Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes
College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(5), 3004; https://doi.org/10.3390/ijms25053004
Submission received: 26 January 2024
/
Revised: 26 February 2024
/
Accepted: 28 February 2024
/
Published: 5 March 2024
(This article belongs to the Section Molecular Genetics and Genomics)
Abstract
:Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of D. filamentosa and P. nigrofasciata measure 16,598 and 16,948 bp, respectively. Both D. filamentosa and P. nigrofasciata exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that D. filamentosa is closely related to the sister group comprising Dawkinsia denisonii and Sahyadria chalakkudiensis. Similarly, P. nigrofasciata forms a sister group with Pethia ticto and Pethia stoliczkana.
1. Introduction
Tan and Armbruster [1] reclassified Puntius and related species under the subfamily Smiliogastrinae, following a phylogenetic analysis of fish genera within the order Cypriniformes. At present, there are 25 genera in the subfamily Smiliogastrinae according to the National Center for Biotechnology Information, including 9 single-species genera. In Bangladesh, extensive research has been conducted on the abundance and distribution of barbs in various habitats, including rivers, floodplains, and mountain streams [2,3]. Most species of the Smiliogastrinae subfamily have bright colors, and accurate identification and monitoring of these fish species are crucial, given their important economic and ornamental value.
Mitochondrial DNA (mtDNA) is a compact genome, typically 15–20 kb in size, and exists as a closed loop separate from the nuclear genome. mtDNA exhibits properties such as maternal inheritance, simple structure, autonomous replication, high mutation rate, and consistent mutation probability, making it an invaluable tool in studying species evolution, phylogenetic relationships, and population genetics. mtDNA has been used to examine genetic differentiation within and between closely related species [4,5,6]. Recent advancements in DNA sequencing technology have greatly facilitated the rapid and accurate acquisition of fish mitochondrial genome data. Moreover, several complete fish mtDNA sequences have been reported, enriching our understanding of classification and systematic evolution within this group. Thus far, complete mitochondrial genome sequences have been reported for only 19 species of Smiliogastrinae [7].
In this study, we employed high-throughput sequencing technology to determine and analyze the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. By comparing these genomes with those of 19 related species, we aimed to elucidate the molecular phylogenetic relationships within this group. These findings are expected to contribute fundamental insights for the germplasm identification and genetic diversity conservation of Smiliogastrinae.
2. Results
2.1. Mitochondrial Genome Analysis
The total mitochondrial genome lengths of D. filamentosa and P. nigrofasciata are 16,598 and 16,948 bp, respectively (Figure 1 and Figure 2). In D. filamentosa, the nucleotide compositions are 33.9, 24.2, 27.3, and 14.7%, for A, T, G, and C, respectively; whereas in P. nigrofasciata the nucleotide compositions are 33.2, 26.7, 24.9, and 15.1%, for A, T, G, and C, respectively. Both species exhibit high AT content in their mitochondrial genomes, which comprise 37 genes (13 protein-coding genes [PCGs], 22 tRNAs, and 2 rRNAs), and one non-coding control region (Table 1 and Table 2). Seven gene overlaps were found in both species, with the longest overlap (7 bp) between ATP8 and ATP6, and ND4L and ND4.
In the mitochondrial genomes of both species, the heavy and light strands encode a different number of genes. The heavy strand encodes 28 genes, including 12 PCGs, 14 tRNAs, and 2 rRNAs; the light strand encodes 9 genes, comprising 1 PCG and 8 tRNAs. The non-coding control regions of D. filamentosa, located between tRNA-Pro and tRNA-Phe, span 931 bp, and the nucleotide compositions of A, T, G, and C are 36.2, 33.0, 11.8, and 19.0%, respectively. The non-coding control area of P. nigrofasciata is similarly positioned with a length of 1288 bp, and the A, T, G, and C compositions are 36.7, 33.4, 11.5, and 18.4%, respectively. The overall AT content of the D. filamentosa mitochondrial genome is 58.1%, with AT skew and GC skew values of 0.166 and −0.300, respectively (Table 3); for P. nigrofasciata, these values are 59.9%, 0.108, and −0.245, respectively (Table 4).
2.2. Protein-Coding Gene Analysis
Among the 13 PCGs in D. filamentosa, only COI uses GTG as the starting codon, while the remaining 12 PCGs initiate with ATG. COII, ND2, ND3, and ND4 have incomplete termination codons (T), ATP6 and COIII terminate with TA-, and the remaining seven PCGs end with the complete termination codons TAA or TAG. Among the 13 PCGs of P. nigrofasciata, only COI starts with GTG, while the remaining 12 PCGs begin with ATG. COII, COIII, Cytb, ND2, ND3, and ND4 have incomplete termination codons (T), ATP6 ends with TA-, and the remaining six PCGs terminate with the complete termination codons TAA or TAG.
A preliminary analysis of the relative synonymous codon usage (RSCU) and amino acid composition of the 13 PCGs in the mitochondrial genomes of D. filamentosa and P. nigrofasciata was performed. The results showed that leucine (Leu) was the most frequently used amino acid, constituting 12.69 and 11.25% of the 3798 and 3800 amino acids encoded, respectively. This was followed by alanine (Ala, 8.23 and 8.8%, respectively) and threonine (Thr, 8.84 and 8.22%, respectively). Cysteine (Cys) was the least abundant, accounting for only 0.66% (Table 5 and Table 6). Dawkinsia filamentosa and P. nigrofasciata showed a preference for 25 and 26 codons (RSCU ≥ 1) in their 13 PCGs, respectively.
