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Phylogenetic trees of 44 Siluriformes species using concatenated nucleotide sequences of 13 protein-coding genes and two rRNAs using the maximum likelihood method. Numbers in the ML tree represent SH-aLRT support/ultrafast bootstrap support values.
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Comparative analysis of the mitogenomes of two Corydoras (Siluriformes, Loricarioidei) with nine known Corydoras, and a phylogenetic analysis of Loricarioidei. ZooKeys Abstract Corydoras is a speciose catfish genus from South America with widely investigated phylogenetic and evolutionary relationships. The complete mitogenomes of C. aeneus and C. p...
Citations
... Among them, H. julii and H. trilineatum are morphologically very similar and are often confused [5]. In addition, previous studies have emphasized the genetic similarity between H. sterbai and H. trilineatum [8,30,31], and our results further support the close genetic relationship among H. julii, H. sterbai, and H. trilineatum. Moreover, within clade 6, the sister species H. concolor and H. panda exhibited the same sequence CYCATCACTTAAGCACT. ...
: Background/Objectives: In this study, we report the complete mitochondrial genome sequence of Hoplisoma concolor Weitzman, 1961 (Siluriformes: Callichthyidae), a callichthyid catfish. Methods: DNA sequencing was performed to obtain its complete mitogenome using the HiSeq platform. To assess the phylogenetic relationships, maximum-likelihood and Bayesian inference phylogenetic trees were constructed using two ribosomal RNA (rRNA) genes and all protein-coding sequences (PCGs) concatenated from the H. concolor mitogenome, along with 31 other Siluriformes mitogenomes. Results: The complete mitogenome of H. concolor is 16,579 base pairs in length, with a nucleotide composition of 32.2% A, 26.0% T, 15.3% G, and 26.5% C. It contains 13 PCGs, 22 transfer RNA genes, and 2 rRNA genes. Phylogenetic analysis based on all PCGs and two rRNAs of the complete mitogenome confirms H. concolor as a sister species of H. panda within the subfamily Corydoradinae. In addition, intergenic sequences between atp6 and cox3 of 21 species of Corydoradinae provide further support for their phylogenetic relationship. Conclusions: Given the lack of detailed descriptions regarding the length and nucleotide composition of these intergenic sequences, our study contributes valuable insights into the genetic diversity and evolutionary complexity of Callichthyidae.
... To the best of our knowledge, this study represents the first assembly of the mitogenomes for two horned toads, B. sangzhiensis and B. tuberogranulata. The exploration of similarities and differences in gene orders, genetic structures, base compositions, evolutionary features, and codon usage offers valuable molecular insights into the taxonomic and phylogenetic characteristics of closely related species (Sun et al., 2022). Overall, the mitogenomes of the two species exhibited similarities in terms of size, organization ( Figure 2 and The sequence obtained in this study. ...
Boulenophrys sangzhiensis and Boulenophrys tuberogranulata, two narrow‐distributed toad species within the Megophryidae family in southern China, are experiencing population declines due to habitat loss and degradation. Despite their critical conservation status, the two species remain largely overlooked in public and scientific spheres. This study presented the first sequencing, assembly, and annotation of the complete mitogenomes of both species using next‐generation sequencing. The mitogenome of B. sangzhiensis was 16,950 bp, while that of B. tuberogranulata was 16,841 bp, each comprising 13 protein‐coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a noncoding control region (D‐loop). The gene content, nucleotide composition, and evolutionary rates of each mitogenome were analyzed. Both mitogenomes exhibited negative AT skew and GC skew with high A + T content. ATP8 exhibited the highest evolutionary rate, while COI had the lowest. A phylogenetic analysis based on 28 mitogenomes revealed two major clades of Megophryidae, supporting the classification of two subfamilies, Megophryinae and Leptobrachiinae. Within the subfamily Megophryinae, the genus Boulenophrys was divided into two species groups. Intriguingly, despite coexisting in Zhangjiajie City, B. sangzhiensis and B. tuberogranulata exhibited distinct origins from the two different species groups, underscoring the unique role of the coexisting area Zhangjiajie in driving their speciation and preserving their current populations. A parallel pattern was also identified in the Leptobrachiinae genus Leptobrachium within the same region. This study provided valuable data references and enhanced our understanding of the molecular characteristics of these threatened amphibian species.
... The caudal fin was collected, and total DNA was extracted using a columnar animal DNA extraction kit (Sun et al. 2022). Sequencing was performed using the Illumina Novaseq 6000 platform (San Diego, CA). ...
... To analyze the relative phylogenetic position of P. padamya in the subfamily Smiliogastrinae, relevant gene sequences (17 species of Smiliogastrinae and one outgroup Corydoras aeneus MZ571336) (Sun et al. 2022) were downloaded from GenBank. Using the tandem sequence set of 13 PCGs and two rRNAs, MrBayes v3.2.6 (Ronquist et al. 2012) was used to construct the Bayesian inference (BI) tree. ...
