Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Mitochondrial Genome Annotation and Analysis
2.3. Phylogenetic Analyses
3. Results and Discussion
3.1. Mitochondrial Structural Characteristics
3.2. Protein Coding Genes
3.3. Genome Comparative Analysis
3.4. Ribosomal RNA and Transfer RNA Genes
3.5. Non-Coding Regions
3.6. Phylogenetic Relationships
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Family | Genus | Species | Assession Number |
---|---|---|---|
Myxocyprinae | Myxocyprinus | Myxocyprinus asiaticus | NC_006401.1 |
Cyprinidae | Danio | Danio rerio | NC_002333.2 |
Cobitidae | Leptobotia | Leptobotia microphthalma | KY307846.1 |
Leptobotia | Leptobotia elongata | OR818399 | |
Leptobotia | Leptobotia pellegrini | NC_031602.1 | |
Leptobotia | Leptobotia taeniops | AP013304.1 | |
Leptobotia | Leptobotia rubrilabris | KY307847.1 | |
Leptobotia | Leptobotia punctata | MH644033.1 | |
Leptobotia | Leptobotia mantschurica | AB242170.1 | |
Parabotia | Parabotia fasciata | AP011437.1 | |
Parabotia | Parabotia banarescui | NC_026127.1 | |
Parabotia | Parabotia kiangsiensis | MT850132.1 | |
Parabotia | Parabotia lijiangensis | MT323118.1 | |
Botia | Botia udomritthiruji | AP011349.1 | |
Botia | Botia lohachata | KP729183.1 | |
Chromobotia | Chromobotia macracanthus | AB242163.1 | |
Yasuhikotakia | Yasuhikotakia morleti | NC_031600.1 | |
Yasuhikotakia modesta | KY131962.1 | ||
Sinibotia | Sinibotia robusta | NC_027853.1 | |
Sinibotia pulchra | KT362179.1 | ||
Sinibotia reevesae | NC_030322.1 | ||
Sinibotia superciliaris | JX683724.1 | ||
Sinibotia superciliaris | KY307848.1 | ||
Acanthocobitis | Acanthocobitis botia | AP012139.1 | |
Acanthocobitis botia | AP012138.1 | ||
Triplophysa | Triplophysa pappenheimi | NC_033972.1 | |
Triplophysa siluroides | NC_024611.1 | ||
Pangio | Pangio kuhlii | NC_031599.1 | |
Pangio cuneovirgata | NC_031594.1 | ||
Cobitis | Cobitis lutheri | NC_022717.1 | |
Cobitis melanoleuca granoei | NC_023473.1 | ||
Cobitis nalbanti | MH349461.1 | ||
Cobitis elongatoides | NC_023947.1 | ||
Cobitis hankugensis | MN841275.1 | ||
Cobitis macrostigma | MK156771.1 | ||
Cobitis sinensis | NC_007229.1 | ||
Cobitis matsubarai | NC_029441.1 |
L. elongata | Size (bp) | A% | T% | G% | C% | A + T% | G + C% | AT-Skew | GC-Skew |
---|---|---|---|---|---|---|---|---|---|
Mitogenome | 16,591 | 30.79 | 24.77 | 16.17 | 28.27 | 55.56 | 44.44 | 0.108 | −0.272 |
PCGs | 11,430 | 28.56 | 26.77 | 15.55 | 29.13 | 55.33 | 44.67 | 0.032 | −0.304 |
tRNAs | 1558 | 28.18 | 25.8 | 23.49 | 22.53 | 53.98 | 46.02 | 0.044 | 0.021 |
rRNAs | 2638 | 34.04 | 19.48 | 21.04 | 25.44 | 53.53 | 46.47 | 0.272 | −0.095 |
Dloop | 926 | 35.64 | 31.75 | 13.71 | 18.9 | 67.39 | 32.61 | 0.058 | −0.159 |
Position | Codon | ||||||
---|---|---|---|---|---|---|---|
Gene | Stand | From | To | Size | Intergenic Length | Start | Stop |
tRNA-phe | H | 1 | 69 | 69 | 0 | ||
12 S rRNA | H | 70 | 1024 | 955 | 0 | ||
tRNA-val | H | 1025 | 1096 | 72 | 0 | ||
16 S rRNA | H | 1097 | 2779 | 1683 | 0 | ||
tRNA-leu | H | 2780 | 2854 | 75 | 0 | ||
nd1 | H | 2855 | 3829 | 975 | 0 | ATG | TAA |
tRNA-ile | H | 3838 | 3909 | 72 | 8 | ||
tRNA-gln | L | 3908 | 3978 | 71 | −2 | ||
tRNA-met | H | 3980 | 4048 | 69 | 1 | ||
nd2 | H | 4049 | 5094 | 1046 | 0 | ATG | TA- |
tRNA-trp | H | 5095 | 5163 | 69 | 0 | ||
tRNA-ala | L | 5166 | 5234 | 69 | 2 | ||
tRNA-asn | L | 5236 | 5308 | 73 | 1 | ||
OL | L | 5310 | 5340 | 39 | 1 | ||
tRNA-cys | L | 5339 | 5404 | 66 | −2 | ||
tRNA-tyr | L | 5406 | 5476 | 71 | 1 | ||
