• 中文核心期刊
  • CSCD来源期刊
  • 中国科技核心期刊
  • CA、CABI、ZR收录期刊

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

瘤胫果实蝇线粒体全基因组分析与系统发育

黄振 郭琼霞

黄振,郭琼霞. 瘤胫果实蝇线粒体全基因组分析与系统发育 [J]. 福建农业学报,2024,39(4):482−491 doi: 10.19303/j.issn.1008-0384.2024.04.013
引用本文: 黄振,郭琼霞. 瘤胫果实蝇线粒体全基因组分析与系统发育 [J]. 福建农业学报,2024,39(4):482−491 doi: 10.19303/j.issn.1008-0384.2024.04.013
HUANG Z, GUO Q X. Mitochondrial Genome and Phylogeny of Bactrocera (B.) tuberculata [J]. Fujian Journal of Agricultural Sciences,2024,39(4):482−491 doi: 10.19303/j.issn.1008-0384.2024.04.013
Citation: HUANG Z, GUO Q X. Mitochondrial Genome and Phylogeny of Bactrocera (B.) tuberculata [J]. Fujian Journal of Agricultural Sciences,2024,39(4):482−491 doi: 10.19303/j.issn.1008-0384.2024.04.013

瘤胫果实蝇线粒体全基因组分析与系统发育

doi: 10.19303/j.issn.1008-0384.2024.04.013
基金项目: 福建省自然科学基金项目 (2011J01066、2012JO1061);福州海关科研项目(fk2022-09)
详细信息
    作者简介:

    黄振(1985 — ),男,硕士,高级农艺师,主要从事植物检疫、农业昆虫与害虫防治研究,E-mail:hz15880010585@126.com

    通讯作者:

    郭琼霞(1954 —),女,研究员,主要从事植物检疫研究,E-mail: gqxfjciq@126.com

  • 中图分类号: Q969

Mitochondrial Genome and Phylogeny of Bactrocera (B.) tuberculata

  • 摘要:   目的  明确瘤胫果实蝇[Bactrocera Bactrocera tuberculata (Bezzi) ]线粒体全基因组序列特征,探究其系统发育地位,为瘤胫果实蝇分子标记、物种鉴定和进化遗传学研究提供参考依据。  方法  采用高通量测序技术对瘤胫果实蝇的线粒体全基因组进行测序、组装、拼接和注释,获得基因组全序列,并对基因组基本结构进行分析;选择NCBI 公布的果实蝇属近缘种20种实蝇的线粒体全基因组序列,基于最大似然法(Maximum likelihood, ML)进行系统发育分析。  结果  瘤胫果实蝇线粒体基因组序列总长度为15 854 bp;具37个基因,其中包含13个蛋白编码基因、22个tRNA基因、2个rRNA基因和1个非编码控制基因。瘤胫果实蝇线粒体基因组全序列A+T含量为 73.2%;13个蛋白质编码基因共有密码子3 755个,在蛋白质所有22种氨基酸密码子中,UUA(leucine)的使用频率 N及相对密码子RSCU使用频率均最高,N(RSCU)为387(3.79);tRNA基因二级结构中,除苯丙氨酸(F)以及苏氨酸(T)缺少假尿嘧啶(T)环和丝氨酸(S1)缺少二氢尿嘧啶DHU环,其余19个tRNA基因均能折叠形成典型的三叶草二级结构,22个 tRNA基因中,共存在178处碱基对错配,错配碱基对均为G-U。通过对其近缘种线粒体全基因组的系统发育分析,瘤胫果实蝇与桔小实蝇(Bactrocera dorsalis)和杨桃实蝇(Bactrocera carambolae)聚在一起,表明3种实蝇的亲缘关系较近,与果实蝇亚属的其他种类聚在同个分支上,结果与形态鉴定一致。  结论  首次报道了瘤胫果实蝇线粒体全基因组,GenBank登录号MW 892726,测定和分析的瘤胫果实蝇线粒体基本结构特征,核苷酸组成、系统进化分析,支持瘤胫果实蝇属于果实蝇亚属,为物种诊断、进化生物学和防治研究提供依据。
  • 图  1  瘤胫果实蝇基因结构

    Figure  1.  Map of mitochondrial genome of B. (B.) tuberculata

    图  2  瘤胫果实蝇线粒体22个tRNA结构

    Figure  2.  Cloverleaf-like structure of 22 inferred tRNAs in mitogenome of B. (B.) tuberculata

