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Hu H, Dong B, Fan X, Wang M, Wang T, Liu Q. Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2023; 16:11. [PMID: 36849744 PMCID: PMC9971424 DOI: 10.1186/s12284-023-00627-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.
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Affiliation(s)
- Huan Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Boran Dong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China
| | - Xiaoji Fan
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Meixia Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China
| | - Tingzhang Wang
- The Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, 310012, People's Republic of China.
| | - Qingpo Liu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A & F University, Lin'an, Hangzhou, 311300, People's Republic of China.
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Wang X, Wang C, Zhang Z, Shi G. Genome-wide Identification of Metal Tolerance Protein Genes in Peanut: Differential Expression in the Root of Two Contrasting Cultivars Under Metal Stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:791200. [PMID: 35432419 PMCID: PMC9011049 DOI: 10.3389/fpls.2022.791200] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/15/2022] [Indexed: 05/23/2023]
Abstract
Metal tolerance proteins (MTP) are Me2+/H+(K+) antiporters that play important roles in the transport of divalent cations in plants. However, their functions in peanut are unknown. In the present study, a total of 24 AhMTP genes were identified in peanut, which were divided into seven groups belonging to three substrate-specific clusters (Zn-CDFs, Zn/Fe-CDFs, and Mn-CDFs). All AhMTP genes underwent whole genome or segmental gene duplication events except AhMTP12. Most AhMTP members within the same subfamily or group generally have similar gene and protein structural characteristics. However, some genes, such as AhMTP1.3, AhMTP2.4, and AhMTP12, showed wide divergences. Most of AhMTP genes preferentially expressed in reproductive tissues, suggesting that these genes might play roles in metal transport during the pod and seed development stages. Excess metal exposure induced expressions for most of AhMTP genes in peanut roots depending on cultivars. By contrast, AhMTP genes in the root of Fenghua 1 were more sensitive to excess Fe, Cd, and Zn exposure than that of Silihong. Stepwise linear regression analysis showed that the percentage of Fe in shoots significantly and positively correlated with the expression of AhMTP4.1, AhMTP9.1, and AhMTPC4.1, but negatively correlated with that of AhMTPC2.1 and AhMTP12. The expression of AhMTP1.1 showed a significant and negative correlation with the percentage of Mn in shoots. The percentage of Zn in shoots was significantly and positively correlated with the expression of AhMTP2.1 but was negatively correlated with that of AhMTPC2.1. The differential responses of AhMTP genes to metal exposure might be, at least partially, responsible for the different metal translocation from roots to shoots between Fenghua 1 and Silihong.
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Aviña-Padilla K, Ramírez-Rafael JA, Herrera-Oropeza GE, Muley VY, Valdivia DI, Díaz-Valenzuela E, García-García A, Varela-Echavarría A, Hernández-Rosales M. Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Front Genet 2021; 12:654256. [PMID: 34306008 PMCID: PMC8302217 DOI: 10.3389/fgene.2021.654256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
The structure of eukaryotic genes is generally a combination of exons interrupted by intragenic non-coding DNA regions (introns) removed by RNA splicing to generate the mature mRNA. A fraction of genes, however, comprise a single coding exon with introns in their untranslated regions or are intronless genes (IGs), lacking introns entirely. The latter code for essential proteins involved in development, growth, and cell proliferation and their expression has been proposed to be highly specialized for neuro-specific functions and linked to cancer, neuropathies, and developmental disorders. The abundant presence of introns in eukaryotic genomes is pivotal for the precise control of gene expression. Notwithstanding, IGs exempting splicing events entail a higher transcriptional fidelity, making them even more valuable for regulatory roles. This work aimed to infer the functional role and evolutionary history of IGs centered on the mouse genome. IGs consist of a subgroup of genes with one exon including coding genes, non-coding genes, and pseudogenes, which conform approximately 6% of a total of 21,527 genes. To understand their prevalence, biological relevance, and evolution, we identified and studied 1,116 IG functional proteins validating their differential expression in transcriptomic data of embryonic mouse telencephalon. Our results showed that overall expression levels of IGs are lower than those of MEGs. However, strongly up-regulated IGs include transcription factors (TFs) such as the class 3 of POU (HMG Box), Neurog1, Olig1, and BHLHe22, BHLHe23, among other essential genes including the β-cluster of protocadherins. Most striking was the finding that IG-encoded BHLH TFs fit the criteria to be classified as microproteins. Finally, predicted protein orthologs in other six genomes confirmed high conservation of IGs associated with regulating neural processes and with chromatin organization and epigenetic regulation in Vertebrata. Moreover, this study highlights that IGs are essential modulators of regulatory processes, such as the Wnt signaling pathway and biological processes as pivotal as sensory organ developing at a transcriptional and post-translational level. Overall, our results suggest that IG proteins have specialized, prevalent, and unique biological roles and that functional divergence between IGs and MEGs is likely to be the result of specific evolutionary constraints.
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Affiliation(s)
- Katia Aviña-Padilla
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | | | - Gabriel Emilio Herrera-Oropeza
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Mexico
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London, United Kingdom
| | | | - Dulce I. Valdivia
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | - Erik Díaz-Valenzuela
- Centro de Investigacioìn y de Estudios Avanzados del IPN, Unidad Irapuato, Guanajuato, Mexico
| | - Andrés García-García
- Centro de Física Aplicada y Tecnología Avanzada, Universidad Nacional Autónoma de México, Querétaro, Mexico
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Jorquera R, González C, Clausen PTLC, Petersen B, Holmes DS. SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6122466. [PMID: 33507271 PMCID: PMC7904048 DOI: 10.1093/database/baab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/01/2020] [Accepted: 01/05/2021] [Indexed: 11/27/2022]
Abstract
Single-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases. Database URL:http://v2.sinex.cl/
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Affiliation(s)
- R Jorquera
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Zañartu 1482, Ñuñoa Santiago 7780132, Chile
- Laboratorio Medicina Traslacional, Fundación Arturo López Pérez, José Manuel Infante 805, Providencia, Santiago 7500691, Chile
| | - C González
- Center for Bioinformatics and Genome Biology, Fundacion Ciencia & Vida, Zañartu 1482, Ñuñoa Santiago 7780132, Chile
- Centro de Genómica y Bioinformática, Universidad Mayor, Camino la pirámide 5750, Huechuraba, Santiago 8580745, Chile
| | - P T L C Clausen
- Department of Global Surveillance, Technical University of Denmark, Kemitorvet building 204, 2800 Kgs. Lyngby, Denmark
| | - B Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Hovedstaden, Øster Voldgade 5–7, Copenhagen 1350, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Batu 3 1/2, Jalan Bukit Air Nasi, 08100 Bedong, Kedah, Malaysia
| | - D S Holmes
- *Corresponding author: Tel: +56 2 22398969;
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