cox1 | H | 5478 | 7028 | 1551 | 1 | GTG | TAA |
tRNA-ser | L | 7030 | 7100 | 71 | 1 | ||
tRNA-asp | H | 7103 | 7174 | 72 | 2 | ||
cox2 | H | 7188 | 7878 | 691 | 13 | ATG | T-- |
tRNA-lys | H | 7879 | 7954 | 76 | 0 | ||
ATPase8 | H | 7956 | 8123 | 168 | 1 | ATG | TAA |
ATPase6 | H | 8114 | 8797 | 684 | −10 | ATG | TAA |
cox3 | H | 8797 | 9581 | 785 | 1 | ATG | TA- |
tRNA-gly | H | 9582 | 9653 | 72 | 0 | ||
nd3 | H | 9654 | 10,002 | 349 | 0 | ATG | T-- |
tRNA-arg | H | 10,003 | 10,072 | 70 | 0 | ||
nd4l | H | 10,073 | 10,369 | 297 | 0 | ATG | TAA |
nd4 | H | 10,363 | 11,744 | 1382 | −7 | ATG | TA- |
tRNA-his | H | 11,745 | 11,814 | 70 | 0 | ||
tRNA-ser | H | 11,815 | 11,881 | 67 | 0 | ||
tRNA-leu | H | 11,883 | 11,955 | 73 | 1 | ||
nd5 | H | 11,956 | 13,794 | 1839 | 0 | ATG | TAA |
nd6 | L | 13,791 | 14,312 | 522 | −4 | ATG | TAA |
tRNA-glu | L | 14,313 | 14,381 | 69 | 0 | ||
cytb | H | 14,386 | 15,526 | 1141 | 4 | ATG | T-- |
tRNA-thr | H | 15,527 | 15,598 | 72 | 0 | ||
tRNA-pro | L | 15,597 | 15,666 | 70 | −2 | ||
CR | H | 15,666 | 16,591 | 926 | 0 |
Codon | No. | RSCU | Codon | No. | RSCU | Codon | No. | RSCU |
---|---|---|---|---|---|---|---|---|
UAA() | 7 | 1 | AAA(K) | 38 | 1.8536 | CGG(R) | 5 | 0.5 |
GCA(A) | 68 | 1.4468 | AAG(K) | 3 | 0.1464 | CGU(R) | 5 | 0.5 |
GCC(A) | 94 | 2 | CUA(L) | 123 | 2.271 | AGC(S) | 24 | 1.161 |
GCG(A) | 3 | 0.064 | CUC(L) | 57 | 1.0524 | AGU(S) | 4 | 0.1938 |
GCU(A) | 23 | 0.4892 | CUG(L) | 22 | 0.4062 | UCA(S) | 50 | 2.4192 |
UGC(C) | 7 | 1.1666 | CUU(L) | 53 | 0.9786 | UCC(S) | 22 | 1.0644 |
UGU(C) | 5 | 0.8334 | UUA(L) | 51 | 0.9414 | UCG(S) | 1 | 0.0486 |
GAC(D) | 25 | 1.3158 | UUG(L) | 19 | 0.351 | UCU(S) | 23 | 1.113 |
GAU(D) | 13 | 0.6842 | AUA(M) | 60 | 2.0226 | ACA(T) | 72 | 1.87 |
GAA(E) | 36 | 1.44 | AUG(M) | 28 | 0.9438 | ACC(T) | 59 | 1.5324 |
GAG(E) | 14 | 0.56 | GUG(M) | 1 | 0.0336 | ACG(T) | 1 | 0.026 |
UUC(F) | 63 | 0.9618 | AAC(N) | 54 | 1.4594 | ACU(T) | 22 | 0.5716 |
UUU(F) | 68 | 1.0382 | AAU(N) | 20 | 0.5406 | GUA(V) | 52 | 1.5524 |
GGA(G) | 48 | 1.4116 | CCA(P) | 47 | 1.6348 | GUC(V) | 23 | 0.6864 |
GGC(G) | 31 | 0.9116 | CCC(P) | 47 | 1.6348 | GUG(V) | 24 | 0.7164 |
GGG(G) | 39 | 1.1472 | CCG(P) | 6 | 0.2088 | GUU(V) | 35 | 1.0448 |
GGU(G) | 18 | 0.5296 | CCU(P) | 15 | 0.5216 | UGA(W) | 45 | 1.6364 |
CAC(H) | 42 | 1.7142 | CAA(Q) | 45 | 1.9148 | UGG(W) | 10 | 0.3636 |
CAU(H) | 7 | 0.2858 | CAG(Q) | 2 | 0.0852 | UAC(Y) | 26 | 0.963 |
AUC(I) | 59 | 0.792 | CGA(R) | 23 | 2.3 | UAU(Y) | 28 | 1.037 |
AUU(I) | 90 | 1.208 | CGC(R) | 7 | 0.7 |
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Ke, Z.; Zhou, K.; Hou, M.; Luo, H.; Li, Z.; Pan, X.; Zhou, J.; Jing, T.; Ye, H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals 2023, 13, 3841. https://doi.org/10.3390/ani13243841
Ke Z, Zhou K, Hou M, Luo H, Li Z, Pan X, Zhou J, Jing T, Ye H. Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals. 2023; 13(24):3841. https://doi.org/10.3390/ani13243841
Chicago/Turabian StyleKe, Zhenlin, Kangqi Zhou, Mengdan Hou, Hui Luo, Zhe Li, Xianhui Pan, Jian Zhou, Tingsen Jing, and Hua Ye. 2023. "Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae" Animals 13, no. 24: 3841. https://doi.org/10.3390/ani13243841
APA StyleKe, Z., Zhou, K., Hou, M., Luo, H., Li, Z., Pan, X., Zhou, J., Jing, T., & Ye, H. (2023). Characterization of the Complete Mitochondrial Genome of the Elongate Loach and Its Phylogenetic Implications in Cobitidae. Animals, 13(24), 3841. https://doi.org/10.3390/ani13243841