    图  3  瘤胫果实蝇的最大似然法(ML)系统发育树

    Figure  3.  ML-generated phylogenetic tree of B. (B.) tuberculata

    表  1  瘤胫果实蝇线粒体基因组特征

    Table  1.   Characteristics of mitochondrial genome of B. (B.) tuberculata

    基因
    Gene
    位置
    Location/bp
    基因长度
    Gene length/bp
    编码链
    Strand
    J(+)、N(-)
    基因间隔
    Intergenic
    sequence/bp
    起始密码子
    Start
    codon
    终止密码子
    Stop
    codon
    trnI-GAU 1~66 66 J
    trnQ-UUG 64~132 69 N −3
    trnM-CAU 201~269 69 J 68
    ND2 270~1292 1023 J 0 ATT TAA
    trnW-UCA 1303~1371 69 J 10
    trnC-GCA 1364~1426 63 N −8
    trnY-GUA 1473~1539 67 N 46
    COX1 1538~3076 1539 J −2 TCG TAA
    trnL-UAA 3072~3137 66 J −5
    COX2 3142~3831 690 J 4 ATG TAA
    trnK-CUU 3836~3906 71 J 4
    trnD-GUC 3910~3976 67 J 2
    ATP8 3977~4138 162 J 0 GTG TAA
    ATP6 4132~4809 678 J −7 ATG TAA
    COX3 4809~5597 789 J −1 ATG TAA
    trnG-UCC 5607~5671 65 J 9
    ND3 5672~6025 354 J 0 ATT TAG
    trnA-UGC 6024~6088 65 J −2
    trnR-UCG 6096~6159 64 J 7
    trnN-GUU 6171~6235 65 J 11
    trnS-GCU 6236~6303 68 J 0
    trnE-UUC 6304~6370 67 J 0
    trnF-GAA 6392~6456 65 N 21
    ND5 6437~8176 1740 N −20 ATT TAG
    trnH-GUG 8192~8257 66 N 15
    ND4 8258~9598 1341 N 0 ATG TAG
    ND4L 9592~9888 297 N −7 ATG TAA
    trnT-UGU 9891~9950 60 J −8
    trnP-UGG 9971~10036 66 N 20
    ND6 10039~10563 525 J 2 ATT TAA
    CYTB 10563~11697 1135 J −1 ATG ATT
    trnS-UGA 11697~12725 1029 N −1 ATA TAA
    ND1 11704~11770 67 J −22
    trnL-UAG 12736~12800 65 N 965
    l-rRNA 12778~14135 1358 N −22
    trnV-UAC 14133~14204 72 N −3
    s-rRNA 14204~14995 791 N −1
    控制区
    Control region
    14996~15943 947 J 0
    下载: 导出CSV

    表  2  瘤胫果实蝇线粒体全基因组碱基组成

    Table  2.   Bases in mitochondrial genome of B. (B.) tuberculata

    区域
    Region
    A/% C/% G/% T/% A+T/% AT偏移
    AT Skew
    GC偏移
    GC Skew
    基因长度
    Gene length/bp
    全基因组
    Whole genome
    39.1 16.4 10.4 34.1 73.2 0.068 −0.224 15943
    PCGs 29.9 14.9 14.4 40.8 70.7 −0.154 −0.017 11302
    PCGs J 32.0 18.7 12.7 36.6 68.6 −0.067 −0.191 6895
    PCGs N 26.7 9.0 17.0 47.2 73.9 −0.277 0.308 4407
    ND2 34.1 16.8 9.1 40.0 74.1 −0.080 −0.297 1023
    COXI 30.1 18.9 16.2 34.8 64.9 −0.072 −0.077 1539
    COX2 33.5 18.4 14.1 34.1 67.6 −0.009 −0.132 690
    ATP8 37.7 17.9 8.6 35.8 73.5 0.026 −0.351 162
    ATP6 30.4 19.9 11.8 37.9 68.3 −0.110 −0.256 678
    COX3 29.7 19.4 15.3 35.6 65.3 −0.090 −0.118 789
    ND3 31.9 16.7 9.9 41.5 73.4 −0.131 −0.256 354
    ND5 27.8 9.0 17.1 46.0 73.8 −0.247 0.310 1740
    ND4 26.3 8.9 16.9 47.8 74.1 −0.290 0.310 1341
    ND4L 26.6 7.1 14.5 51.9 78.5 −0.322 0.343 297
    ND6 37.0 16.6 6.9 39.6 76.6 −0.034 −0.413 525
    CYTB 30.9 20.7 13.5 34.9 65.8 −0.061 −0.211 1135
    ND1 25.5 9.7 17.6 47.2 72.7 −0.298 0.289 1029
    tRNA 36.9 11.1 14.1 37.8 74.7 −0.012 0.119 1462
    tRNA J 37.2 12.7 13.2 36.8 74.0 0.005 0.019 929
    tRNA N 36.4 8.4 15.6 39.6 76.0 −0.042 0.300 533
    rRNA 35.7 8.0 14.6 41.7 77.4 −0.078 0.292 2149
    1-rRNA 36.7 7.1 13.8 42.5 79.2 −0.073 0.321 1358
    s-rRNA 34.1 9.5 16.1 40.3 74.4 −0.083 0.258 791
    控制区
    Control region
    46.9 6.6 5.0 41.5 88.4 0.061 0.138 947
    下载: 导出CSV

