1
|
Hatchett WJ, Jueterbock AO, Kopp M, Coyer JA, Coelho SM, Hoarau G, Lipinska AP. Evolutionary dynamics of sex-biased gene expression in a young XY system: insights from the brown alga genus Fucus. THE NEW PHYTOLOGIST 2023; 238:422-437. [PMID: 36597732 DOI: 10.1111/nph.18710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.
Collapse
Affiliation(s)
- William J Hatchett
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - James A Coyer
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, 03824, USA
| | - Susana M Coelho
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - Agnieszka P Lipinska
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
| |
Collapse
|
2
|
Chen M, Li M, Zhao L, Song H. Deciphering evolutionary dynamics of WRKY genes in Arachis species. BMC Genomics 2023; 24:48. [PMID: 36707767 PMCID: PMC9881300 DOI: 10.1186/s12864-023-09149-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Cultivated peanut (Arachis hypogaea), a progeny of the cross between A. duranensis and A. ipaensis, is an important oil and protein crop from South America. To date, at least six Arachis genomes have been sequenced. WRKY transcription factors (TFs) play crucial roles in plant growth, development, and response to abiotic and biotic stresses. WRKY TFs have been identified in A. duranensis, A. ipaensis, and A. hypogaea cv. Tifrunner; however, variations in their number and evolutionary patterns across various Arachis spp. remain unclear. RESULTS WRKY TFs were identified and compared across different Arachis species, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cultivars (cv.) Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The results showed that the WRKY TFs underwent dynamic equilibrium between diploid and tetraploid peanut species, characterized by the loss of old WRKY TFs and retention of the new ones. Notably, cultivated peanuts inherited more conserved WRKY orthologs from wild tetraploid peanuts than their wild diploid donors. Analysis of the W-box elements and protein-protein interactions revealed that different domestication processes affected WRKY evolution across cultivated peanut varieties. WRKY TFs of A. hypogaea cv. Fuhuasheng and Shitouqi exhibited a similar domestication process, while those of cv. Tifrunner of the same species underwent a different domestication process based on protein-protein interaction analysis. CONCLUSIONS This study provides new insights into the evolution of WRKY TFs in Arachis spp.
Collapse
Affiliation(s)
- Mingwei Chen
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Meiran Li
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Longgang Zhao
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- grid.412608.90000 0000 9526 6338Key Laboratory of National Forestry and Grassland Administration On Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, China ,grid.412608.90000 0000 9526 6338High-Efficiency Agricultural Technology Industry Research Institute of Saline and Alkaline Land of Dongying, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
3
|
Allen SR, Stewart RK, Rogers M, Ruiz IJ, Cohen E, Laederach A, Counter CM, Sawyer JK, Fox DT. Distinct responses to rare codons in select Drosophila tissues. eLife 2022; 11:e76893. [PMID: 35522036 PMCID: PMC9116940 DOI: 10.7554/elife.76893] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Codon usage bias has long been appreciated to influence protein production. Yet, relatively few studies have analyzed the impacts of codon usage on tissue-specific mRNA and protein expression. Here, we use codon-modified reporters to perform an organism-wide screen in Drosophila melanogaster for distinct tissue responses to codon usage bias. These reporters reveal a cliff-like decline of protein expression near the limit of rare codon usage in endogenously expressed Drosophila genes. Near the edge of this limit, however, we find the testis and brain are uniquely capable of expressing rare codon-enriched reporters. We define a new metric of tissue-specific codon usage, the tissue-apparent Codon Adaptation Index (taCAI), to reveal a conserved enrichment for rare codon usage in the endogenously expressed genes of both Drosophila and human testis. We further demonstrate a role for rare codons in an evolutionarily young testis-specific gene, RpL10Aa. Optimizing RpL10Aa codons disrupts female fertility. Our work highlights distinct responses to rarely used codons in select tissues, revealing a critical role for codon bias in tissue biology.
Collapse
Affiliation(s)
- Scott R Allen
- Department of Cell Biology, Duke UniversityDurhamUnited States
| | - Rebeccah K Stewart
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Michael Rogers
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Ivan Jimenez Ruiz
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Erez Cohen
- Department of Cell Biology, Duke UniversityDurhamUnited States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel HillChapel HillUnited States
| | | | - Jessica K Sawyer
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| | - Donald T Fox
- Department of Cell Biology, Duke UniversityDurhamUnited States
- Department of Pharmacology and Cancer Biology, Duke UniversityDurhamUnited States
| |
Collapse
|
4
|
Dong S, Zhang L, Pang W, Zhang Y, Wang C, Li Z, Ma L, Tang W, Yang G, Song H. Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:213-222. [PMID: 33707864 PMCID: PMC7907404 DOI: 10.1007/s12298-021-00938-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 06/09/2023]
Abstract
Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.