2.3. tRNAs and rRNAs Gene Analysis
The 22 tRNA genes in D. filamentosa are 67–77 bp long. The longest gene, Leu2-tRNA, is 74 bp long, while the shortest, Cys-tRNA, is 67 bp (Table 1). In P. nigrofasciata, the sequence length of the 22 tRNAs genes is 67–77 bp, with Lys-tRNA being the longest at 77 bp, and Cys-tRNA being the shortest at 67 bp (Table 2). Of the 24 RNA genes of D. filamentosa and P. nigrofasciata, 8 are located on the L chain and 16 on the H chain.
The total length of the 16S rRNA gene in the mitochondrial genome of D. filamentosa is 1695 bp (Table 3), with an AT content of 57.4%. The 12S rRNA measures 955 bp (Table 3), with an AT content of 51.8%. In P. nigrofasciata, the 16S rRNA gene is 1684 bp in length (Table 4), with an AT content of 59.1%, and the 12S rRNA gene is 956 bp (Table 4), with an AT content of 51.7%.
2.4. Phylogenetic Analysis
Using the mitochondrial genomes of 23 Cyprinidae fish, 13 PCG tandem sequences were used to construct Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees (Figure 3). The trees consistently supported the monophyly of Enteromius, Hampala, and Pethia. However, further research is required regarding the monophyletic relationships of the other three genera: Barbodes, Dawkinsia, and Puntius. Notably, both phylogenetic trees strongly support D. filamentosa forming a sister group with Dawkinsia denisonii and Sahyadria chalakkudiensis (BS = 100, PP = 1). Similarly, P. nigrofasciata is strongly indicated to be a sister group of Pethia ticto and Pethia stoliczkana (BS = 100, PP = 1).
3. Discussion
We used high-throughput sequencing technology to obtain the complete mitochondrial genome sequences of D. filamentosa and P. nigrofasciata, measuring 16,598 and 16,948 bp, respectively. The structural characteristics of these sequences align with those of previously published studies of Smiliogastrinae fish, underscoring the high evolutionary conservation of the mitochondrial genome in this group [8]. AT and GC skew values are indicative of base content differences between the heavy and light chains, and larger absolute values indicate more significant differences in the base composition between the two [9]. Dawkinsia filamentosa and P. nigrofasciata mitochondrial DNA sequences exhibit a higher AT content and a lower GC content, thus exhibiting a clear AT preference. This preference has also been observed in other Smiliogastrinae species, but the content varies slightly depending on the species. This base preference may be related to natural mutations and selection pressure during replication and transcription. Unless there are significant changes in the number of coding regions and tRNA bases, each gene is similar to other species of Smiliogastrinae and has a high homology. Typical features of AT duplication also exist in non-coding regions [10]. The base distribution in PCGs was relatively uniform, except for the first codon, whereas both the second and third codons exhibited significant anti-G bias. This uneven distribution is likely due to limitations imposed by amino acid compositions and differences in codon usage frequencies [11].
Leucine, a hydrophobic amino acid, was the most frequently used in the 20 amino acid-encoding proteins, a trend consistent with 19 other fish species of Smiliogastrinae [8]. This may be related to the composition of transmembrane proteins encoded by mitochondrial genes. Notably, the absolute value of AT skew is the highest in the base composition of the ND6 gene, and the GC skew value is the only positive value, with significant fluctuations in AT/GC bias values. The proton-transporting NADH-quinone oxidoreductase, also known as complex I, is a multi-subunit membrane protein complex that catalyzes electron transfer in the NADH respiratory chain and provides approximately 40% of the proton power required for ATP synthesis in vertebrates [12,13]. The ND6 subunit, a critical component of complex I, suggests differential selection and mutation pressures related to respiratory metabolism compared to other genes.
The total lengths of the two rRNA genes of D. filamentosa and P. nigrofasciata were 2650 and 2640 bp, respectively. The intervals between the 12S rRNA and 16S rRNA gene were consistent with Val-tRNA, aligning with the typical characteristics of Smiliogastrinae. Given its stability, the 12S rRNA is often used for fish identification and phylogenetic studies [14]. Studies have shown that base mismatches are also commonly present in the secondary structure of tRNA, as they help to mitigate harmful mutations in the non-recombinant mitochondrial genome [15]. The mitochondrial control region, containing elements regulating mitochondrial genome replication and gene expression, offers insights into DNA replication, transcription mechanisms, and evolutionary laws. The significant difference in D-loop length variance as it was observed in our work was also reported previously in the investigated subfamily Smiliogastrinae [7].
Most current phylogenetic studies of Smiliogastrinae rely on individual genes [16,17]. However, in our study we used concatenated sequences of 13 PCGs to construct partial Smiliogastrinae phylogenetic trees using ML and BI methods. These analyses confirmed the monophyletic relationships of Enteromius, Hampala, and Pethia, while suggesting the need for further research on the monophyly of Barbodes, Dawkinsia, and Puntius. In addition, both analyses identified D. filamentosa (comprising Dawkinsia denisonii and Sahyadria chalakkudiensis) and P. nigrofasciata (alongside Pethia ticto and Pethia stoliczkana) as sister groups.