    表  3  瘤胫果实蝇线粒体基因组蛋白质编码基因密码子使用统计

    Table  3.   Statistics of codon usage in mitochondria of B. (B.) tuberculata

    密码子 Codon N R 密码子 Codon N R 密码子 Codon N R 密码子 Codon N R
    UUU(F) 235 1.42 UCU (S) 114 2.68 UAU(Y) 144 1.73 UGU(C) 41 1.91
    UUC(F) 96 0.58 UCC (S) 10 0.24 UAC(Y) 22 0.27 UGC(C) 2 0.9
    UUA(L) 387 3.79 UCA (S) 95 2.24 UAA(*) 0 0.00 UGA(W) 95 1.88
    UUG(L) 68 0.67 UCG (S) 2 0.05 UAG(*) 0 0.00 UGG(W) 6 0.12
    CUU(L) 66 0.65 CCU(P) 75 2.17 CAU(H) 55 1.39 CGU(R) 15 1.02
    CUC(L) 5 0.05 CCC(P) 13 0.38 CAC(H) 24 0.61 CGC(R) 3 0.20
    CUA(L) 81 0.79 CCA(P) 48 1.39 CAA(Q) 74 1.87 CGA(R) 37 2.51
    CUG(L) 5 0.05 CCG(P) 2 0.06 CAG(Q) 5 0.13 CGG(R) 4 0.27
    AUU(I) 298 1.76 ACU (T) 79 1.57 AAU(N) 163 1.72 AGU(S) 47 1.11
    AUC(I) 40 0.24 ACC (T) 19 0.38 AAC(N) 26 0.28 AGC(S) 9 0.21
    AUA(M) 174 1.73 ACA (T) 101 2.01 AAA(K) 63 1.42 AGA(S) 63 1.48
    AUG(M) 27 0.27 ACG (T) 2 0.04 AAG(K) 26 0.58 AGG(S) 0 0.00
    GUU(V) 84 1.53 GCU(A) 116 2.43 GAU(D) 58 1.63 GGU(G) 71 1.23
    GUC(V) 8 0.15 GCC(A) 22 0.46 GAC(D) 13 0.37 GGC(G) 3 0.05
    GUA(V) 112 2.02 GCA(A) 50 1.05 GAA(E) 73 1.95 GGA(G) 126 2.18
    GUG(V) 16 0.29 GCG(A) 3 0.06 GAG(E) 2 0.05 GGG(G) 31 0.54
    N为线粒体全基因组蛋白质编码基因的密码子使用个数;R:RSCU为相对同义密码子的使用频率。*:终止密码子。
    N: number of codons used for protein-coding genes of whole mitochondrial genome; R: frequency of use of relative synonymous codon (RSCU). *: stop codon.
    下载: 导出CSV
  • [1] 邓裕亮, 李正跃, 蒋小龙, 等. 缅甸第四特区实蝇类害虫调查 [J]. 植物检疫, 2005, 19(5):316−318.

    DENG Y L, LI Z Y, JIANG X L, et al. Investigation on fruit fly pests in the fourth special zone of Myanmar [J]. Plant Quarantine, 2005, 19(5): 316−318. (in Chinese)
    [2] 邓裕亮, 李志红, 白永华, 等. 老挝中北部地区果实蝇属(Bactrocera)害虫种类初步调查 [J]. 植物检疫, 2010, 24(1):52−53. doi: 10.3969/j.issn.1005-2755.2010.01.021