Collapse
Affiliation(s)
- Shuwei Dong
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Long Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wenhui Pang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Chang Wang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhenyi Li
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Lichao Ma
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Wei Tang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
5
|
Song H, Sun J, Yang G. Old and young duplicate genes reveal different responses to environmental changes in Arachis duranensis. Mol Genet Genomics 2019; 294:1199-1209. [PMID: 31076861 DOI: 10.1007/s00438-019-01574-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/03/2019] [Indexed: 11/24/2022]
Abstract
Old and young duplicate genes have been reported in some organisms. However, little is known about the properties of old and young duplicate genes in Arachis. Here, we have identified old and young duplicate genes in Arachis duranensis, and analyzed the evolution, gene complexity, gene expression pattern, and functional divergence between old and young duplicate genes. Our results showed different evolutionary, gene complexity and gene expression patterns, as well as differing correlations between old and young duplicate genes. Gene ontology results showed that old duplicate genes play a crucial role in lipid and amino acid biosynthesis and the oxidation-reduction process and that young duplicate genes are preferentially involved in photosynthesis and response to biotic stimulus. Transcriptome data sets revealed that most old and young duplicate genes had asymmetric function, and only a few duplicate genes exhibited symmetric function under drought and nematode stress. We found that old duplicate genes are preferentially involved in lipid and amino acid metabolism and response to abiotic stress, while young duplicate genes are likely to participate in photosynthesis and response to biotic stress. This work provides a better understanding of the evolution and functional divergence of old and young duplicate genes in A. duranensis.
Collapse
Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, China.
| |
Collapse
|
6
|
Song H, Sun J, Yang G. Comparative analysis of selection mode reveals different evolutionary rate and expression pattern in Arachis duranensis and Arachis ipaënsis duplicated genes. PLANT MOLECULAR BIOLOGY 2018; 98:349-361. [PMID: 30298428 DOI: 10.1007/s11103-018-0784-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Our results reveal that Ks is a determining factor affecting selective pressure and different evolution and expression patterns are detected between PSGs and NSGs in wild Arachis duplicates. Selective pressure, including purifying (negative) and positive selection, can be detected in organisms. However, studies on comparative evolutionary rates, gene expression patterns and gene features between negatively selected genes (NSGs) and positively selected genes (PSGs) are lagging in paralogs of plants. Arachis duranensis and Arachis ipaënsis are ancestors of the cultivated peanut, an important oil and protein crop. Here, we carried out a series of systematic analyses, comparing NSG and PSG in paralogs, using genome sequences and transcriptome datasets in A. duranensis and A. ipaënsis. We found that synonymous substitution rate (Ks) is a determining factor affecting selective pressure in A. duranensis and A. ipaënsis duplicated genes. Lower expression level, lower gene expression breadth, higher codon bias and shorter polypeptide length were found in PSGs and not in NSGs. The correlation analyses showed that gene expression breadth was positively correlated with polypeptide length and GC content at the first codon site (GC1) in PSGs and NSGs, respectively. There was a negative correlation between expression level and polypeptide length in PSGs. In NSGs, the Ks was positively correlated with expression level, gene expression breadth, GC1, and GC content at the third codon site (GC3), but selective pressure was negatively correlated with expression level, gene expression breadth, polypeptide length, GC1, and GC3 content. The function of most duplicated gene pairs was divergent under drought and nematode stress. Taken together, our results show that different evolution and expression patterns occur between PSGs and NSGs in paralogs of two wild Arachis species.
Collapse
Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, 700# Changcheng Road, Qingdao, China.
| |
Collapse
|
7
|
Song H, Sun W, Yang G, Sun J. WRKY transcription factors in legumes. BMC PLANT BIOLOGY 2018; 18:243. [PMID: 30332991 PMCID: PMC6192229 DOI: 10.1186/s12870-018-1467-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/03/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND WRKY transcription factors, so named because of the WRKYGQK heptapeptide at the N-terminal end, are widely distributed in plants and play an important role in physiological changes and response to biotic and abiotic stressors. Many previous studies have focused on the evolution of WRKY transcription factors in a given plant; however, little is known about WRKY evolution in legumes. The gene expression pattern of duplicated WRKY transcription factors remains unclear. RESULTS We first identified the WRKY proteins in 12 legumes. We found that the WRKYGQK heptapeptide tended to mutate into WRKYGKK. The Q site in WRKYGQK preferentially mutated, while W, K, and Y were conserved. The phylogenetic tree shows that the WRKY proteins in legumes have multiple origins, especially group IIc. For example, WRKY64 from Lupinus angustifolius (LaWRKY64) contains three WRKY domains, of which the first two clustered together in the N-terminal WRKY domain of the group I WRKY protein, and the third WRKY domain grouped in the C-terminal WRKY domain of the group I WRKY protein. Orthologous WRKY genes have a faster evolutionary rate and are subject to constrained selective pressure, unlike paralogous WRKY genes. Different gene features were observed between duplicated WRKY genes and singleton WRKY genes. Duplicated Glycine max WRKY genes with similar gene features have gene expression divergence. CONCLUSIONS We analyzed the WRKY number and type in 12 legumes, concluding that the WRKY proteins have multiple origins. A novel WRKY protein, LaWRKY64, was found in L. angustifolius. The first two WRKY domains of LaWRKY64 have the same origin. The orthologous and paralogous WRKY proteins have different evolutionary rates. Duplicated WRKY genes have gene expression divergence under normal growth conditions in G. max. These results provide insight into understanding WRKY evolution and expression.
Collapse
Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Weihong Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Guofeng Yang
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| | - Juan Sun
- Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao, 266109 China
| |
Collapse
|