In summary, this study is the first to analyze the mitochondrial DNA genome structure of D. filamentosa and P. nigrofasciata and to explore their phylogenetic relationships based on multi-gene tandem sequences. These results provide new insights and reference points for further research into the species evolution, classification, identification, and diversity of Smiliogastrinae.
4. Materials and Methods
4.1. Experimental Materials and DNA Extraction
In September 2021, fish samples were collected from the Huadiwan Flower, Bird, Fish, and Insect Wholesale Market in Liwan District, Guangzhou City, Guangdong Province (23°3′48″ N, 113°12′18″ E). Following preliminary morphological identification, fresh muscle tissue from the back and abdomen were excised and stored in 1.5 mL Eppendorf centrifuge tubes. These samples were soaked in 95% alcohol for 48 h and then preserved at −20 °C. Genomic DNA was extracted using the traditional chloroform tris-saturated phenol method [18]. The concentration of genomic DNA was measured with a NanoDrop ultra-micro spectrophotometer, and DNA integrity was verified by 1% agarose gel electrophoresis.
4.2. High-Throughput Sequencing and Gene Annotation
DNA samples that passed the quality inspection were fragmented to approximately 200 bp using a Covaris ultrasonic crusher (Covaris, Woburn, MA, USA) for small genomic DNA library construction. The HiSeq 2500 high-throughput sequencing platform was used for sequencing (Guangzhou Tianyi Huiyuan Gene Technology Co., Ltd., Guangzhou, China). SOAPdenovo 2.04 software (http://soap.genomics.org.cn/soapdenovo.html, accessed on 25 January 2024) [19] was used to assemble clean reads and optimize local assembly based on read parings and overlap with default parameters; gaps introduced during scaffold splicing were compensated and repaired using GapCloser 1.12 software (http://soap.genomics.org.cn/soapdenovo.html, accessed on 25 January 2024) [20], with a redundant segment subsequently removed to obtain the final assembly result. The mitochondrial genome was extracted and assembled using NOVOPlasty v4.3.1 software [21]. The assembled complete mitochondrial genome sequence was annotated on the MITOS web server (http://mitofish.aori.u-tokyo.ac.jp/, accessed on 25 January 2024), involving PCGs, RNA, and non-coding regions. This was supplemented by manual comparison and correction to precisely determine the position and length of each gene. MitoAnnotator (https://mitofish.aori.u-tokyo.ac.jp/annotation/input/, accessed on 25 January 2024) was used to create mitochondrial genome structure maps for D. filamentosa and P. nigrofasciata.
4.3. Data Analysis
The tRNA genes were predicted using the online tool tRNAscan-SE (http://trna. ucsc. edu/tRNAscan-SE/, accessed on 25 January 2024) [22]. Base composition and codon usage were analyzed, and AT and GC skew values were calculated using MEGA-X software [23]. We retrieved and downloaded the complete mitochondrial genome sequences of 19 Smiliogastrinae fish species from GenBank (https://www.ncbi.nlm.nih.gov/, accessed on 25 January 2024; Table 7), using Lepidopygopsis typus (OR685011) [24] as outgroup. Phylogenetic trees of Smiliogastrinae fish were constructed based on the tandem sequences of 13 PCGs, using the maximum likelihood [25] and Bayesian inference [26] methods, respectively.
Multiple sequence alignment was performed using MAFFT v7.313 [27]. The optimal partition model was determined using ModelFinder [28], based on the Akaike Information Criterion [29]. An ML tree was constructed with IQ-TREE [30] under the edge-linked partition model for 50,000 ultrafast bootstraps, as well as the Shimodaira–Hasegawa-like approximate likelihood-ratio test. To construct the BI tree, the following steps were conducted. The aligned FASTA file was converted into a NEXUS file and imported into CIPRES software (https://www.phylo.org/, accessed on 25 January 2024) under the partition model (two parallel runs, 100,000,000 generations), in which the initial 25% of sampled data were discarded as burn-in [31]. The phylogenetic tree was then edited using FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/, accessed on 25 January 2024).
Author Contributions
Conceptualization, C.-H.S. and C.-H.L.; methodology, C.-H.S.; software, C.-H.S.; formal analysis, C.-H.S.; writing—original draft preparation, C.-H.S.; writing—review and editing, C.-H.S. and C.-H.L.; funding acquisition, C.-H.L. All authors have read and agreed to the published version of the manuscript.
Funding
The present study was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).
Institutional Review Board Statement
All specimens in this study were collected in accordance with Chinese laws. The collection and sampling of specimens were reviewed and approved by the Animal Ethics Committee of Nanjing Forestry University (NFU2017-2023187, 1 July 2021). All experiments were conducted with respect to animal welfare and care. This study was compliant with CBD and Nagoya protocols.
Informed Consent Statement
Not applicable.
Data Availability Statement
The complete mitochondrial genome sequences and annotations of D. filamentosa and P. nigrofasciata are available in the National Center for Biotechnology Information (NCBI) GenBank database https://www.ncbi.nlm.nih.gov/genbank/, accessed on 25 January 2024) under accession numbers OP595699 and OP581953, respectively.
