The Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of the Stephanitis chinensis

YANG Jinhong; XIE Manchao; WEN Xinru; CHEN Ruiru; KONG Weiqing

doi:10.13305/j.cnki.jts.2022.06.007

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Journal of Tea Science ›› 2022, Vol. 42 ›› Issue (6) : 839-850. DOI: 10.13305/j.cnki.jts.2022.06.007

Research Paper

The Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of the Stephanitis chinensis

YANG Jinhong¹, XIE Manchao¹, WEN Xinru¹, CHEN Ruiru¹, KONG Weiqing^2,*

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Abstract

In order to obtain the characteristics of the mitochondrial genome (mitogenome) and explore phylogenetic relationship, the mitogenome sequence of Stephanitis chinensis collected from Ankang city, Shaanxi Province was determined by Illumina and Sanger sequencing methods. The result shows that the mitogenome of S. chinensis is 18 085 bp in length, including 37 coding genes [13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs], and one control region of 3 678 bp. The gene organization of S. chinensis is the same as the ancestral gene order of insect mitogenome. The AT content of whole mitogenome is 78.10%. Among the 13 PCGs, six start with the typical ATG, seven start with ATT or ATA, and ten end with the typical TAA or TAG. Only cox2, atp6 and cox3 terminate with T. The highly occurred codons in the PCGs are UUA, AUU, UUU and AUA, and the top 4 amino acids are Leu, Ile, Phe and Ser. There are 23 mismatches of GU, UU, GA and AA in 22 tRNAs. All the tRNAs could form the common clover-leaf secondary structures, except trnS1(GCU), which lacks the DHU arm. The control region contains 3 type of non-tandem repeats and 4 (TTAG)_n in the front-end region (FER) and one tandem repeat in the back-end region (BER), and several stem-loop structures. Phylogenetic analysis shows that Stephanitis mendica has the closest relationship with S. chinensis. All the insects from Tingidae were clustered together, and placed at the base part of the phylogenetic tree.

Key words

Stephanitis chinensis / mitochondrial genome / phylogenetic relationship / sequence analysis

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YANG Jinhong, XIE Manchao, WEN Xinru, CHEN Ruiru, KONG Weiqing. The Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of the Stephanitis chinensis[J]. Journal of Tea Science. 2022, 42(6): 839-850 https://doi.org/10.13305/j.cnki.jts.2022.06.007

