Mitochondrial Genome and Phylogenetics of Philonthus spinipes (Sharp, 1874)
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摘要:
目的 探究大赤隐翅虫Philonthus spinipes（Sharp, 1874）的线粒体基因组结构特征及隐翅虫亚科的系统发育关系。 方法 利用高通量测序技术获得大赤隐翅虫线粒体基因组的全序列。在系统发育分析中，选择隐翅虫亚科的21个物种和毒隐翅虫亚科的8个物种作为内群，并选择2个蚁甲亚科Pselaphinae的物种作为外群，利用最大似然法和贝叶斯法重建隐翅虫亚科的系统发育关系。 结果 大赤隐翅虫的线粒体基因组包含37个基因（13个蛋白质编码基因、22个tRNA基因和2个rRNA基因）和一段非编码控制区。整个线粒体基因组全长为16 219 bp（GenBank登录号：OL998729）。大赤隐翅虫线粒体基因组的13个蛋白质编码基因的起始密码子除nad6和nad1利用ATC和TTG开头外，其余蛋白质编码基因都是以ATT、ATA和ATG开头。4个蛋白质编码基因（cox1、cox2、cox3和nad5）以不完整的终止密码子T或TA结尾，其余9个蛋白质编码基因以完整的终止密码子TAA或TAG结尾。除trnS1因缺少DHU臂而形成一个简单的环，无法形成稳定的三叶草结构外，其余tRNA基因均能形成典型的三叶草结构。rrnL基因的全长为1 275 bp，A+T含量为79.84%。rrnS基因全长为765 bp，A+T含量为76.47%。 结论 两种不同的系统发育分析方法构建的隐翅虫亚科的系统发育关系是基本一致的，均表明隐翅虫亚科为非单系群；毒隐翅虫亚科为单系群；毒隐翅虫亚科嵌套在隐翅虫亚科中。 Abstract:Objective Mitochondrial genome and phylogenetic relationship in Staphylininae subfamily of Philonthus spinipes (Sharp, 1874) were determined. Method The high-throughput sequencing technique was applied to secure the full length mitochondrial genome of P. spinipes. A phylogenetic analysis was conducted to decipher the beetle’s relationship in the Staphylininae subfamily. Using 21 exemplars of Staphylininae and 8 of Paederinae as ingroups as well as two Pselaphinae species as outgroups, the phylogeny was reconstructed with the maximum likelihood (ML) and Bayesian inference (BI) methods. Result The mitochondrial genome of P. spinipes was a circular molecule of 16 219 bp with the GenBank accession number of OL998729. It contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region. Most of the protein-coding genes started with ATT, ATA, or ATG, but nad6 did with ATC and nad1 with TTG. And cox1, cox2, cox3, and nad5 had an incomplete T or TA as the stop codon, while the remaining 9 genes terminated with TAA or TAG. All tRNA genes, except trnS1 which lacked the DHU arm, could be folded into a typical cloverleaf-like structure. The lengths of rrnL and rrnS were 1 275 bp and 765 bp with the A+T contents of 79.84% and 76.47%, respectively. Conclusion The two applied phylogenetic inference methods produced a similar tree topological structure that showed Paederinae to be monophyletic, Staphylininae non-monophyletic, and Paederinae nested within the Staphylininae subfamily. -
Key words:
- Coleoptera /
- Staphylininae /
- Philonthus spinipes /
- mitochondrial genome /
- phylogeny
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图 1 大赤隐翅虫线粒体基因组结构
箭头表示转录方向。
Figure 1. Structure of P. spinipes mitochondrial genome
Arrow indicates direction of transcription.