Acknowledgments
We are very grateful to the editor and reviewers for critically evaluating this manuscript and providing constructive comments for its improvement.
Conflicts of Interest
The authors declare no conflicts of interest.
References
- Tan, M.; Armbruster, J.W. Phylogenetic classification of extant genera of fishes of the order Cypriniformes (Teleostei: Ostariophysi). Zootaxa 2018, 4476, 6–39. [Google Scholar] [CrossRef] [PubMed]
- Mian, S.; Ferdous, M.J.; Sarker, M.Y.; Islam, M.J.; Reza, A.M.; Iqbal, M.M.; Hossain, M.A.R. Status of biodiversity and conservation of freshwater barbs in Bangladesh. World J. Fish Mar. Sci. 2013, 5, 701–708. [Google Scholar]
- Mohsin, A.B.M.; Haque, S.M.M.; Chaki, N.; Fazad, F.H. Seasonal abundance of finfish in the Padma River in the Rajshahi District, Bangladesh. World J. Fish Mar. Sci. 2013, 5, 680–685. [Google Scholar]
- Inoue, J.G.; Miya, M.; Tsukamoto, K.; Nishida, M. A mitogenomic perspective on basal teleostean phylogeny: Resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 2001, 20, 275–285. [Google Scholar] [CrossRef] [PubMed]
- Harrison, R.G. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 1989, 4, 6–11. [Google Scholar] [CrossRef] [PubMed]
- Boore, J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27, 1767–1780. [Google Scholar] [CrossRef] [PubMed]
- Behura, S.K.; Severson, D.W. Codon usage bias: Causative factors, quantification methods and genome-wide patterns: With emphasis on insect genomes. Biol. Rev. Camb. Philos. Soc. 2013, 88, 49–61. [Google Scholar] [CrossRef] [PubMed]
- Sun, C.H.; Sun, P.Y.; Lao, Y.L.; Wu, T.; Zhang, Y.N.; Huang, Q.; Zhang, Q. Mitogenome of a monotypic genus, Oliotius Kottelat, 2013 (Cypriniformes: Cyprinidae): Genomic characterization and phylogenetic position. Gene 2023, 851, 147035. [Google Scholar] [CrossRef]
- Perna, N.T.; Kocher, T.D. Patterns of nucleotide composition at four-fold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 1995, 41, 353–358. [Google Scholar] [CrossRef]
- Mullens, N.; Sonet, G.; Decru, E.; Virgilio, M.; Snoeks, K.; Emmanuel, V. Mitogenomic characterization and systematic placement of the Congo blind barb Caecobarbus geertsii (Cypriniformes: Cyprinidae). Int. J. Biol. Macromol. 2020, 161, 292–298. [Google Scholar] [CrossRef]
- Frank, A.C.; Lobry, J.R. Asymmetric substitution patterns: A review of possible underlying mutational or selective mechanisms. Gene 1999, 238, 65–77. [Google Scholar] [CrossRef]
- Lazarou, M.; Thorburn, D.R.; Ryan, M.T.; McKenzie, M. Assembly of mitochondrial complex I and defects in disease. Biochim. Biophys. Acta 2009, 1793, 78–88. [Google Scholar] [CrossRef]
- Efremov, R.G.; Baradaran, R.; Sazanov, L.A. The architecture of respiratory complex I. Nature 2010, 465, 441–445. [Google Scholar] [CrossRef]
- Miya, M.; Sato, Y.; Fukunaga, T.; Sado, T.; Poulsen, J.Y.; Sato, K.; Minamoto, T.; Yamamoto, S.; Yamanaka, H.; Araki, H.; et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fish: Detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2015, 2, 150088. [Google Scholar] [CrossRef]
- Lynch, M. Mutation accumulation in nuclear, organelle and prokaryotic transfer RNA genes. Mol. Biol. Evol. 1997, 14, 914–925. [Google Scholar] [CrossRef]
- Ahmed, M.S.; Islam, N.N.; Akter, J.A.; Sanzida, N.J. DNA barcoding of Smiliogastrinae (Teleostei: Cypriniformes) of Bangladesh based on cytochrome c oxidase subunit I (coi) sequences. Zool. Ecol. 2021, 67, 78. [Google Scholar] [CrossRef]
- Sudasinghe, H.; Rüber, L.; Meegaskumbura, M. Molecular phylogeny and systematics of the South Asian freshwater-fish genus Puntius (Teleostei: Cyprinidae). Zool. Scr. 2023, 52, 571–587. [Google Scholar] [CrossRef]
- Mamiatis, T.; Fritsch, F.; Sambrook, J.; Engel, J. Molecular Cloning of a Laboratory Manual. New York, NY: Cold Spring Harbor Laboratory. Acta Biotechnol. 1985, 5, 104. [Google Scholar]
- Li, R.Q.; Zhu, H.M.; Ruan, J.; Qian, W.; Fang, X.; Shi, Z.; Li, Y.; Li, S.; Shan, G.; Kristiansen, K.; et al. De novo assembly of human genome using massive parallel short-read sequencing. Genome Res. 2010, 20, 265–272. [Google Scholar] [CrossRef]
- Zhao, Q.Y.; Wang, Y.; Kong, Y.M.; Luo, D.; Li, X.; Hao, P. Optimizing de novo transcriptome assembly from short-read RNA-seq data: A comparative study. BMC Bioinform. 2011, 12, S2. [Google Scholar] [CrossRef]
- Dierckxsens, N.; Mardulyn, P.; Smits, G. NOVOPlasty: De novo assembly of organelle genomes from whole-genome data. Nucleic Acids Res. 2017, 45, e18. [Google Scholar]