References

[1] 吴平昌, 李尤学. 陕南茶区茶脊冠网蝽发生现状和防控研究[J]. 陕西农业科学, 2014, 60(3): 73-76.
Wu P C, Li Y X.Study of the occurrence and control of Stephanitis chinensis Drake in the tea field of south Shaanxi[J]. Shaanxi Journal of Agricultural Sciences, 2014, 60(3): 73-76.
[2] 田忠正. 茶脊冠网蝽发生规律与防治技术研究[D]. 杨凌: 西北农林科技大学, 2017.
Tian Z Z.Study of occurrence and control techniques on Stephanitis chinensis Drake[D]. Yangling: Northwest A&F University, 2017.
[3] 陈孝钧, 吴平昌, 马荣彬, 等. 镇巴茶区一种新发生的害虫——茶网蝽[J]. 中国茶叶, 2013, 35(8): 16-17.
Chen X J, Wu P C, Ma R B, et al.A new pest in Zhenba tea area: Stephanitis chinensis Drake[J]. China Tea, 2013, 35(8): 16-17.
[4] 张锡友, 罗碧安, 孙光德, 等. 陕南茶脊冠网蝽蔓延威胁及有效防控对策思考[J]. 茶业通报, 2017, 39(3): 130-132.
Zhang X Y, Luo B A, Sun G D, et al.Spreading threat and effective control strategy of Stephanitis chinensis Drake in south Shaanxi[J]. Journal of Tea Business, 2017, 39(3): 130-132.
[5] 王梦思. 茶脊冠网蝽的生物学特性及防治研究[D]. 武汉: 湖北大学, 2019.
Wang M S.Study on the biological characteristics and control of Stephanitis chinensis Drake[D]. Wuhan: Hubei University, 2019.
[6] Crampton-Platt A, Yu D W, Zhou X, et al.Mitochondrial metagenomics: letting the genes out of the bottle[J]. GigaScience, 2016, 5(1): 15. doi: 10.1186/s13742-016-0120-y.
[7] Song F, Li H, Jiang P, et al.Capturing the phylogeny of holometabola with mitochondrial genome data and Bayesian site-heterogeneous mixture models[J]. Genome Biology and Evolution, 2016, 8(5): 1411-1426.
[8] Yang H H, Li T, Dang K, et al.Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera)[J]. BMC Genomics, 2018, 19: 264. doi: 10.1186/s12864-018-4650-9.
[9] 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: 241. doi: 10.1186/s13059-020-02154-5.
[10] Dierckxsens N, Mardulyn P, Smits G.NOVOPlasty: de novo assembly of organelle genomes from whole genome data[J]. Nucleic Acids Research, 2017, 45(4): e18. doi: 10.1093/nar/gkw955.
[11] Wick R R, Schultz M B, Zobel J, et al.Bandage: interactive visualization of de novo genome assemblies[J]. Bioinformatics, 2015, 31: 3350-3352.
[12] 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.
[13] 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-W64.
[14] Chan P P, Lowe T M. tRNAscan-SE: searching for tRNA genes in genomic sequences[J]. Methods in Molecular Biology, 2019, 1962: 1-14.
[15] Benson G.Tandem repeats finder: a program to analyze DNA sequences[J]. Nucleic Acids Research, 1999, 27(2): 573-580.
[16] Beier S, Thiel T, Münch T, et al.MISA-web: a web server for microsatellite prediction[J]. Bioinformatics, 2017, 33: 2583-2585.
[17] Zuker M.Mfold web server for nucleic acid folding and hybridization prediction[J]. Nucleic Acids Research, 2003, 31(13): 3406-3415.
[18] Tamura K, Stecher G, Kumar S.MEGA11: molecular evolutionary genetics analysis version 11[J]. Molecular Biology and Evolution, 2021, 38(7): 3022-3027.
[19] Perna N T, Kocher T D.Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes[J]. Journal of Molecular Evolution, 1995, 41(3): 353-358.
[20] Ranwez V, Harispe S, Delsuc F, et al.MACSE: multiple alignment of coding sequences accounting for frameshifts and stop codons[J]. PLoS One, 2011, 6(9): e22594. doi: 10.1371/journal.pone.0022594.
[21] Stamatakis A.RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models[J]. Bioinformatics, 2006, 22(21): 2688-2690.
[22] Clary D O, Wolstenholme D R.The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code[J]. Journal of Molecular Evolution, 1985, 22(3): 252-271.
[23] 张玉波, 史娅琴, 孙翠英. 长尾管蚜蝇Eristalis tenax (Linnaeus, 1758)线粒体基因组测序及分析[J]. 基因组学与应用生物学, 2019, 38(12): 5371-5378.
Zhang Y B, Shi Y Q, Sun C Y.Sequencing and analysis of the mitochondrial genome of Eristalis tenax (Linnaeus, 1758)[J]. Genomics and Applied Biology, 2019, 38(12): 5371-5378.
[24] 钟健, 刘增虎, 杨伟克, 等. 琥珀蚕线粒体全基因组测序及序列分析[J]. 昆虫学报, 2017, 60(8): 936-949.
Zhong J, Liu Z H, Yang W K, et al.Sequencing and analysis of the complete mitochondrial genome of Antheraea assama (Lepidoptera: Saturniidae)[J]. Acta Entomologica Sinica, 2017, 60(8): 936-949.
[25] 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: 978-985.
[26] 俞鹏飞, 李倩, 王梦馨, 等. 凹大叶蝉线粒体全基因组序列分析及系统发育关系[J]. 农业生物技术学报, 2019, 27(7): 1246-1258.
Yu P F, Li Q, Wang M X, et al.Analysis of complete mitochondrial genome and phylogenetic relationship of Bothrogonia ferruginea[J]. Journal of Agricultural Biotechnology, 2019, 27(7): 1246-1258.
[27] Zhang D X, Hewitt G M.Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies[J]. Biochemical Systematics and Ecology, 1997, 25(2): 99-120.
[28] Boyce T M, Zwick M E, Aquadro C F.Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy[J]. Genetics, 1989, 123(4): 825-836.
[29] Taanman J W.The mitochondrial genome: structure, transcription, translation and replication[J]. Biochimica et Biophysica Acta, 1999, 1410(2): 103-123.
[30] Cui Y, Dong P Z, Hua J M, et al.The complete mitochondrial genome of Aquarius paludum (Fabricius) (Insecta, Hemiptera, Gerridae)[J]. Acta Zootaxonomica Sinica, 2012, 37(2): 255-262.
[31] 郭鹏磊, 吴燕卓, 王艳会, 等. 大黑毛肩长蝽(半翅目:异翅亚目:地长蝽科)线粒体基因组及地长蝽科系统发育地位探讨[J]. 环境昆虫学报, 2017, 39(2): 314-331.
Guo P L, Wu Y Z, Wang Y H, et al.The complete mitochondrial genome of Neolethaeus assamensis (Hemiptera: Heteroptera: Rhyparochromidae) and the implication for the phylogenetic position of Rhyparochromidae in Lygaeoidea[J]. Journal of Environmental Entomology, 2017, 39(2): 314-331.
[32] Li P W, Wang X Q, Chen S C, et al.The complete mitochondrial genome of the tea lace bug, Stephanitis chinensis (Hemiptera: Tingidae)[J]. Mitochondrial DNA Part B, 2017, 2(2): 607-608.
[33] Monroe J G, Srikant T, Carbonell-Bejerano P, et al.Mutation bias reflects natural selection in Arabidopsis thaliana[J]. Nature, 2022, 602(7895): 101-105.
[34] Wilson J J, Sing K W, Jaturas N.DNA barcoding: bioinformatics workflows for beginners[J]. Encyclopedia of Bioinformatics and Computational Biology, 2019, 3: 985-995.
[35] Coucheron D H, Nymark M, Breines R, et al.Characterization of mitochondrial mRNAs in codfish reveals unique features compared to mammals[J]. Current Genetics, 2011, 57(3): 213-222.
[36] Schuh R T, Weirauch C, Wheeler W C.Phylogenetic relationships within the Cimicomorpha (Hemiptera: Heteroptera): a total-evidence analysis[J]. Systematic Entomology, 2009, 34(1): 15-48.
[37] Wang Y H, Cui Y, Rédei D, et al.Phylogenetic divergences of the true bugs (Insecta: Hemiptera: Heteroptera), with emphasis on the aquatic lineages: the last piece of the aquatic insect jigsaw originated in the Late Permian/Early Triassic[J]. Cladistics, 2016, 32(4): 390-405.
[38] Wang Y H, Wu H Y, Rédei D, et al.When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera[J]. Cladistics, 2019, 35(1): 42-66.
[39] Liu Y, Song F, Jiang P, et al.Compositional heterogeneity in true bug mitochondrial phylogenomics[J]. Molecular Phylogenetics and Evolution, 2018, 118: 135-144.
[40] Li H, Leavengood J M, Chapman E G, et al.Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs[J]. Proceedings of the Royal Society B, 2017, 284: 20171223. doi: 10.1098/rspb.2017.1223.