Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop)

Pasa, Rubens; Menegídio, Fabiano Bezerra; Rodrigues‐Oliveira, Igor Henrique; Silva, Iuri Batista da; Campos, Matheus Lewi Cruz Bonaccorsi de; Reis, Dinaíza Abadia Rocha; Heslop‐Harrison, J.; Schwarzacher, Trude; Kavalco, Karine Frehner

doi:10.3389/fevo.2021.650783

Cited by 8 publications

(7 citation statements)

References 38 publications

(53 reference statements)

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“…The karyotype formulas were 3m+5sm+6st+11a for P. bockmanni , 3m+5sm+12st+4a for P. fasciatus (Araras), 4m+7sm+9st+3a for P. fasciatus (Alambari), and 3m+9sm+9st+4a for A. lacustris . The species P. fasciatus is part of a “species complex”, with diploid numbers varying between 45 and 49, so our results are consistent with the literature ( Kantek et al, 2009 ; Pasa et al, 2021 ). None of the analyzed individuals had B chromosomes.…”

Section: Resultssupporting

confidence: 92%

Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics

Goes¹,

Santos²,

Aguiar³

et al. 2022

Front. Genet.

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Eukaryotic genomes are usually enriched in repetitive DNA sequences, which can be classified as dispersed or tandemly repeated elements. Satellite DNAs are noncoding monomeric sequences organized in a head-to-tail fashion that are generally located on the subtelomeric and/or pericentromeric heterochromatin. In general, a single species incorporates a diverse group of satellite DNA families, which collection is called satellitome. Here, we characterized three new satellitomes from distinct characid fish (Psalidodon fasciatus, P. bockmanni, and Astyanax lacustris) using a combination of genomic, cytogenetic, and bioinformatic protocols. We also compared our data with the available satellitome of P. paranae. We described 57 satellite DNA (satDNA) families of P. fasciatus (80 variants), 50 of P. bockmanni (77 variants), and 33 of A. lacustris (54 variants). Our analyses demonstrated that several sequences were shared among the analyzed species, while some were restricted to two or three species. In total, we isolated 104 distinctive satDNA families present in the four species, of which 10 were shared among all four. Chromosome mapping revealed that the clustered satDNA was mainly located in the subtelomeric and pericentromeric areas. Although all Psalidodon species demonstrated the same pattern of clusterization of satDNA, the number of clusters per genome was variable, indicating a high dynamism of these sequences. In addition, our results expand the knowledge of the As51 satellite DNA family, revealing that P. bockmanni and P. paranae exhibited an abundant variant of 39 bp, while P. fasciatus showed a variant of 43 bp. The majority of satDNAs in the satellitomes analyzed here presented a common library repetitive sequence in Psalidodon and Astyanax, with abundance variations in each species, as expected for closely related groups. In addition, we concluded that the most abundant satDNA in Psalidodon (As51) passed through a diversification process in this group, resulting in new variants exclusive of Psalidodon.

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Section: Resultssupporting

confidence: 92%

Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics

Goes¹,

Santos²,

Aguiar³

et al. 2022

Front. Genet.

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“…We found tandem repeats in the D-loop of all three species of the genus Kali , with three repeating sequences in K. macrura and five in K. macrodon and K. normani (Supplementary Material 3), but we did not find repeat regions in the mitogenomes of C. niger , D. oligoscolus , and P. astronesthidens . Repetitive sequences in the D-loop shared between species of the same genus have already been reported for fishes from the tribe Gymnocharacini and may play a key role in the study of the evolutionary history of these groups [ 26 ].…”

Section: Resultsmentioning

confidence: 99%

“…The increase in the number of published mitogenomes associated with the stable organization of this genome among vertebrates, the improvement of assembly techniques, and its maternal nature without recombination make the mitochondrial genome a tool with great potential to solve taxonomic problems and phylogenetic relationships [ 26 , 27 ]. Furthermore, as all mitochondrial genes are linked on the same chromosome, they have a very similar phylogenetic signal and share a unique phylogenetic history, allowing them to be used concatenated and partitioned in phylogenetic analyses [ 28 ].…”

Section: Resultsmentioning

confidence: 99%

Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family

Rodrigues‐Oliveira

Pasa²,

Menegídio

et al. 2023

Genomics Inform

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The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

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“…Phylogenetic analysis was performed using the same genomes reported previously [9]. We created a concatenated set of base sequences from 35 species to examine the phylogenetic relationships of the Characidae (see Supplementary Table S1; [10,[23][24][25][26][27][28][29][30][31][32][33][34][35][36][37]). Geneious ® software (version 9.0.5) was used to generate the alignments [38] and Lebiasina astrigata (Regan, 1903) was used as an outgroup.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

The Complete Mitogenome of Amazonian Hyphessobrycon heterorhabdus (Characiformes: Characidae) as a Valuable Resource for Phylogenetic Analyses of Characidae

Montag

Koroiva

Ribeiro-dos-Santos

et al. 2023

Fishes

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Hyphessobrycon heterorhabdus (Ulrey, 1894), popularly known as ‘Flag Tetra’ in English speaking countries, belongs to the genus Hyphessobrycon of the family Characidae, and is widely present in the eastern Amazon basin. Here, using Illumina sequencing, we report the complete mitogenome sequence of H. heterorhabdus. Overall, the mitogenome has 17,021 bp, containing 13 protein-coding, 22 tRNA, and 2 rRNA genes. Non-ambiguous nucleotide compositions of the H. heterorhabdus mitogenome are A: 29.2%, T: 29.4%, G: 15.6%, and C: 25.8%. As recently indicated, the phylogenetic analyses did not support four separate genera (Hemigrammus, Hyphessobrycon, Moenkhausia, and Psalidodon) of Characidae. Understanding the H. heterorhabdus mitogenome is important for taxonomic purposes as well as for the molecular characterization of environmental pollutants. Thus, the mitogenome described here will be a valuable resource for studies on environmental changes, evolutionary genetics, species delimitation, and phylogenetic analyses in Characidae.

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Ten Complete Mitochondrial Genomes of Gymnocharacini (Stethaprioninae, Characiformes). Insights Into Evolutionary Relationships and a Repetitive Element in the Control Region (D-loop)

Cited by 8 publications

References 38 publications

Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics

Revealing the Satellite DNA History in Psalidodon and Astyanax Characid Fish by Comparative Satellitomics

Characterization of six new complete mitochondrial genomes of Chiasmodontidae (Scombriformes, Percomorpha) and considerations about the phylogenetic relationships of the family

The Complete Mitogenome of Amazonian Hyphessobrycon heterorhabdus (Characiformes: Characidae) as a Valuable Resource for Phylogenetic Analyses of Characidae

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