瘤胫果实蝇线粒体全基因组分析与系统发育

黄振; 郭琼霞

瘤胫果实蝇线粒体全基因组分析与系统发育

黄振^{1, 2,},
郭琼霞^2, ,

1.
福州长乐机场海关，福建　福州　350209
2.
福州海关技术中心，福建　福州　350001

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
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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

Mitochondrial Genome and Phylogeny of Bactrocera (B.) tuberculata

HUANG Zhen^{1, 2
,},
GUO Qiongxia^{2
, ,}

1.
Fuzhou Changle Airport Customs，Fuzhou, Fujian　350209, China
2.
Fuzhou Customs Technical Center, Fuzhou, Fujian　350001, China

摘要

摘要: 目的明确瘤胫果实蝇线粒体全基因组序列特征，探究系统发育地位，为分子标记、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 上已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和洋桃实蝇聚在一起，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。
- 瘤胫果实蝇 /
- 线粒体全基因组 /
- 序列分析 /
- 相对密码子使用频率 /
- tRNA基因二级结构 /
- 系统发育
Abstract: Objective Mitochondrial genome and phylogeny of Bactrocera (B.) tuberculata were studied for advancement on the molecular markers design, species identification, and evolutionary genetics relating to the destructive fruit fly. Methods High-throughput sequencing was applied to determine, assemble, join, and annotate the complete genome of B. (B.) tuberculata mitochondria. With the sequences on selected 20 species published on NCBI, the phylogeny of fruit flies was analyzed using the maximum likelihood method (ML). Results The total mitochondrial genome sequence was 15 854 bp long containing 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and one non-coding control gene with 73.2% A+T. There were 3 755 codons in the 13 protein-coding genes. Of the 22 amino acid codons in the protein, UUA (leucine) had the highest frequency (N) of 387 and relative codon (RSCU) of 3.79. Aside from the phenylalanine (F) and threonine (T) that lacked pseuduracine (T) rings and the serine (S1) without a dihydrouracil DHU ring, the secondary structures of the remaining 19 tRNA genes shaped typically like a canonical cloverleaf. And the 22 genes had 178 mismatched G-U base pairs. Based on the mitochondrial analysis, the phylogeny of B. (B.) tuberculate, B. (B.) dorsalis, and B. (B.) carambolae were closely related and in the same branch as other subgenera. The result agreed with what was revealed by the morphological observation. Conclusion For the first time, the complete mitochondrial genome of B. (B.) tuberculata was obtained with a GenBank accession number of MW 892726. The information secured on the structure and nucleotide composition of the mitochondria and the phylogenetic relation with other subgenera would aid further studies on the species identification, evolutionary biology, and pest control of the devastating pest.
- Bactrocera Bactrocera tuberculata (Bezzi) /
- mitochondrial genome /
- sequence analysis /
- relative codon usage frequency /
- secondary structure of tRNA genes /
- phylogeny

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图 1 瘤胫果实蝇基因结构图

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

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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

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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

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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 Interenic 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

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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

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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的使用个数；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.

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