DNA methylation regulates growth traits by influencing metabolic pathways in Pacific white shrimp (Litopenaeus vannamei)

被引：0

作者：

Zhang, Xin ^{[1
]}

Hu, Chaoqun ^{[1
]}

Chen, Ting ^{[1
]}

Li, Pengying ^{[2
]}

Tan, Yehui ^{[1
]}

Ren, Chunhua ^{[1
]}

Wang, Yanhong ^{[1
]}

Jiang, Xiao ^{[1
]}

Ma, Bo ^{[1
,3
]}

Yin, Jiayue ^{[1
,3
]}

Huang, Yunyi ^{[1
,3
]}

Liu, Liyan ^{[4
]}

Li, Huo ^{[5
]}

Luo, Peng ^{[1
]}

机构：

[1] Chinese Acad Sci, South China Sea Inst Oceanol, Key Lab Breeding Biotechnol & Sustainable Aquacult, Guangdong Prov Key Lab Appl Marine Biol LAMB, Guangzhou, Peoples R China

[2] Shanghai Ocean Univ, Shanghai, Peoples R China

[3] Univ Chinese Acad Sci, Beijing, Peoples R China

[4] Yuehai Feed Grp Co Ltd, Zhanjiang, Peoples R China

[5] Guangdong Jinyang Biotechnol Co Ltd, Maoming, Peoples R China

来源：

BMC GENOMICS | 2025年 / 26卷 / 01期

关键词：

Litopenaeus vannamei; Growth trait; DNA methylation; Gene expression; MESSENGER-RNA EXPRESSION; IMMUNE-RESPONSES; RESISTANCE; TOLERANCE;

D O I：

10.1186/s12864-025-11688-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

BackgroundDNA methylation is a critical epigenetic modification that dynamically regulates gene expression associated with economic traits. Pacific white shrimp (Litopenaeus vannamei) is one of the most important aquatic species for culturing, and growth trait is one of the most important economic traits for its production. However, research on DNA methylation regulation of growth traits is still at an early stage. This study explored DNA methylome dynamics and their associations with the regulatory mechanism behind growth traits using full-subfamily individuals with discrepant growth performance.ResultsThe DNA methylation-related genes in L. vannamei were identified, and the expression of DNA methylation genes showed significantly higher levels in the slow growth (SG) group compared to the fast-growing (FG) individuals. The Whole Genome Bisulfite Sequencing (WGBS) analysis revealed that the methylation levels in the muscles of shrimp were notably decreased in SG individuals compared to FG individuals. A total of 532 differentially methylated promoters and 2,067 differentially methylated regions were identified. Through integrative analysis of DNA methylation and transcriptomic data from SG and FG group shrimp, a total of 47 genes were screened out with differential methylation levels (DMGs) and expression levels (DEGs). Functional enrichment analysis revealed that the overlapping DEGs/DMGs were enriched mainly in metabolic pathways, starch and sucrose metabolism, linoleic acid metabolism, ascorbate and aldarate metabolism, pentose and glucuronate interconversions.ConclusionsDNA methylation plays a role in the regulation of growth traits in L. vannamei. The level of DNA methylation was found to be negatively correlated with growth traits. Through comprehensive analysis, it was discovered that DNA methylation predominantly affects growth performance by up-regulating the expression of genes involved in metabolic pathways, such as glucose metabolism and amino acid metabolism in L. vannamei. This suggests a higher metabolism activity in SG individuals derived DNA methylation to cope with some unknown internal stress or environmental stress rather than being allocated for growth.

引用

页数：14

共 70 条

[1] Accumulation of Palmitoylcarnitine and Its Effect on Pro-Inflammatory Pathways and Calcium Influx in Prostate Cancer [J].

Al-Bakheit, Ala'a ;

Traka, Maria ;

Saha, Shikha ;

Mithen, Richard ;

Melchini, Antonietta .

PROSTATE, 2016, 76 (14) :1326-1337

[2] Gene Body Methylation Patterns in Daphnia Are Associated with Gene Family Size [J].

Asselman, Jana ;

De Coninck, Dieter I. M. ;

Pfrender, Michael E. ;

De Schamphelaere, Karel A. C. .

GENOME BIOLOGY AND EVOLUTION, 2016, 8 (04) :1185-1196

[3] The MEME Suite [J].

Bailey, Timothy L. ;

Johnson, James ;

Grant, Charles E. ;

Noble, William S. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W39-W49

[4] DNA Methylation Dynamics in Atlantic Salmon (Salmo salar) Challenged With High Temperature and Moderate Hypoxia [J].

Beemelmanns, Anne ;

Ribas, Laia ;

Anastasiadi, Dafni ;

Moraleda-Prados, Javier ;

Zanuzzo, Fabio S. ;

Rise, Matthew L. ;

Gamperl, A. Kurt .

FRONTIERS IN MARINE SCIENCE, 2021, 7

[5]

Bommarito PA, 2019, TOXICOEPIGENETICS: CORE PRINCIPLES AND APPLICATIONS, P127, DOI 10.1016/B978-0-12-812433-8.00005-8

[6] Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator [J].

Bonasio, Roberto ;

Li, Qiye ;

Lian, Jinmin ;

Mutti, Navdeep S. ;

Jin, Lijun ;

Zhao, Hongmei ;

Zhang, Pei ;

Wen, Ping ;

Xiang, Hui ;

Ding, Yun ;

Jin, Zonghui ;

Shen, Steven S. ;

Wang, Zongji ;

Wang, Wen ;

Wang, Jun ;

Berger, Shelley L. ;

Liebig, Juergen ;

Zhang, Guojie ;

Reinberg, Danny .

CURRENT BIOLOGY, 2012, 22 (19) :1755-1764

[7] TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data [J].

Chen, Chengjie ;

Chen, Hao ;

Zhang, Yi ;

Thomas, Hannah R. ;

Frank, Margaret H. ;

He, Yehua ;

Xia, Rui .

MOLECULAR PLANT, 2020, 13 (08) :1194-1202

[8] DNA Methyltransferases, DNA Methylation, and Age-Associated Cognitive Function [J].

Cui, Di ;

Xu, Xiangru .

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2018, 19 (05)

[9] Comparative transcriptome analysis of the Pacific White Shrimp (Litopenaeus vannamei) muscle reveals the molecular basis of residual feed intake [J].

Dai, Ping ;

Luan, Sheng ;

Lu, Xia ;

Luo, Kun ;

Kong, Jie .

SCIENTIFIC REPORTS, 2017, 7

[10] Widespread dynamic DNA methylation in response to biotic stress [J].

Dowen, Robert H. ;

Pelizzola, Mattia ;

Schmitz, Robert J. ;

Lister, Ryan ;

Dowen, Jill M. ;

Nery, Joseph R. ;

Dixon, Jack E. ;

Ecker, Joseph R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (32) :E2183-E2191

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