The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling Collection and DNA Extraction
2.2. PCR Amplification and Sequencing
2.3. Mitogenome Assembly and Annotation
2.4. Phylogenetic Analysis
3. Results and Discussion
3.1. Characteristics of the Mitogenome
3.2. Base Composition
3.3. Protein Coding Genes
3.4. Transfer RNA Genes
3.5. The Control Region
3.6. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Family | Species | Number (bp) | GenBank Number | References |
---|---|---|---|---|
Nemouridae | Sphaeronemoura grandicauda | 15,661 | MH085454 | [20] |
Sphaeronemoura acutispina | 15,016 | MH085455 * | [35] | |
Sphaeronemoura hainana | 15,260 | MK111420 * | [17] | |
Sphaeronemoura elephas | 15,846 | MN944385 | [36] | |
Mesonemoura tritaenia | 15,778 | MH085451 | [37] | |
Mesonemoura metafiligera | 15,739 | MH085450 | [37] | |
Protonemura kohnoae | 15,707 | MH085452 | [20] | |
Protonemura datongensis | 15,756 | MT276842 | [38] | |
Protonemura orbiculata | 15,758 | MH085453 | [20] | |
Amphinemura claviloba | 15,707 | MN720741 | [39] | |
Amphinemura bulla | 15,827 | MW339348 | [40] | |
Amphinemura longispina | 15,709 | MH085446 | [20] | |
Indonemoura nohirae | 15,738 | MH085449 | [20] | |
Indonemoura jacobsoni | 15,642 | MH085448 | [20] | |
Nemoura papilla | 15,774 | MK290826 | [41] | |
Nemoura nankinensis | 16,602 | KY940360 | [42] | |
Nemoura meniscata | 15,895 | MN944386 | [43] | |
Notonemouridae | Neonemura barrosi | 14,852 | MK111418 * | [17] |
Capniidae | Mesocapnia daxingana | 15,524 | KY568983 * | [27] |
Mesocapnia arizonensis | 14,921 | KP642637 * | [44] | |
Capnia zijinshana | 16,310 | KX094942 | [28] | |
Apteroperla tikumana | 15,564 | NC_027698 | [35] | |
Zwicknia bifrons | 15,380 | MT872688* | [35] | |
Isocapnia anguis | 16,200 | OQ735414 | This study | |
Taeniopterygidae | Doddsia occidentalis | 16,020 | MG589787 | [19] |
Strophopteryx fasciata | 15,527 | ON500674 | [24] | |
Taeniopteryx ugola | 15,353 | MG589786 | [19] | |
Leuctridae | Paraleuctra cercia | 15,625 | MK492251 | [21] |
Rhopalopsole bulbifera | 15,599 | MK111419 * | [17] | |
Perlomyia isobeae | 15,795 | MK492252 | [21] | |
Perlodidae(Outgroup) | Isoperla eximia | 16,034 | MG910457 | [45] |
Pseudomegarcys japonica | 16,067 | MG910458 | [45] |
Feature | Proportion of Nucleotides | No. of Nucleotides | |||||||
---|---|---|---|---|---|---|---|---|---|
T% | C% | A% | G% | AT% | GC% | AT Skew | GC Skew | ||
Genome | 31.28 | 20.64 | 34.91 | 13.17 | 66.19 | 33.81 | 0.05 | −0.22 | 16,200 |
Protein coding genes | 37.63 | 18.62 | 27.15 | 16.60 | 64.78 | 35.22 | −0.16 | −0.06 | 11,219 |
First position | 36.58 | 18.61 | 27.38 | 17.41 | 63.96 | 36.02 | −0.14 | −0.03 | 3739 |
Second position | 37.94 | 18.00 | 27.14 | 16.90 | 65.08 | 34.90 | −0.17 | 0.03 | 3739 |
Third position | 38.37 | 19.25 | 26.90 | 15.46 | 65.27 | 34.71 | −0.18 | −0.11 | 3739 |
PCG−J | 34.34 | 22.55 | 28.61 | 14.50 | 62.95 | 37.05 | −0.09 | −0.22 | 6904 |
First codon position | 28.67 | 22.42 | 34.01 | 14.90 | 62.68 | 37.32 | 0.09 | −0.20 | 2302 |
Second codon position | 35.16 | 22.56 | 24.12 | 18.17 | 59.28 | 40.72 | −0.19 | −0.11 | 2301 |
Third codon position | 39.20 | 22.69 | 27.68 | 10.43 | 66.88 | 33.12 | −0.17 | −0.37 | 2301 |
PCG−N | 40.88 | 14.82 | 25.64 | 18.67 | 66.52 | 33.48 | −0.23 | 0.12 | 5609 |
First codon position | 40.91 | 12.62 | 26.68 | 19.79 | 67.59 | 32.41 | −0.21 | 0.22 | 1870 |
Second codon position | 40.77 | 17.71 | 20.65 | 20.87 | 61.42 | 38.58 | −0.33 | 0.08 | 1869 |
Third codon position | 40.96 | 14.12 | 29.57 | 15.35 | 70.53 | 29.47 | −0.16 | 0.04 | 1870 |
tRNA genes | 34.24 | 13.69 | 34.78 | 17.29 | 69.02 | 30.98 | 0.01 | 0.12 | 1475 |
rRNA genes | 37.51 | 10.45 | 33.69 | 18.35 | 71.20 | 28.80 | −0.05 | 0.27 | 2125 |
lrRNA | 37.66 | 9.08 | 34.81 | 18.45 | 72.47 | 27.53 | −0.04 | 0.34 | 1333 |
srRNA | 37.25 | 12.75 | 31.82 | 18.18 | 69.07 | 30.93 | −0.08 | 0.18 | 792 |
CR | 30.08 | 20.67 | 36.54 | 12.71 | 66.62 | 33.38 | 0.10 | −0.24 | 1393 |
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Rehman, A.; Huo, Q.-B.; Du, Y.-Z. The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea. Genes 2023, 14, 965. https://doi.org/10.3390/genes14050965
Rehman A, Huo Q-B, Du Y-Z. The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea. Genes. 2023; 14(5):965. https://doi.org/10.3390/genes14050965
Chicago/Turabian StyleRehman, Abdur, Qing-Bo Huo, and Yu-Zhou Du. 2023. "The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea" Genes 14, no. 5: 965. https://doi.org/10.3390/genes14050965
APA StyleRehman, A., Huo, Q.-B., & Du, Y.-Z. (2023). The First Complete Mitochondrial Genome of Genus Isocapnia (Plecoptera: Capniidae) and Phylogenetic Assignment of Superfamily Nemouroidea. Genes, 14(5), 965. https://doi.org/10.3390/genes14050965