图 2 大赤隐翅虫 22 个 tRNA基因的二级结构
Figure 2. Secondary structures of 22 tRNAs genes of P. spinipes
图 3 大赤隐翅虫12S rRNA基因二级结构预测
Figure 3. Predicted secondary structure of 16S rRNA gene of P. spinipes mitogenome
图 4 大赤隐翅虫12S rRNA基因二级结构预测
Figure 4. Predicted secondary structure of 12S rRNA gene of P. spinipes mitogenome
表 1 大赤隐翅虫线粒体基因组注释
Table 1. Annotation of P. spinipes mitochondrial genome
基因
Gene基因长度
Gene length/bp起始位置
Start position/bp终止位置
Stop position/bp起始密码子
Start codon终止密码子
Stop codon编码链
Coding strand控制区Control region 1 521 1 1 521 非编码序列Non-coding sequence trnI 64 1 522 1 585 H trnQ 69 1 651 1 583 L trnM 69 1 651 1 719 H nad2 1 017 1 720 2 736 ATT TAA H trnW 67 2 735 2 801 H trnC 62 2 878 2 817 L trnY 64 2 944 2 881 L cox1 1 540 2 937 4 476 ATT T H trnL2 65 4 477 4 541 H cox2 688 4 540 5 227 ATG T H trnK 71 5 228 5 298 H trnD 66 5 298 5 363 H atp8 156 5 364 5 519 ATA TAA H atp6 669 5 513 6 181 ATG TAA H cox3 788 6 181 6 968 ATG TA H trnG 61 6 970 7 030 H nad3 354 7 033 7 386 ATT TAG H trnA 65 7 385 7 449 H trnR 66 7 449 7 514 H trnN 66 7 571 7 636 H trnS1 66 7 637 7 702 H trnE 68 7 703 7 770 H trnF 67 7 835 7 769 L nad5 1 717 9 552 7 836 ATT T L trnH 65 9 617 9 553 L nad4 1 338 10 954 9 617 ATG TAA L nad4l 288 11 235 10 948 ATG TAA L trnT 63 11 238 11 300 H trnP 64 11 364 11 301 L nad6 498 11 366 11 863 ATC TAA H Cob 1 143 11 863 13 005 ATG TAG H trnS2 66 13 004 13 069 H nad1 951 14 037 13 087 TTG TAG L trnL1 65 14 103 14 039 L rrnL 1 275 15 378 14 104 L trnV 73 15 454 15 382 L rrnS 765 16 219 15 455 L H：重链；L：轻链；T或TA表示不完全密码子。
H: Heavy strand; L: light strand; T or TA: incomplete stop codon.
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表 2 大赤隐翅虫线粒体基因组13个蛋白质编码基因的相对密码子使用频率
Table 2. Relative synonymous codon usage of 13 protein-coding genes of P. spinipes mitochondrial genome
密码子
Codon次数
CountRSCU 密码子
Codon次数
CountRSCU 密码子
Codon次数
CountRSCU 密码子
Codon次数
CountRSCU UUU(F) 280 1.53 UCU(S) 72 1.58 UAU(Y) 173 1.54 UGU(C) 51 1.17 UUC(F) 85 0.47 UCC(S) 42 0.92 UAC(Y) 52 0.46 UGC(C) 36 0.83 UUA(L) 185 2.44 UCA(S) 73 1.6 UAA(*) 127 1.23 UGA(W) 60 1.3 UUG(L) 61 0.8 UCG(S) 22 0.48 UAG(*) 80 0.77 UGG(W) 32 0.7 CUU(L) 78 1.03 CCU(P) 57 1.78 CAU(H) 59 1.53 CGU(R) 12 1.2 CUC(L) 38 0.5 CCC(P) 34 1.06 CAC(H) 18 0.47 CGC(R) 4 0.4 CUA(L) 53 0.7 CCA(P) 30 0.94 CAA(Q) 51 1.38 CGA(R) 16 1.6 CUG(L) 40 0.53 CCG(P) 7 0.22 CAG(Q) 23 0.62 CGG(R) 8 0.8 AUU(I) 240 1.57 ACU(T) 54 1.64 AAU(N) 159 1.55 AGU(S) 36 0.79 AUC(I) 65 0.43 ACC(T) 33 1 AAC(N) 46 0.45 AGC(S) 27 0.59 AUA(M) 122 1.37 ACA(T) 39 1.18 AAA(K) 99 1.49 AGA(S) 46 1.01 AUG(M) 56 0.63 ACG(T) 6 0.18 AAG(K) 34 0.51 AGG(S) 47 1.03 GUU(V) 35 1.46 GCU(A) 17 1.58 GAU(D) 60 1.48 GGU(G) 17 0.78 GUC(V) 15 0.63 GCC(A) 11 1.02 GAC(D) 21 0.52 GGC(G) 13 0.6 GUA(V) 26 1.08 GCA(A) 12 1.12 GAA(E) 56 1.24 GGA(G) 33 1.52 GUG(V) 20 0.83 GCG(A) 3 0.28 GAG(E) 34 0.76 GGG(G) 24 1.1 RSCU：相对密码子使用频率; *终止密码子。
RSCU: Relative synonymous codon usage; *: stop codon.
