Complete Mitochondrial (mtDNA) Genome Analysis of Economically Significant Fish Cirrhinus cirrhosus in Bangladesh
Abstract
1. Introduction
2. Results
2.1. Mitochondrial Genome Assembly
2.2. Protein-Coding Genes
2.3. Transfer RNA Genes, Ribosomal RNA Genes, and Control Region
2.4. Selective Pressure Analysis
2.5. Nucleotide Diversity
2.6. Phylogenetic Analysis
3. Discussion
4. Materials and Methods
4.1. Ethics Statement
4.2. Sample Collection, DNA Extraction, and Quality Assessment
4.3. Next-Generation Sequencing
4.4. Mitogenome Assembly and Annotation
4.5. Phylogenetic Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Gene Type | Location | Intergenic Nucleotides | Size |
---|---|---|---|---|
trnF(gaa) | tRNA | 1–69 | 0 | 69 |
s-rRNA | rRNA | 70–1026 | 0 | 957 |
trnV(uac) | tRNA | 1027–1098 | 0 | 72 |
l-rRNA | rRNA | 1099–2786 | 0 | 1688 |
trnL(uaa) | tRNA | 2787–2862 | 0 | 76 |
ND1 | CDS | 2864–3838 | 1 | 975 |
trnI(gau) | tRNA | 3843–3914 | 4 | 72 |
trnQ(uug) | tRNA | 3913–3983 | −2 | 71 |
trnM(cau) | tRNA | 3985–4053 | 1 | 69 |
ND2 | CDS | 4054–5098 | 0 | 1045 |
trnW(uca) | tRNA | 5099–5169 | 0 | 71 |
trnA(ugc) | tRNA | 5172–5240 | 2 | 69 |
trnN(guu) | tRNA | 5242–5314 | 1 | 73 |
trnC(gca) | tRNA | 5348–5414 | 33 | 67 |
trnY(gua) | tRNA | 5415–5484 | 0 | 70 |
COX1 | CDS | 5486–7036 | 1 | 1551 |
trnS(uga) | tRNA | 7037–7107 | 0 | 71 |
trnD(guc) | tRNA | 7111–7182 | 3 | 72 |
COX2 | CDS | 7196–7886 | 13 | 691 |
trnK(uuu) | tRNA | 7887–7962 | 0 | 76 |
ATP8 | CDS | 7964–8128 | 1 | 165 |
ATP6 | CDS | 8122–8804 | −7 | 683 |
COX3 | CDS | 8805–9590 | 0 | 786 |
trnG(ucc) | tRNA | 9591–9662 | 0 | 72 |
ND3 | CDS | 9663–10,011 | 0 | 349 |
trnR(ucg) | tRNA | 10,012–10,081 | 0 | 70 |
ND4L | CDS | 10,082–10,378 | 0 | 297 |
ND4 | CDS | 10,372–11,752 | −7 | 1381 |
trnH(gug) | tRNA | 11,753–11,821 | 0 | 69 |
trnS(gcu) | tRNA | 11,822–11,890 | 0 | 69 |
trnL(uag) | tRNA | 11,892–11,964 | 1 | 73 |
ND5 | CDS | 11,968–13,791 | 3 | 1824 |
ND6 | CDS | 13,788–14,309 | −4 | 522 |
trnE(uuc) | tRNA | 14,310–14,378 | 0 | 69 |
CYTB | CDS | 14,384–15,524 | 5 | 1141 |
trnT(ugu) | tRNA | 15,525–15,596 | 0 | 72 |
tRNA-Pro | tRNA | 15,596–15,665 | −1 | 70 |
D-loop | misc_feature | 15,666–16,593 | 0 | 928 |
Gene | Total Bases | Number of Individual Bases | Percentage of Bases (%) | Percentage Content | AT Skew | GC Skew | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | T | G | C | A | T | G | C | AT% | GC% | ||||
trnF(gaa) | 69 | 26 | 14 | 14 | 15 | 37 | 22 | 20 | 21 | 59 | 41 | 0.3 | −0.03 |
s-rRNA | 957 | 305 | 184 | 210 | 258 | 31 | 22 | 21 | 26 | 53 | 47 | 0.24 | −0.10 |
