jinming Wang
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Youquan Li
- Department of Veterinary Medicine, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China.
- State Key Laboratory of Veterinary Etiological Biology/Key Laboratory of Veterinary Parasitology of Gansu Province/Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
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