    DENG Y L, LI Z H, BAI Y H, et al. Preliminary investigation on insect species of Bactrocera in central and northern Laos [J]. Plant Quarantine, 2010, 24(1): 52−53. (in Chinese) doi: 10.3969/j.issn.1005-2755.2010.01.021
    [3] DREW R A I, ROMIG M C, DORJI C. Records of Dacine fruit flies and new species of Dacus (Diptera: Tephritidae) in Bhutan [J]. The Raffles Bulletin of Zoology, 2007, 55(1): 1−21.
    [4] LEBLANC L, HOSSAIN M A, KHAN S, et al. Additions to the Fruit Fly Fauna (Diptera: Tephritidae: Dacinae) of Bangladesh, with a Key to the Species [J]. Proceedings of the Hawaiian Entomological Society, 2014, 46: 31−40.
    [5] 蒋小龙. 云南边境检疫性实蝇风险分析研究 [J]. 西南农业大学学报, 2002, 24(5):402−405,421. doi: 10.3969/j.issn.1673-9868.2002.05.006

    JIANG X L. Risk analysis of quarantine fruit flies along Yunnan borber [J]. Journal of Southwest Agricultural University, 2002, 24(5): 402−405,421. (in Chinese) doi: 10.3969/j.issn.1673-9868.2002.05.006
    [6] 黄振, 侯有明, 郭琼霞, 等. 利用物种特异性PCR技术快速鉴定南瓜实蝇 [J]. 福建农业学报, 2021, 36(2):215−220.

    HUANG Z, HOU Y M, GUO Q X, et al. Rapid species-specific PCR identification of Bactrocera tau(Diptera: Tephritidae) [J]. Fujian Journal of Agricultural Sciences, 2021, 36(2): 215−220. (in Chinese)
    [7] 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
    [8] 徐浪, 余道坚, 张润杰, 等. 桔小实蝇线粒体基因组全序列及其分析 [J]. 昆虫学报, 2007, 50(8):755−761. doi: 10.3321/j.issn:0454-6296.2007.08.001

    XU L, YU D J, ZHANG R J, et al. Sequencing and analysis of the complete mitochondrial genome of the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) [J]. Acta Entomologica Sinica, 2007, 50(8): 755−761. (in Chinese) doi: 10.3321/j.issn:0454-6296.2007.08.001
    [9] 叶军, 房蕊, 易建平, 等. 4种实蝇线粒体DNA全序列测定 [J]. 植物检疫, 2010, 24(3):11−14. doi: 10.3969/j.issn.1005-2755.2010.03.004

    YE J, FANG R, YI J P, et al. The complete sequence determination and analysis of four species of bactrocera mitochondrial genome [J]. Plant Quarantine, 2010, 24(3): 11−14. (in Chinese) doi: 10.3969/j.issn.1005-2755.2010.03.004
    [10] 梅琰, 岳巧云, 贾凤龙. 双翅目昆虫线粒体基因组研究进展 [J]. 环境昆虫学报, 2012, 34(4):497−503. doi: 10.3969/j.issn.1674-0858.2012.04.15

    MEI Y, YUE Q Y, JIA F L. Research progress on mitochondrial genomes of Dipteral insect [J]. Journal of Environmental Entomology, 2012, 34(4): 497−503. (in Chinese) doi: 10.3969/j.issn.1674-0858.2012.04.15
    [11] 姜帆, 李志红, 梁亮, 等. 实蝇科昆虫线粒体基因组研究进展 [J]. 植物检疫, 2016, 30(3):12−17.

    JIANG F, LI Z H, LIANG L, et al. Research progress in mitochondrial genomes of Tephritidae insect [J]. Plant Quarantine, 2016, 30(3): 12−17. (in Chinese)
    [12] 梁亮, 江威, 余慧, 等. 中国果实蝇属种类的DNA条形码鉴定(双翅目, 实蝇科)[J]. 动物分类学报, 2011, 36(4): 925−932.

    LIANG L, JIANG W, YU H, et al. Identification of Chinese bactrocera species through DNA barcoding (Diptera, Tephritidae)[J]. Acta Zootaxonomica Sinica, 2011, 36(4): 925−932. (in Chinese)
    [13] 范京安, 顾海丰, 陈世界, 等. 实蝇科昆虫mtDNA-COI基因序列分析及系统发育研究[J]. 西南大学学报: 自然科学版, 2009, 31(10): 88-95.

    FAN J A, GU H F, CHEN S J, et al. Sequence analysis of mtDNA-COI gene and molecular phylogeny of Fruitfly(Tepbritidae)[J]. Journal of Southwest University (Natural Science Edition), 2009, 31(10): 88-95. (in Chinese)
    [14] 刘慎思, 张桂芬, 万方浩. 基于mtDNA COI基因的离腹寡毛实蝇属常见种DNA条形码识别和系统发育分析 [J]. 昆虫学报, 2014, 57(3):343−355.