- Lowe, T.M.; Chan, P.P. TRNAscan-SE online: Integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016, 44, W54–W57. [Google Scholar] [CrossRef]
- Kumar, S.; Nei, M.; Dudley, J.; Tamura, K. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 2008, 9, 299–306. [Google Scholar] [CrossRef]
- Chandra, S.; Abhilash, R.; Sidharthan, A.; Raghavan, R.; Dahanukar, N. Complete mitogenome of Lepidopygopsis typus, an evolutionarily distinct, endangered cyprinid fish from the Western Ghats Biodiversity Hotspot: Phylogenetic relationships and implications for conservation. Gene 2023, 898, 148098. [Google Scholar] [CrossRef]
- Guindon, S.; Gascuel, O. A simple, fast, and accurate algorithm for estimating large phylogenies using maximum likelihood. Syst. Biol. 2003, 52, 696–704. [Google Scholar] [CrossRef]
- Huelsenbeck, J.P.; Ronquist, F. MBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17, 754–755. [Google Scholar] [CrossRef]
- Katoh, K.; Misawa, K.; Kuma, K.I.; Miyata, T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30, 3059–3066. [Google Scholar] [CrossRef]
- Kalyaanamoorthy, S.; Minh, B.Q.; Wong, T.K.F.; von Haeseler, A.; Jermiin, L.S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 2017, 14, 587–589. [Google Scholar] [CrossRef]
- Vrieze, S.I. Model selection and psychological theory: A discussion of the differences between the Akaike information criterion (AIC) and Bayesian information criterion (BIC). Psychol. Methods 2012, 17, 228–243. [Google Scholar] [CrossRef]
- Nguyen, L.T.; Schmidt, H.A.; Von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015, 32, 268–274. [Google Scholar] [CrossRef]
- Mark, A.M.; Terri, S.; Wayne, P. Embedding CIPRES Science Gateway Capabilities in Phylogenetics Software Environments. In XSEDE ‘13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery; Association for Computing Machinery: New York, NY, USA, 2013; Volume 40, pp. 1–8. [Google Scholar]
Figure 1.
Structure of Dawkinsia filamentosa mitochondrial genome.
Figure 2.
Structure of Pethia nigrofasciata mitochondrial genome.
Figure 3.
Phylogenetic tree inferred from the nucleotide sequences of 13 protein-coding genes. Numbers at nodes represent the posterior probability values for Bayesian analysis and bootstrap values for maximum likelihood analysis.
Figure 3.
Phylogenetic tree inferred from the nucleotide sequences of 13 protein-coding genes. Numbers at nodes represent the posterior probability values for Bayesian analysis and bootstrap values for maximum likelihood analysis.
Table 1.
Annotation of the mitochondrial genome of Dawkinsia filamentosa.
| Gene | Position | Size | Intergenic Nucleotides | Codon | Strand | ||
|---|---|---|---|---|---|---|---|
| From | To | Start | Stop | ||||
| tRNA-Phe | 1 | 69 | 69 | 0 | H | ||
| 12S rRNA | 70 | 1024 | 955 | 0 | H | ||
| tRNA-Val | 1025 | 1096 | 72 | 0 | H | ||
| 16S rRNA | 1097 | 2791 | 1695 | 0 | H | ||
| tRNA-Leu2 | 2792 | 2868 | 77 | 0 | H | ||
| ND1 | 2870 | 3844 | 975 | 1 | ATG | TAA | H |
| tRNA-Ile | 3849 | 3920 | 72 | 4 | H | ||
| tRNA-Gln | 3919 | 3989 | 71 | −2 | L | ||
| tRNA-Met | 3992 | 4061 | 70 | 2 | H | ||
| ND2 | 4062 | 5106 | 1045 | 0 | ATG | T | H |
| tRNA-Trp | 5107 | 5177 | 71 | 0 | H | ||
| tRNA-Ala | 5179 | 5247 | 69 | 1 | L | ||
| tRNA-Asn | 5249 | 5321 | 73 | 1 | L | ||
| tRNA-Cys | 5357 | 5423 | 67 | 35 | L | ||
| tRNA-Tyr | 5423 | 5493 | 71 | −1 | L | ||
| COI | 5495 | 7045 | 1551 | 1 | GTG | TAA | H |
| tRNA-Ser2 | 7046 | 7116 | 71 | 0 | L | ||
| tRNA-Asp | 7118 | 7189 | 72 | 1 | H | ||
| COII | 7202 | 7892 | 691 | 12 | ATG | T | H |
| tRNA-Lys | 7893 | 7968 | 76 | 0 | H | ||
| ATP8 | 7970 | 8134 | 165 | 1 | ATG | TAG | H |
| ATP6 | 8128 | 8810 | 683 | −7 | ATG | TA | H |
| COIII | 8811 | 9595 | 785 | 0 | ATG | TA | H |
| tRNA-Gly | 9596 | 9668 | 73 | 0 | H | ||
| ND3 | 9669 | 10017 | 349 | 0 | ATG | T | H |
| tRNA-Arg | 10018 | 10087 | 70 | 0 | H | ||
| ND4L | 10088 | 10384 | 297 | 0 | ATG | TAA | H |
| ND4 | 10378 | 11758 | 1381 | −7 | ATG | T | H |
| tRNA-His | 11759 | 11827 | 69 | 0 | H | ||
| tRNA-Ser1 | 11828 | 11896 | 69 | 0 | H | ||
| tRNA-Leu1 | 11898 | 11970 | 73 | 1 | H | ||
| ND5 | 11972 | 13792 | 1821 | 1 | ATG | TAA | H |
| ND6 | 13789 | 14310 | 522 | −4 | ATG | TAA | L |
| tRNA-Glu | 14311 | 14378 | 68 | 0 | L | ||
| Cytb | 14385 | 15521 | 1137 | 6 | ATG | TAA | H |
| tRNA-Thr | 15525 | 15597 | 73 | 3 | H | ||
| tRNA-Pro | 15597 | 15667 | 71 | −1 | L | ||
| D-loop | 15668 | 16598 | 931 | 0 | H | ||
Table 2.