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[1] THAYER M K. Morphology and Systematics (Archostemata, Adephaga, Myxophaga, Polyphaga partim)[M]. Berlin: Walter de Gruyter, 2016: 394-442. [2] CAI C Y, WANG Y L, LIANG L, et al. Congruence of morphological and molecular phylogenies of the rove beetle subfamily Staphylininae (Coleoptera: Staphylinidae) [J]. Scientific Reports, 2019, 9(1): 1−11. doi: 10.1038/s41598-018-37186-2 [3] KASULE F K. The larvae of Paederinae and Staphylininae (Coleoptera: Staphylinidae) with keys to the known British Genera [J]. Transactions of the Royal Entomological Society of London, 2009, 122(2): 49−80. doi: 10.1111/j.1365-2311.1970.tb00527.x [4] NEWTON A F, THAYER M K. In American Beetles (Archostemata, Myxophaga, Adephaga, Polyphaga: Staphyliniformia)[M]. London: CRC Press, 2000: 272–418. [5] GREBENNIKOV V V, NEWTON A F. Good-bye Scydmaenidae, or why the ant-like stone beetles should become megadiverse Staphylinidae sensu latissimo (Coleoptera) [J]. European Journal of Entomology, 2009, 106(2): 275−301. doi: 10.14411/eje.2009.035 [6] NEWTON A F, THAYER M K, CHICAGO N N H M. Current classification and family-group names in Staphyliniformia (Coleoptera)[M]. Chicago: Field Museum of Natural History, 1992. [7] SOLODOVNIKOV A Y, NEWTON A F. Phylogenetic placement of Arrowinini trib. n. within the subfamily Staphylininae (Coleoptera: Staphylinidae), with revision of the relict South African genusArrowinusand description of its larva [J]. Systematic Entomology, 2005, 30(3): 398−441. doi: 10.1111/j.1365-3113.2004.00283.x [8] MCKENNA D D, WILD A L, KANDA K, et al. The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution [J]. Systematic Entomology, 2015, 40(4): 835−880. doi: 10.1111/syen.12132 [9] CHATZIMANOLIS S, COHEN I M, SCHOMANN A, et al. Molecular phylogeny of the mega-diverse rove beetle tribe Staphylinini (Insecta, Coleoptera, Staphylinidae) [J]. Zoologica Scripta, 2010, 39(5): 436−449. doi: 10.1111/j.1463-6409.2010.00438.x [10] MCKENNA D D, FARRELL B D, CATERINO M S, et al. Phylogeny and evolution of Staphyliniformia and Scarabaeiformia: Forest litter as a stepping stone for diversification of nonphytophagous beetles [J]. Systematic Entomology, 2015, 40(1): 35−60. doi: 10.1111/syen.12093 [11] BRUNKE A J, CHATZIMANOLIS S, SCHILLHAMMER H, et al. Early evolution of the hyperdiverse rove beetle tribe Staphylinini (Coleoptera: Staphylinidae: Staphylininae) and a revision of its higher classification [J]. Cladistics, 2016, 32(4): 427−451. doi: 10.1111/cla.12139 [12] SCHOMANN A M, SOLODOVNIKOV A. Phylogenetic placement of the austral rove beetle genus Hyperomma triggers changes in classification of Paederinae (Coleoptera: Staphylinidae) [J]. Zoologica Scripta, 2017, 46(3): 336−347. doi: 10.1111/zsc.12209 [13] CAMERON S L. Insect mitochondrial genomics: Implications for evolution and phylogeny [J]. Annual Review of Entomology, 2014, 59: 95−117. doi: 10.1146/annurev-ento-011613-162007 [14] BOORE J L. Animal mitochondrial genomes [J]. Nucleic Acids Research, 1999, 27(8): 1767−1780. doi: 10.1093/nar/27.8.1767 [15] SONG N, ZHANG H, LI H, et al. All 37 mitochondrial genes of aphid Aphis craccivora obtained from transcriptome sequencing: Implications for the evolution of aphids [J]. PLoS One, 2016, 11(6): e0157857. doi: 10.1371/journal.pone.0157857 [16] JIN J J, YU W B, YANG J B, et al. GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes [J]. Genome Biology, 2020, 21(1): 241. doi: 10.1186/s13059-020-02154-5 [17] BERNT M, DONATH A, JÜHLING F, et al. MITOS: Improved de novo metazoan mitochondrial genome annotation [J]. Molecular Phylogenetics and Evolution, 2013, 69(2): 313−319. doi: 10.1016/j.ympev.2012.08.023 [18] KUMAR S, STECHER G, TAMURA K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets [J]. Molecular Biology and Evolution, 2016, 33(7): 1870−1874. doi: 10.1093/molbev/msw054 [19] KATOH K, STANDLEY D M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability [J]. Molecular Biology and Evolution, 2013, 30(4): 772−780. doi: 10.1093/molbev/mst010 [20] ABASCAL F, ZARDOYA R, TELFORD M J. TranslatorX: Multiple alignment of nucleotide sequences guided by amino acid translations [J]. Nucleic Acids Research, 2010, 38(S2): W7−13. doi: 10.1093/nar/gkq291 [21] CAPELLA-GUTIÉRREZ S, SILLA-MARTÍNEZ J M, GABALDÓN T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses [J]. Bioinformatics, 2009, 25(15): 1972−1973. doi: 10.1093/bioinformatics/btp348 [22] KÜCK P, LONGO G C. FASconCAT-G: Extensive functions for multiple sequence alignment preparations concerning phylogenetic studies [J]. Frontiers in Zoology, 2014, 11(1): 1−8. doi: 10.1186/1742-9994-11-1 [23] NGUYEN L T, SCHMIDT H A, VON HAESELER A, et al. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies [J]. Molecular Biology and Evolution, 2015, 32(1): 268−274. doi: 10.1093/molbev/msu300 [24] LARTILLOT N, LEPAGE T, BLANQUART S. PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating [J]. Bioinformatics, 2009, 25(17): 2286−2288. doi: 10.1093/bioinformatics/btp368 [25] GREINER S, LEHWARK P, BOCK R. OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: Expanded toolkit for the graphical visualization of organellar genomes [J]. Nucleic Acids Research, 2019, 47(W1): W59−64. doi: 10.1093/nar/gkz238 [26] BAE J S, KIM I, SOHN H D, et al. The mitochondrial genome of the firefly, Pyrocoelia rufa: Complete DNA sequence, genome organization, and phylogenetic analysis with other insects [J]. Molecular Phylogenetics and Evolution, 2004, 32(3): 978−985. doi: 10.1016/j.ympev.2004.03.009 [27] 林爱丽, 李欣欣, 赵新成, 等. 黑毛皮蠹线粒体基因组分析及皮蠹科系统发育分析 [J]. 昆虫学报, 2018, 61(4):477−487. doi: 10.16380/j.kcxb.2018.04.010LIN A L, LI X X, ZHAO X C, et al. Analysis of the mitochondrial genome of Attagenus unicolor japonicus (Coleoptera: Dermestidae) and a phylogenetic analysis of Dermestidae [J]. Acta Entomologica Sinica, 2018, 61(4): 477−487.(in Chinese) doi: 10.16380/j.kcxb.2018.04.010 [28] SONG N, ZHANG H, ZHAO T. Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling [J]. Molecular Phylogenetics and Evolution, 2019, 137: 236−249. doi: 10.1016/j.ympev.2019.05.009 [29] SONG N, ZHAI Q, ZHANG Y L. Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences [J]. Mitochondrial DNA Part A, 2021, 32(3): 98−105. doi: 10.1080/24701394.2021.1882444 [30] 林兴雨, 翟卿, 宋南, 等. 锯谷盗线粒体基因组及扁甲总科系统发育分析 [J]. 河南农业大学学报, 2023, 57(1):109−117. doi: 10.3969/j.issn.1000-2340.2023.1.hennannydxxb202301012LIN X Y, ZHAI Q, SONG N, et al. The mitochondrial genome of Oryzaephilus surinamensis and a phylogenetic analysis of cucujoidea [J]. Journal of Henan Agricultural University, 2023, 57(1): 109−117.(in Chinese) doi: 10.3969/j.issn.1000-2340.2023.1.hennannydxxb202301012 -
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