trnV(uac) | 72 | 20 | 15 | 18 | 19 | 27 | 22 | 25 | 26 | 49 | 51 | 0.14 | −0.02 |
l-rRNA | 1688 | 624 | 334 | 328 | 402 | 36 | 22 | 19 | 23 | 58 | 42 | 0.30 | −0.10 |
trnL(uaa) | 76 | 19 | 18 | 20 | 19 | 25 | 24 | 26 | 25 | 49 | 51 | 0.02 | 0.02 |
ND1 | 975 | 292 | 235 | 141 | 307 | 29 | 26 | 14 | 31 | 55 | 45 | 0.10 | −0.37 |
trnI(gau) | 72 | 19 | 18 | 17 | 18 | 26 | 26 | 23 | 25 | 52 | 48 | 0.02 | −0.02 |
trnQ(uug) | 71 | 17 | 24 | 19 | 11 | 23 | 36 | 26 | 15 | 59 | 41 | −0.17 | 0.26 |
trnM(cau) | 69 | 15 | 13 | 17 | 24 | 21 | 21 | 24 | 34 | 42 | 58 | 0.07 | −0.17 |
ND2 | 1045 | 353 | 218 | 121 | 353 | 33 | 23 | 11 | 33 | 56 | 44 | 0.23 | −0.48 |
trnW(uca) | 71 | 26 | 18 | 14 | 13 | 36 | 27 | 19 | 18 | 63 | 37 | 0.18 | 0.03 |
trnA(ugc) | 69 | 23 | 26 | 13 | 7 | 33 | 39 | 18 | 10 | 72 | 28 | −0.06 | 0.3 |
trnN(guu) | 73 | 15 | 23 | 21 | 14 | 20 | 33 | 28 | 19 | 53 | 47 | −0.21 | 0.2 |
trnC(gca) | 67 | 20 | 16 | 18 | 13 | 29 | 26 | 26 | 19 | 55 | 45 | 0.11 | 0.16 |
trnY(gua) | 70 | 12 | 19 | 25 | 14 | 17 | 28 | 35 | 20 | 45 | 55 | −0.22 | 0.28 |
COX1 | 1551 | 416 | 446 | 277 | 412 | 26 | 31 | 17 | 26 | 57 | 43 | −0.03 | −0.19 |
trnS(uga) | 71 | 16 | 20 | 21 | 14 | 22 | 30 | 29 | 19 | 52 | 48 | −0.11 | 0.2 |
trnD(guc) | 72 | 25 | 21 | 12 | 14 | 34 | 31 | 16 | 19 | 65 | 35 | 0.08 | −0.07 |
COX2 | 691 | 215 | 175 | 111 | 190 | 31 | 26 | 16 | 27 | 57 | 43 | 0.10 | −0.26 |
trnK(uuu) | 76 | 23 | 18 | 17 | 18 | 30 | 25 | 22 | 23 | 55 | 45 | 0.12 | −0.02 |
ATP8 | 165 | 59 | 41 | 19 | 46 | 35 | 27 | 11 | 27 | 62 | 38 | 0.18 | −0.41 |
ATP6 | 683 | 208 | 184 | 90 | 201 | 30 | 28 | 13 | 29 | 58 | 42 | 0.06 | −0.38 |
COX3 | 786 | 224 | 199 | 125 | 238 | 28 | 27 | 15 | 30 | 55 | 45 | 0.05 | −0.31 |
trnG(ucc) | 72 | 25 | 21 | 12 | 14 | 34 | 31 | 16 | 19 | 65 | 35 | 0.08 | −0.07 |
ND3 | 349 | 96 | 98 | 53 | 102 | 27 | 29 | 15 | 29 | 56 | 44 | −0.01 | −0.31 |
trnR(ucg) | 70 | 20 | 18 | 14 | 18 | 28 | 27 | 20 | 25 | 55 | 45 | 0.05 | −0.12 |
ND4L | 297 | 78 | 75 | 48 | 96 | 26 | 26 | 16 | 32 | 52 | 48 | 0.01 | −0.33 |
ND4 | 1381 | 449 | 345 | 181 | 406 | 32 | 26 | 13 | 29 | 58 | 42 | 0.13 | −0.38 |
trnH(gug) | 69 | 26 | 19 | 10 | 14 | 37 | 29 | 14 | 20 | 66 | 34 | 0.15 | −0.16 |
trnS(gcu) | 69 | 23 | 18 | 13 | 15 | 33 | 28 | 18 | 21 | 61 | 39 | 0.12 | −0.07 |
trnL(uag) | 73 | 23 | 19 | 16 | 15 | 31 | 28 | 21 | 20 | 59 | 41 | 0.09 | 0.03 |
ND5 | 1824 | 612 | 463 | 220 | 529 | 33 | 26 | 12 | 29 | 59 | 41 | 0.13 | −0.41 |
ND6 | 522 | 59 | 227 | 176 | 60 | 11 | 45 | 33 | 11 | 56 | 44 | −0.58 | 0.49 |