Annotation of the mitochondrial genome of Pethia nigrofasciata.
| Gene | Position | Size | Intergenic Nucleotides | Codon | Strand | ||
|---|---|---|---|---|---|---|---|
| From | To | Start | Stop | ||||
| tRNA-Phe | 1 | 69 | 69 | 0 | H | ||
| 12S rRNA | 70 | 1025 | 956 | 0 | H | ||
| tRNA-Val | 1026 | 1097 | 72 | 0 | H | ||
| 16S rRNA | 1098 | 2781 | 1684 | 0 | H | ||
| tRNA-Leu2 | 2782 | 2856 | 75 | 0 | H | ||
| ND1 | 2858 | 3832 | 975 | 1 | ATG | TAA | H |
| tRNA-Ile | 3845 | 3916 | 72 | 12 | H | ||
| tRNA-Gln | 3916 | 3986 | 71 | −1 | L | ||
| tRNA-Met | 3988 | 4057 | 70 | 1 | H | ||
| ND2 | 4058 | 5102 | 1045 | 0 | ATG | T | H |
| tRNA-Trp | 5103 | 5173 | 71 | 0 | H | ||
| tRNA-Ala | 5175 | 5243 | 69 | 1 | L | ||
| tRNA-Asn | 5245 | 5317 | 73 | 1 | L | ||
| tRNA-Cys | 5350 | 5416 | 67 | 32 | L | ||
| tRNA-Tyr | 5416 | 5485 | 70 | −1 | L | ||
| COI | 5487 | 7037 | 1551 | 1 | GTG | TAA | H |
| tRNA-Ser2 | 7038 | 7108 | 71 | 0 | L | ||
| tRNA-Asp | 7110 | 7181 | 72 | 1 | H | ||
| COII | 7191 | 7881 | 691 | 9 | ATG | T | H |
| tRNA-Lys | 7882 | 7958 | 77 | 0 | H | ||
| ATP8 | 7960 | 8124 | 165 | 1 | ATG | TAG | H |
| ATP6 | 8118 | 8800 | 683 | −7 | ATG | TA | H |
| COIII | 8801 | 9584 | 784 | 0 | ATG | T | H |
| tRNA-Gly | 9585 | 9657 | 73 | 0 | H | ||
| ND3 | 9658 | 10006 | 349 | 0 | ATG | T | H |
| tRNA-Arg | 10007 | 10076 | 70 | 0 | H | ||
| ND4L | 10077 | 10373 | 297 | 0 | ATG | TAA | H |
| ND4 | 10367 | 11747 | 1381 | −7 | ATG | T | H |
| tRNA-His | 11748 | 11816 | 69 | 0 | H | ||
| tRNA-Ser1 | 11817 | 11884 | 68 | 0 | H | ||
| tRNA-Leu1 | 11886 | 11958 | 73 | 1 | H | ||
| ND5 | 11962 | 13785 | 1824 | 3 | ATG | TAA | H |
| ND6 | 13782 | 14303 | 522 | −4 | ATG | TAA | L |
| tRNA-Glu | 14304 | 14372 | 69 | 0 | L | ||
| Cytb | 14379 | 15519 | 1141 | 6 | ATG | T | H |
| tRNA-Thr | 15520 | 15591 | 72 | 0 | H | ||
| tRNA-Pro | 15591 | 15660 | 70 | −1 | L | ||
| D-loop | 15661 | 16948 | 1288 | 0 | H | ||
Table 3.
Nucleotide composition and skewness of Dawkinsia filamentosa mitochondrial genome.
| Regions | Strand | Size (bp) | AT (%) | AT Skewness | GC Skewness |
|---|---|---|---|---|---|
| PCGs | H | 10,872 | 58.1 | 0.139 | −0.371 |
| PCGs | L | 522 | 57.9 | −0.497 | 0.509 |
| tRNAs | H | 1006 | 56 | 0.130 | −0.070 |
| tRNAs | L | 561 | 54.9 | −0.136 | 0.233 |
| rRNAs | H | 2650 | 55.4 | 0.290 | −0.107 |
| 16S rRNA | H | 1695 | 57.4 | 0.289 | −0.091 |
| 12S rRNA | H | 955 | 51.8 | 0.293 | −0.130 |
| Full genome | H | 16,598 | 58.1 | 0.166 | −0.300 |
Table 4.
