The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families
Abstract
:1. Introduction
2. Results and Discussion
2.1. Mitogenome Organization and Nucleotide Composition
2.2. PCGs (Protein-Coding Genes)
2.3. The tRNA Genes and rRNA Genes
2.4. The D-Loop Region
2.5. Intergenic Spacer and Overlapping Regions
2.6. Rearrangement
2.7. Phylogenetic Analyses
3. Materials and Methods
3.1. Sampling and DNA Extraction
3.2. PCR Amplification, Sequencing and Sequence Assembly
3.3. Sequence Analysis
3.4. Phylogenetic Analysis
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
atp6 | ATPase subunit 6 |
atp8 | ATPase subunit 8 |
cox1-3 | cytochrome c oxidase subunit I-III |
cytb | cytochrome b |
nad1-6, 4L | NADH dehydrogenase subunit 1-6, 4L |
PCGs | protein-coding genes |
tRNA | transfer RNA genes |
rRNA | ribosomal RNA genes |
12/16S | small and large subunit of ribosomal RNA genes |
ML | maximum likelihood analyses |
BI | bayesian inference analyses |
RSCU | relative synonymous codon usage |
IGS | intergenic spacer region |
BPP | bayesian posterior probabilities |
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Gene | C. meridianus | C. relictus | C. kyebangensis | |||
---|---|---|---|---|---|---|
Size (bp) | A + T (%) | Size (bp) | A + T (%) | Size (bp) | A + T (%) | |
PCGs | 11,186 | 73.3 | 11,183 | 72.5 | 11,184 | 73.4 |
tRNAs | 1450 | 74.9 | 1450 | 74.4 | 1451 | 74.6 |
rRNAs | 2060 | 76.2 | 2063 | 75.8 | 2067 | 76.5 |
D-loop | 240 | 77.5 | 672 | 80.3 | 1009 | 80.2 |
Genome | 15,322 | 74.2 | 15,373 | 73.5 | 15,720 | 74.4 |
Gene Name | Strand | Location | Size (bp) | IGS | Anticodon | Start/Stop Codon | |
---|---|---|---|---|---|---|---|
tRNA-Ile | H | 1–65 | 65 | GAT | |||
tRNA-Gln | L | 64–132 | 69 | −2 | TTG | ||
tRNA-Met | H | 140–205 | 66 | 7 | CAT | ||
nad2 | H | 206–1233 | 1028 | 0 | ATG/TA* | ||
tRNA-Trp | H | 1234–1299 | 66 | 0 | TCA | ||
tRNA-Cys | L | 1292–1355 | 64 | −8 | GCA | ||
tRNA-Tyr | L | 1356–1424 | 69 | 0 | GTA | ||
cox1 | H | 1429–2964 | 1536 | 4 | TTG/TAA | ||
tRNA-LeuUUR | H | 2967–3032 | 66 | 2 | TAA | ||
cox2 | H | 3033–3717 | 685 | 0 | ATA/T** | ||
tRNA-Lys | H | 3718–3787 | 70 | 0 | CTT | ||
tRNA-Asp | H | 3788–3849 | 62 | 0 | GTC | ||
atp8 | H | 3850–4008 | 159 | 0 | ATT/TAA | ||
atp6 | H | 4002–4682 | 681 | −7 | ATG/TAA | ||
cox3 | H | 4682–5470 | 789 | −1 | ATG/TAA | ||
tRNA-Gly | H | 5475–5538 | 64 | 4 | TCC | ||
nad3 | H | 5536–5892 | 357 | −3 | ATA/TAA | ||
tRNA-SerAGN | H | 6040–6108 | 69 | 147 | GCT | ||
tRNA-Ala | H | 6283–6347 | 65 | 174 | TGC | ||
tRNA-Arg | H | 6348–6410 | 63 | 0 | TCG | ||
tRNA-Asn | H | 6414–6478 | 65 | 3 | GTT | ||
tRNA-Glu | H | 6541–6604 | 64 | 62 | TTC | ||
tRNA-Phe | L | 6605–6671 | 67 | 0 | GAA | ||
nad5 | L | 6672–8400 | 1729 | 0 | ATG/T** | ||
tRNA-His | L | 8401–8464 | 64 | 0 | GTG | ||
nad4 | L | 8467–9807 | 1341 | 2 | ATG/TAA | ||
nad4L | L | 9801–10,088 | 288 | −7 | ATG/TAA | ||
tRNA-Thr | H | 10,093–10,157 | 65 | 4 | TGT | ||
tRNA-Pro | L | 10,158–10,221 | 64 | 0 | TGG | ||
nad6 | H | 10,224–10,721 | 498 | 2 | ATT/TAA | ||