Pethia padamya (Kullander and Britz, 2008) is a freshwater fish distributed in the Mekong River basin of Thailand. It has beautiful colors and can be used as an ornamental fish. The complete mitochondrial genome of P. padamya was determined using next-generation sequencing technology and its characteristics were analyzed. The mitochondrial genome is a closed circular molecule comprising 16,792 bp, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a major non-coding region. The overall base composition of the mitochondrial genome is 32.47% A, 25.39% C, 26.08% T, and 16.06% G, with a high A + T bias of 58.55%. Phylogenetic analysis revealed P. padamya as a sister group of Pethia conchonius+(Pethia ticto+Pethia cumingii) and Pethia gelius with maximal support, providing support for the monophyly of the genus Pethia based on concatenated nucleotide sequences. The results of this study proved the monophyly of the genus Pethia. These data for the first time provide information on the complete mitochondrial genome of P. padamya and can contribute to further studies on the biodiversity and management of P. padamya.
... The A+T content (59.7%) was higher than the G+C content (40.3%) in the mitochondrial genome of P. stoliczkana, revealing a preference for A+T and base anti-G bias. These results are consistent with the preference for A+T bases in vertebrates (Sun et al., 2020(Sun et al., , 2022(Sun et al., , 2023. ...
... They are found in South America. Almost all the main and tributary water systems of the Amazon River contain pikes, but the composition of species in the watersheds where various species are distributed is different (Huysentruyt and Adriaens 2005;Liu et al. 2019;Lv et al. 2020;Tencatt et al. 2021;Sun et al. 2022). For instance, most mouse fish gather in the middle and lower reaches, where the water flow is relatively gentle, and a few strong swift warriors live in the upper reaches of the river. ...
The Pygmy corydoras Corydoras pygmaeus Knaack, 1966, is the smallest member of the genus Corydoras, belonging to the family Callichthyidae and order Siluriformes. The complete mitochondrial genome of C. pygmaeus was sequenced and assembled using next-generation sequencing technology, and phylogenetically compared with those of other species of this genus. The mitochondrial genome of C. pygmaeus is a circular DNA molecule with a size of 16,840 bp (GenBank no. ON729306). A phylogenetic tree was constructed based on 13 protein-coding genes of C. pygmaeus and 13 species of the family Callichthyidae, which showed that C. pygmaeus clustered with other species of this genus, but was the first branch to differentiate. These results could provide basic data for phylogenetic analysis and population genetic diversity protection of Corydoras and Callichthyidae fish in the future.
The complete mitogenome of four Scleromystax barbatus populations distributed along the species natural range was reconstructed, comprising the first study with this genus and the second with Corydoradinae specimens sampled from their natural environment and deposited in permanent collections. The mitogenome of S. barbatus is a circular molecule of 16,694 base pairs (bp) comprising 37 genes, 22 of which are tRNA, two are rRNA, 13 are protein-coding genes and one control region (D-loop). An 18-nucleotide insertion sequence was found between the ATPase subunit 6 and COIII genes. Most genes are encoded on the heavy strand, while the ND6 and eight tRNAs are found on the light strand. Phylogenetic analyses using other available Callichthyidae mitogenomes confirmed the monophyly of Callichthyinae and Corydoradinae and indicate that S. barbatus populations form a separate and more closely related branch of Corydoras nattereri + Corydoras paleatus.
We examined the evolutionary status of the genus Oliotius Kottelat, 2013, clarified the mitogenome structure of Smiliogastrinae, and analyzed its phylogenetic information to provide a reference for the taxonomy, evolutionary genetics, and germplasm identification of Smiliogastrinae. Using next-generation sequencing, the complete mitogenome sequence of the monotypic species Oliotius oligolepis was obtained, annotated, and characterized. The mitogenomic sequences of Smiliogastrinae fish were compared and analyzed, and a phylogenetic tree was constructed. The mitogenome of O. oligolepis was 16,636 base pairs long and contained 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and 1 D-loop. The Smiliogastrinae species exhibited gene arrangement consistency, with slight differences in their genome lengths and compositions. Among the 13 protein-coding genes, ND3 showed the highest polymorphism rate and largest genetic distance. Our phylogenetic analysis showed that the target species O. oligolepis is closely related to Barbodes binotatus. The genus Oliotius is monotypic, and the genus Barbodes is not supported as a monophyletic group. This molecular information provides a foundation for further research on the phylogeny of the genera Oliotius and Barbodes and provides insight into the phylogenetic features of fishes belonging to Smiliogastrinae.
