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Marques-Neto JC, de Lima GM, Maciel CMT, Maciel BR, Abrunhosa FA, Sampaio I, Maciel CR. In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data. BMC Genomics 2023; 24:677. [PMID: 37950193 PMCID: PMC10637016 DOI: 10.1186/s12864-023-09770-y] [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: 07/18/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Macrobrachium amazonicum is a freshwater prawn widely distributed in South America that is undergoing speciation, so the denomination "M. amazonicum complex" is used for it. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used to elucidate this speciation, but heteroplasmies and pseudogenes have been recorded, making separation difficult. Obtaining genes from cDNA (RNA) rather than genomic DNA is an effective tool to mitigate those two types of occurrences. The aim of this study was to assemble in silico the mitochondrial DNA (mtDNA) of the Amazonian coastal population of M. amazonicum inhabiting the state of Pará. RESULTS Sequences were obtained from the prawn's transcriptome using the de novo approach. Six libraries of cDNA from the androgen gland, hepatopancreas, and muscle tissue were used. The mtDNA of M. amazonicum was 14,960 bp in length. It contained 13 protein-coding genes, 21 complete transfer RNAs, and the 12S and 16S subunits of ribosomal RNA. All regions were found on the light strand except tRNAGln, which was on the heavy strand. The control region (D-loop) was not recovered, making for a gap of 793 bp. The cladogram showed the formation of the well-defined Macrobrachium clade, with high support value in the established branches (91-100). The three-dimensional spatial conformation of the mtDNA-encoded proteins showed that most of them were mainly composed of major α-helices that typically shows in those proteins inserted in the membrane (mitochondrial). CONCLUSIONS It was possible to assemble a large part of the mitochondrial genome of M. amazonicum in silico using data from other genomes deposited in GenBank and to validate it through the similarities between its COI and 16S genes and those from animals of the same region deposited in GenBank. Depositing the M. amazonicum mtDNA sequences in GenBank may help solve the taxonomic problems recorded for the species, in addition to providing complete sequences of candidate coding genes for use as biomarkers in ecological studies.
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Affiliation(s)
- Jerônimo Costa Marques-Neto
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Gabriel Monteiro de Lima
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Carlos Murilo Tenório Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Bruna Ramalho Maciel
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Fernando Araujo Abrunhosa
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Carcinology, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Iracilda Sampaio
- Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil
| | - Cristiana Ramalho Maciel
- Laboratory of Aquaculture, Coastal Studies Institute, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
- Coastal Studies Institute, School of Biological Sciences, Laboratory of Aquaculture/BioDatta, Federal University of Pará, Alameda Leandro Ribeiro S/N, Aldeia, Bragança, Pará, CEP: 68600-000, Brazil.
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Mioduser O, Goz E, Tuller T. Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis. BMC Genomics 2017; 18:866. [PMID: 29132309 PMCID: PMC5683454 DOI: 10.1186/s12864-017-4248-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Background Viruses undergo extensive evolutionary selection for efficient replication which effects, among others, their codon distribution. In the current study, we aimed at understanding the way evolution shapes the codon distribution in early vs. late viral genes in terms of their expression during different stages in the viral replication cycle. To this end we analyzed 14 bacteriophages and 11 human viruses with available information about the expression phases of their genes. Results We demonstrated evidence of selection for distinct composition of synonymous codons in early and late viral genes in 50% of the analyzed bacteriophages. Among others, this phenomenon may be related to the time specific adaptation of the viral genes to the translation efficiency factors involved at different bacteriophage developmental stages. Specifically, we showed that the differences in codon composition in different temporal gene groups cannot be explained only by phylogenetic proximities between the analyzed bacteriophages, and can be partially explained by differences in the adaptation to the host tRNA pool, nucleotide bias, GC content and more. In contrast, no difference in temporal regulation of synonymous codon usage was observed in human viruses, possibly because of a stronger selection pressure due to a larger effective population size in bacteriophages and their bacterial hosts. Conclusions The codon distribution in large fractions of bacteriophage genomes tend to be different in early and late genes. This phenomenon seems to be related to various aspects of the viral life cycle, and to various intracellular processes. We believe that the reported results should contribute towards better understanding of viral evolution and may promote the development of relevant procedures in synthetic virology. Electronic supplementary material The online version of this article (10.1186/s12864-017-4248-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oriah Mioduser
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel
| | - Eli Goz
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel.,SynVaccineLtd. Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel. .,SynVaccineLtd. Ramat Hachayal, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel-Aviv University, Ramat Aviv, Israel.
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Zhang J, Zhang W, Yang H. In search of coding and non- coding regions of DNA sequences based on balanced estimation of diffusion entropy. J Biol Phys 2015; 42:99-106. [PMID: 26318090 DOI: 10.1007/s10867-015-9399-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 07/30/2015] [Indexed: 11/30/2022] Open
Abstract
Identification of coding regions in DNA sequences remains challenging. Various methods have been proposed, but these are limited by species-dependence and the need for adequate training sets. The elements in DNA coding regions are known to be distributed in a quasi-random way, while those in non-coding regions have typical similar structures. For short sequences, these statistical characteristics cannot be extracted correctly and cannot even be detected. This paper introduces a new way to solve the problem: balanced estimation of diffusion entropy (BEDE).
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Affiliation(s)
- Jin Zhang
- Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China. .,School of Information Science and Engineering, University of Jinan, Jinan, 250022, China.
| | - Wenqing Zhang
- Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Huijie Yang
- Business School, University of Shanghai for Science and Technology, Shanghai, 200093, China
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