cytb | H | 10,724–11,855 | 1132 | 2 | ATG/T** | ||
tRNA-SerUCN | H | 11,856–11,923 | 68 | 0 | TGA | ||
nad1 | L | 11,920–12,886 | 967 | −4 | ATG/T** | ||
tRNA-LeuCUN | L | 12,888–12,954 | 67 | 1 | TAG | ||
16S | L | 12,955–14,237 | 1283 | 0 | |||
tRNA-Val | L | 14,238–14,305 | 68 | 0 | TAC | ||
12S | L | 14,306–15,082 | 777 | 0 | |||
D-loop | 15,083–15,322 | 240 | 0 |
Gene | C. meridianus | C. relictus | C. kyebangensis | |||
---|---|---|---|---|---|---|
AT Skew | GC Skew | AT Skew | GC Skew | AT Skew | GC Skew | |
PCGs | 0.22 | −0.23 | 0.24 | −0.23 | 0.23 | −0.23 |
tRNAs | 0.12 | −0.16 | 0.15 | −0.16 | 0.14 | −0.15 |
rRNAs | 0.29 | −0.36 | 0.30 | −0.34 | 0.31 | −0.34 |
D-loop | 0.37 | −0.52 | 0.15 | −0.09 | 0.27 | −0.33 |
Genome | 0.22 | −0.25 | 0.23 | −0.23 | 0.24 | −0.24 |
Order | Species | Accession Number | Reference |
---|---|---|---|
Ephemeroptera | Parafronurus youi | EU349015 | [42] |
Odonata | Brachythemis contaminata | NC_026305 | [49] |
Mantophasmatodea | Sclerophasma paresisense | NC_007701 | [50] |
Orthoptera | Deracantha onos | EU137664 | [51] |
Physemacris variolosa | NC_014491 | [52] | |
Atractomorpha sinensis | NC_011824 | [53] | |
Plecoptera | Kamimuria wangi | KC894944 | [54] |
Phasmatodea | Bacillus rossius | GU001956 | [55] |
Heteropteryx dilatata | AB477468 | [56] | |
Mantodea | Tamolanica tamolana | NC_007702 | [35] |
Leptomantella albella | NC_024028 | [57] | |
Isoptera | Mastotermes darwiniensis | NC_018120 | [35] |
Microhodotermes viator | NC_018122 | [35] | |
Neotermes insularis | NC_018124 | [35] | |
Zootermopsis nevadensis | NC_024658 | [58] | |
Zootermopsis angusticollis | NC_018123 | [35] | |
Macrotermes natalensis | NC_025522 | [59] | |
Coptotermes formosanus | AB626147 | [60] | |
Porotermes adamsoni | NC_018121 | [35] | |
Blattodea | Cryptocercus meridianus | MG518617 | this study |
Cryptocercus relictus | NC_018132 | [35] | |
Cryptocercus kyebangensis | KP872847 | [12] | |
Blattella germanica | NC_012901 | [61] | |
Eupolyphaga sinensis | NC_014274 | [62] | |
Blattella bisignata | NC_018549 | [63] | |
Periplaneta americana | NC_016956 | [61] | |
Periplaneta fuliginosa | AB126004 | [64] | |
Opisthoplatia orientalis | KT893460 | [65] | |
Panchlota nivea | KU684412 | [20] | |
Shelfordella lateralis | KU684413 | [20] | |
Gromphadorhina | KU684411 | [20] | |
portentosa | |||
Blaptica dubia | KU684410 | [20] |
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Li, W.; Wang, Z.; Che, Y. The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families. Int. J. Mol. Sci. 2017, 18, 2397. https://doi.org/10.3390/ijms18112397
Li W, Wang Z, Che Y. The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families. International Journal of Molecular Sciences. 2017; 18(11):2397. https://doi.org/10.3390/ijms18112397
Chicago/Turabian StyleLi, Weijun, Zongqing Wang, and Yanli Che. 2017. "The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families" International Journal of Molecular Sciences 18, no. 11: 2397. https://doi.org/10.3390/ijms18112397