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Luan H, Song D, Huang K, Li S, Xu H, Kachroo P, Kachroo A, Zhao L. Genome-wide analysis of the soybean eEF gene family and its involvement in virus resistance. FRONTIERS IN PLANT SCIENCE 2024; 15:1421221. [PMID: 39224853 PMCID: PMC11366645 DOI: 10.3389/fpls.2024.1421221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024]
Abstract
Eukaryotic elongation factors (eEFs) are protein factors that mediate the extension of peptide chain, among which eukaryotic elongation factor 1 alpha (eEF1A) is one of the most abundant protein synthesis factors. Previously we showed that the P3 protein of Soybean mosaic virus (SMV), one of the most destructive and successful viral pathogens of soybean, targets a component of the soybean translation elongation complex to facilitate its pathogenesis. Here, we conducted a systematic analyses of the soybean eEF (GmeEF) gene family in soybean and examinedits role in virus resistance. In this study, GmeEF family members were identified and characterized based on sequence analysis. The 42 members, which were unevenly distributed across the 15 chromosomes, were renamed according to their chromosomal locations. The GmeEF members were further divided into 12 subgroups based on conserved motif, gene structure, and phylogenetic analyses. Analysis of the promoter regions showed conspicuous presence of myelocytomatosis (MYC) and ethylene-responsive (ERE) cis-acting elements, which are typically involved in drought and phytohormone response, respectively, and thereby in plant stress response signaling. Transcriptome data showed that the expression of 15 GmeEF gene family members changed significantly in response to SMV infection. To further examine EF1A function in pathogen response, three different Arabidopsis mutants carrying T-DNA insertions in orthologous genes were analyzed for their response to Turnip crinkle virus (TCV) and Cucumber mosaic virus (CMV). Results showed that there was no difference in viral response between the mutants and the wild type plants. This study provides a systematic analysis of the GmeEF gene family through analysis of expression patterns and predicted protein features. Our results lay a foundation for understanding the role of eEF gene in soybean anti-viral response.
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Affiliation(s)
- Hexiang Luan
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Daiqiao Song
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Kai Huang
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Shuxin Li
- Institute of Plant Genetic Engineering, College of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hao Xu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Pradeep Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States
| | - Longgang Zhao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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Han FY, Wu RX, Miao BB, Niu SF, Wang QH, Liang ZB. Whole-Genome Sequencing Analyses Reveal the Whip-like Tail Formation, Innate Immune Evolution, and DNA Repair Mechanisms of Eupleurogrammus muticus. Animals (Basel) 2024; 14:434. [PMID: 38338077 PMCID: PMC10854985 DOI: 10.3390/ani14030434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Smallhead hairtail (Eupleurogrammus muticus) is an important marine economic fish distributed along the northern Indian Ocean and the northwest Pacific coast; however, little is known about the mechanism of its genetic evolution. This study generated the first genome assembly of E. muticus at the chromosomal level using a combination of PacBio SMRT, Illumina Nova-Seq, and Hi-C technologies. The final assembled genome size was 709.27 Mb, with a contig N50 of 25.07 Mb, GC content of 40.81%, heterozygosity rate of 1.18%, and repetitive sequence rate of 35.43%. E. muticus genome contained 21,949 protein-coding genes (97.92% of the genes were functionally annotated) and 24 chromosomes. There were 143 expansion gene families, 708 contraction gene families, and 4888 positively selected genes in the genome. Based on the comparative genomic analyses, we screened several candidate genes and pathways related to whip-like tail formation, innate immunity, and DNA repair in E. muticus. These findings preliminarily reveal some molecular evolutionary mechanisms of E. muticus at the genomic level and provide important reference genomic data for the genetic studies of other trichiurids.
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Affiliation(s)
- Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Ben-Ben Miao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China;
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
| | - Qing-Hua Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Sciences School, Sun Yat-sen University, Guangzhou 510275, China;
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China; (F.-Y.H.); (S.-F.N.); (Z.-B.L.)
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