trnE(uuc) | 69 | 18 | 24 | 17 | 10 | 26 | 36 | 24 | 14 | 62 | 38 | −0.14 | 0.25 |
CYTB | 1141 | 339 | 305 | 161 | 336 | 29 | 28 | 14 | 29 | 57 | 43 | 0.05 | −0.35 |
trnT(ugu) | 72 | 18 | 18 | 16 | 20 | 25 | 26 | 22 | 27 | 51 | 49 | 0 | −0.11 |
tRNA-Pro | 70 | 17 | 24 | 20 | 9 | 24 | 36 | 28 | 12 | 60 | 40 | −0.17 | 0.37 |
D-loop | 928 | 320 | 309 | 117 | 182 | 34 | 35 | 12 | 19 | 69 | 31 | 0.017 | −0.21 |
Sequence | Ka | Ks | Ka/Ks | p-Value (Fisher) | Substitutions | Syn-Subs | Non-syn-Subs |
---|---|---|---|---|---|---|---|
ND1 | 0.00155 | 0.004498 | 0.344636 | 0.580742 | 2 | 0.882608 | 1.11739 |
ND2 | 1.75 × 10−5 | 0.017535 | 0.001 | 0.001957 | 3 | 2.98596 | 0.014036 |
COX1 | 1.39 × 10−5 | 0.013891 | 0.001 | 0.000623 | 4 | 3.98442 | 0.01558 |
COX2 | 1.25 × 10−5 | 0.012476 | 0.001 | 0.023376 | 2 | 1.9941 | 0.005899 |
ATP8 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
ATP6 | 2.26 × 10−5 | 0.022563 | 0.001 | 0.002104 | 4 | 3.98957 | 0.010428 |
COX3 | 0.001867 | 0.006831 | 0.273377 | 0.54937 | 2 | 0.922892 | 1.07711 |
ND3 | 3.42 × 10−5 | 0.034179 | 0.001 | 0.00688 | 3 | 2.99182 | 0.008185 |
ND4L | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
ND4 | 0.002198 | 0.018689 | 0.117584 | 0.005217 | 7 | 4.81737 | 2.18263 |
ND5 | 2.09 × 10−5 | 0.020923 | 0.001 | 3.87 × 10−6 | 7 | 6.97138 | 0.028618 |
ND6 | 1.37 × 10−5 | 0.013684 | 0.001 | 0.053704 | 1 | 0.994184 | 0.005816 |
CYTB | 3.50 × 10−5 | 0.035013 | 0.001 | 1.40 × 10−6 | 8 | 7.9705 | 0.029501 |
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Huda, T.; Kabir, M.A.; Rabbane, M.G. Complete Mitochondrial (mtDNA) Genome Analysis of Economically Significant Fish Cirrhinus cirrhosus in Bangladesh. Int. J. Mol. Sci. 2025, 26, 7473. https://doi.org/10.3390/ijms26157473
Huda T, Kabir MA, Rabbane MG. Complete Mitochondrial (mtDNA) Genome Analysis of Economically Significant Fish Cirrhinus cirrhosus in Bangladesh. International Journal of Molecular Sciences. 2025; 26(15):7473. https://doi.org/10.3390/ijms26157473
Chicago/Turabian StyleHuda, Tajmirul, Md. Alamgir Kabir, and Md. Golam Rabbane. 2025. "Complete Mitochondrial (mtDNA) Genome Analysis of Economically Significant Fish Cirrhinus cirrhosus in Bangladesh" International Journal of Molecular Sciences 26, no. 15: 7473. https://doi.org/10.3390/ijms26157473
APA StyleHuda, T., Kabir, M. A., & Rabbane, M. G. (2025). Complete Mitochondrial (mtDNA) Genome Analysis of Economically Significant Fish Cirrhinus cirrhosus in Bangladesh. International Journal of Molecular Sciences, 26(15), 7473. https://doi.org/10.3390/ijms26157473