    LIU S S, ZHANG G F, WAN F H. DNA barcoding and phylogenetic analysis of common species of the genus Bactrocera(Diptera: Tephritidae) based on mtDNA COI gene sequences [J]. Acta Entomologica Sinica, 2014, 57(3): 343−355. (in Chinese)
    [15] KROSCH M N, SCHUTZE M K, ARMSTRONG K F, et al. A molecular phylogeny for the Tribe Dacini (Diptera: Tephritidae): Systematic and biogeographic implications [J]. Molecular Phylogenetics and Evolution, 2012, 64(3): 513−523. doi: 10.1016/j.ympev.2012.05.006
    [16] CLARY D O, WOLSTENHOLME D R. The mitochondrial DNA molecule ofDrosophila yakuba: Nucleotide sequence, gene organization, and genetic code [J]. Journal of Molecular Evolution, 1985, 22(3): 252−271. doi: 10.1007/BF02099755
    [17] BOORE J L. Animal mitochondrial genomes [J]. Nucleic Acids Research, 1999, 27(8): 1767−1780. doi: 10.1093/nar/27.8.1767
    [18] CLARY D O, WOLSTENHOLME D R. Drosophila mitochondrial DNA: Conserved sequences in the A+T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA [J]. Journal of Molecular Evolution, 1987, 25(2): 116−125. doi: 10.1007/BF02101753
    [19] 林兴雨, 刘向阳, 宋南. 大赤隐翅虫的线粒体基因组研究及系统发育分析 [J]. 福建农业学报, 2023, 38(5):607−615.

    LIN X Y, LIU X Y, SONG N. Mitochondrial genome and phylogenetics of Philonthus spinipes(Sharp, 1874) [J]. Fujian Journal of Agricultural Sciences, 2023, 38(5): 607−615. (in Chinese)
    [20] BOORE J L, LAVROV D V, BROWN W M. Gene translocation links insects and crustaceans [J]. Nature, 1998, 392(6677): 667−668. doi: 10.1038/33577
    [21] 王菊平, 宣善滨, 张育平, 等. 武铠蛱蝶线粒体基因组全序列测定和分析 [J]. 昆虫学报, 2015, 58(3):319−328.

    WANG J P, XUAN S B, ZHANG Y P, et al. Sequencing and analysis of the complete mitochondrial genome of Chitoria ulupi(Lepidoptera: Nymphalidae) [J]. Acta Entomologica Sinica, 2015, 58(3): 319−328. (in Chinese)
    [22] ZHANG Y, FENG S Q, ZENG Y Y, et al. The first complete mitochondrial genome of Bactrocera tsuneonis (Miyake) (Diptera: Tephritidae) by next-generation sequencing and its phylogenetic implications[J]. International Journal of Biological Macromolecules, 2018, 118(Pt A): 1229-1237.
    [23] 黄振, 郭琼霞. 基于种特异性SS-COⅠ技术快速鉴定瘤胫实蝇 [J]. 生物安全学报, 2022, 31(2):179−184. doi: 10.3969/j.issn.2095-1787.2022.02.013

    HUANG Z, GUO Q X. Rapid identification of Bactrocera tuberculata (Diptera: Tephritidae) by species-specific SS-COⅠ technique [J]. Journal of Biosafety, 2022, 31(2): 179−184. (in Chinese) doi: 10.3969/j.issn.2095-1787.2022.02.013
    [24] ISAZA J P, ALZATE J F, CANAL N A. Complete mitochondrial genome of the Andean morphotype of Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) [J]. Mitochondrial DNA Part B, Resources, 2017, 2(1): 210−211. doi: 10.1080/23802359.2017.1307706
    [25] 周志军, 杨明茹, 常岩林, 等. 两种纺织娘线粒体基因组的比较分析 [J]. 昆虫学报, 2013, 56(4):408−418.

    ZHOU Z J, YANG M R, CHANG Y L, et al. Comparative analysis of mitochondrial genomes of two long-legged katydids (Orthoptera: Tettigoniidae) [J]. Acta Entomologica Sinica, 2013, 56(4): 408−418. (in Chinese)
  • 加载中
图(3) / 表(3)
计量
  • 文章访问数:  67
  • HTML全文浏览量:  40
  • PDF下载量:  13
  • 被引次数: 0
出版历程
  • 收稿日期:  2023-12-05
  • 修回日期:  2024-04-01
  • 网络出版日期:  2024-06-26
  • 刊出日期:  2024-04-28

目录

    /

    返回文章
    返回