1
|
Muhala V, Guimarães-Costa A, Bessa-Silva AR, Rabelo LP, Carneiro J, Macate IE, Watanabe L, Balcázar OD, Gomes GE, Vallinoto M, Sampaio I. Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species. Sci Rep 2024; 14:3358. [PMID: 38336845 PMCID: PMC10858209 DOI: 10.1038/s41598-024-52979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.
Collapse
Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil.
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chokwe, 1204, Mozambique.
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Jeferson Carneiro
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Oscar David Balcázar
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| | - Grazielle Evangelista Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
- Laboratório Associado, Campus agrário de Vairão, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Iracilda Sampaio
- Laboratório de Evolução Bragança, Instituto de Estudos Costeiros, Universidade Federal do Pará, Pará, Brazil
| |
Collapse
|
2
|
Conferring the Midas Touch on Integrative Taxonomy: A Nanogold-Oligonucleotide Conjugate-Based Quick Species Identification Tool. INTERNATIONAL JOURNAL OF ECOLOGY 2022. [DOI: 10.1155/2022/1009066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nanogold or functionalized gold nanoparticles (GNPs) have myriad applications in medical sciences. GNPs are widely used in the area of nanodiagnostics and nanotherapeutics. Applications of GNPs in taxonomic studies have not been studied vis-à-vis its extensive medical applications. GNPs have great potential in the area of integrative taxonomy. We have realized that GNPs can be used to visually detect animal species based on molecular signatures. In this regard, we have synthesized gold nanoparticles (<20 nm) and have developed a method based on interactions between thiolated DNA oligonucleotides and small-sized GNPs, interactions between DNA oligonucleotides and target DNA molecules, and self-aggregating properties of small-sized GNPs under high salt concentrations leading to a visible change in colour. Exploiting these intermolecular and interparticle interactions under aqueous conditions, in the present work, we have demonstrated the application of our procedure by using a DNA oligonucleotide probe designed against a portion of the mitochondrial genome of the codling moth Cydia pomonella. This method is accurate, quick, and easy to use once devised and can be used as an additional tool along with DNA barcoding. This tool can be used for distinguishing cryptic species, identification of morphovariants of known species, diet analysis, and identification of pest species in quarantine facilities without any need of performing repetitive DNA sequencing. We suggest that designing and selecting a highly specific DNA probe is crucial in increasing the specificity of the procedure. Present work may be considered as an effort to introduce nanotechnology as a new discipline to the extensive field of integrative taxonomy with which disciplines like palaeontology, embryology, anatomy, ethology, ecology, biochemistry, and molecular biology are already associated for a long time.
Collapse
|