Nucleotide composition and skewness of Pethia nigrofasciata mitochondrial genome.
| Regions | Strand | Size (bp) | AT (%) | AT Skewness | GC Skewness |
|---|---|---|---|---|---|
| PCGs | H | 10,878 | 60.2 | 0.067 | −0.301 |
| PCGs | L | 522 | 60.2 | −0.452 | 0.442 |
| tRNAs | H | 1003 | 56.9 | 0.103 | −0.042 |
| tRNAs | L | 560 | 54.4 | −0.121 | 0.224 |
| rRNAs | H | 2640 | 56.3 | 0.250 | −0.082 |
| 16S rRNA | H | 1684 | 59.1 | 0.260 | −0.078 |
| 12S rRNA | H | 956 | 51.7 | 0.231 | −0.087 |
| Full genome | H | 16,948 | 59.9 | 0.108 | −0.245 |
Table 5.
Relative synonymous codon usage of 13 protein-coding genes of the Dawkinsia filamentosa mitochondrial genome.
Table 5.
Relative synonymous codon usage of 13 protein-coding genes of the Dawkinsia filamentosa mitochondrial genome.
| Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU |
|---|---|---|---|---|---|---|---|---|---|---|---|
| UUU (F) | 79 | 0.7 | UCU (S) | 27 | 0.69 | UAU (Y) | 49 | 0.84 | UGU (C) | 6 | 0.48 |
| UUC (F) | 146 | 1.3 | UCC (S) | 51 | 1.31 | UAC (Y) | 68 | 1.16 | UGC (C) | 19 | 1.52 |
| UUA (L) | 113 | 1.12 | UCA (S) | 98 | 2.51 | UAA (*) | 6 | 3.43 | UGA (W) | 114 | 1.92 |
| UUG (L) | 14 | 0.14 | UCG (S) | 5 | 0.13 | UAG (*) | 1 | 0.57 | UGG (W) | 5 | 0.08 |
| CUU (L) | 62 | 0.61 | CCU (P) | 18 | 0.34 | CAU (H) | 16 | 0.32 | CGU (R) | 10 | 0.54 |
| CUC (L) | 66 | 0.65 | CCC (P) | 34 | 0.64 | CAC (H) | 85 | 1.68 | CGC (R) | 8 | 0.43 |
| CUA (L) | 333 | 3.29 | CCA (P) | 159 | 2.97 | CAA (Q) | 97 | 1.96 | CGA (R) | 54 | 2.92 |
| CUG (L) | 20 | 0.2 | CCG (P) | 3 | 0.06 | CAG (Q) | 2 | 0.04 | CGG (R) | 2 | 0.11 |
| AUU (I) | 140 | 0.93 | ACU (T) | 33 | 0.39 | AAU (N) | 29 | 0.47 | AGU (S) | 11 | 0.28 |
| AUC (I) | 161 | 1.07 | ACC (T) | 124 | 1.48 | AAC (N) | 94 | 1.53 | AGC (S) | 42 | 1.08 |
| AUA (M) | 168 | 1.73 | ACA (T) | 172 | 2.05 | AAA (K) | 76 | 1.9 | AGA (*) | 0 | 0 |
| AUG (M) | 26 | 0.27 | ACG (T) | 6 | 0.07 | AAG (K) | 4 | 0.1 | AGG (*) | 0 | 0 |
| GUU (V) | 42 | 0.81 | GCU (A) | 46 | 0.59 | GAU (D) | 14 | 0.37 | GGU (G) | 29 | 0.48 |
| GUC (V) | 28 | 0.54 | GCC (A) | 133 | 1.71 | GAC (D) | 62 | 1.63 | GGC (G) | 38 | 0.63 |
| GUA (V) | 126 | 2.42 | GCA (A) | 128 | 1.64 | GAA (E) | 98 | 1.9 | GGA (G) | 145 | 2.39 |
| GUG (V) | 12 | 0.23 | GCG (A) | 5 | 0.06 | GAG (E) | 5 | 0.1 | GGG (G) | 31 | 0.51 |
* termination codons.
Table 6.
Relative synonymous codon usage of 13 protein-coding genes of the Pethia nigrofasciata mitochondrial genome.
Table 6.
Relative synonymous codon usage of 13 protein-coding genes of the Pethia nigrofasciata mitochondrial genome.
| Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU | Codon | Count | RSCU |
|---|---|---|---|---|---|---|---|---|---|---|---|
| UUU (F) | 124 | 1.09 | UCU(S) | 33 | 0.85 | UAU (Y) | 60 | 1.01 | UGU (C) | 11 | 0.88 |
| UUC (F) | 103 | 0.91 | UCC(S) | 42 | 1.08 | UAC (Y) | 59 | 0.99 | UGC (C) | 14 | 1.12 |
| UUA (L) | 176 | 1.73 | UCA(S) | 107 | 2.74 | UAA (*) | 5 | 3.33 | UGA (W) | 109 | 1.85 |
| UUG (L) | 9 | 0.09 | UCG(S) | 3 | 0.08 | UAG (*) | 1 | 0.67 | UGG (W) | 9 | 0.15 |
| CUU (L) | 92 | 0.9 | CCU(P) | 30 | 0.58 | CAU (H) | 38 | 0.72 | CGU (R) | 7 | 0.38 |
| CUC (L) | 65 | 0.64 | CCC(P) | 28 | 0.54 | CAC (H) | 67 | 1.28 | CGC (R) | 5 | 0.27 |
| CUA (L) | 243 | 2.38 | CCA(P) | 144 | 2.77 | CAA (Q) | 98 | 1.92 | CGA (R) | 58 | 3.14 |
| CUG (L) | 27 | 0.26 | CCG(P) | 6 | 0.12 | CAG (Q) | 4 | 0.08 | CGG (R) | 4 | 0.22 |
| AUU (I) | 204 | 1.43 | ACU(T) | 63 | 0.81 | AAU (N) | 46 | 0.8 | AGU (S) | 10 | 0.26 |
| AUC (I) | 81 | 0.57 | ACC(T) | 90 | 1.15 | AAC (N) | 69 | 1.2 | AGC (S) | 39 | 1 |
| AUA (M) | 165 | 1.66 | ACA(T) | 153 | 1.96 | AAA (K) | 81 | 1.91 | AGA (*) | 0 | 0 |
| AUG (M) | 34 | 0.34 | ACG(T) | 6 | 0.08 | AAG (K) | 4 | 0.09 | AGG (*) | 0 | 0 |
| GUU (V) | 55 | 1 | GCU(A) | 55 | 0.66 | GAU (D) | 18 | 0.47 | GGU (G) | 28 | 0.46 |
| GUC (V) | 30 | 0.55 | GCC(A) | 133 | 1.59 | GAC (D) | 58 | 1.53 | GGC (G) | 39 | 0.64 |
| GUA (V) | 120 | 2.19 | GCA(A) | 139 | 1.66 | GAA (E) | 91 | 1.77 | GGA (G) | 132 | 2.18 |
| GUG (V) | 14 | 0.26 | GCG(A) | 7 | 0.08 | GAG (E) | 12 | 0.23 | GGG (G) | 43 | 0.71 |
* termination codons.
Table 7.
Species taxonomy used in phylogenetic analysis.
| Subfamily | Species | Length (bp) | A + T (%) | GenBank Accession No. |
|---|---|---|---|---|
| Smiliogastrinae | Barbodes binotatus | 16,573 | 57.0 | KY305681 |
| Barbodes semifasciolatus | 16,594 | 58.2 | KC113209 | |
| Dawkinsia denisonii | 16,899 | 58.6 | KF019637 | |
| Dawkinsia filamentosa | 16,598 | 58.1 | OP595699 | |
| Enteromius thysi | 16,688 | 60.5 | OP819561 | |
| Enteromius trimaculatus | 16,417 | 60.8 | NC_008666 | |
| Hampala macrolepidota | 16,766 | 58.2 | KF670818 | |
| Hampala salweenensis | 16,913 | 58.9 | MW548258 | |
| Oliotius oligolepis | 16,636 | 58.4 | ON864407 | |
| Oreichthys crenuchoides | 16,596 | 60.2 | MK456608 | |
| Osteobrama belangeri | 16,602 | 60.7 | KY887473 | |
| Pethia nigrofasciata | 16,948 | 59.9 | OP581953 | |
| Pethia padamya | 16,792 | 58.6 | ON864408 | |
| Pethia stoliczkana | 16,996 | 59.7 | OP785085 | |
| Pethia ticto | 17,302 | 60.0 | AB238969 | |
| Prolabeops melanhypopterus | 13,571 | 62.8 | ON323520 | |
| Puntigrus tetrazona | 16,550 | 59.8 | EU287909 | |
| Puntius sachsii | 16,587 | 58.2 | MZ364158 | |
| Puntius snyderi | 16,578 | 59.3 | KC113210 | |
| Sahyadria chalakkudiensis | 16,989 | 59.9 | JX311437 | |
| Systomus sarana | 16,590 | 58.6 | KU886061 | |
| Torinae | Lepidopygopsis typus | 16,729 | 56.7 | OR685011 |
| Cyprininae | Carassius auratus | 16,580 | 57.7 | OR950752 |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
MDPI and ACS Style
Sun, C.-H.; Lu, C.-H. Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes. Int. J. Mol. Sci. 2024, 25, 3004. https://doi.org/10.3390/ijms25053004
AMA Style
Sun C-H, Lu C-H. Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes. International Journal of Molecular Sciences. 2024; 25(5):3004. https://doi.org/10.3390/ijms25053004
Chicago/Turabian StyleSun, Cheng-He, and Chang-Hu Lu. 2024. "Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes" International Journal of Molecular Sciences 25, no. 5: 3004. https://doi.org/10.3390/ijms25053004
APA StyleSun, C. -H., & Lu, C. -H. (2024). Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes. International Journal of Molecular Sciences, 25(5), 3004. https://doi.org/10.3390/ijms25053004
Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.
