茸毛小长蝽的线粒体基因组测序和分析

doi:10.3969/j.issn.1004-1524.20230316

浙江农业学报 ›› 2023, Vol. 35 ›› Issue (12): 2878-2889.DOI: 10.3969/j.issn.1004-1524.20230316

茸毛小长蝽的线粒体基因组测序和分析

林兴雨(), 宋南()

河南农业大学植物保护学院,河南郑州 450046

收稿日期:2023-03-15 出版日期:2023-12-25 发布日期:2023-12-27
作者简介:林兴雨(1999—),男,河南安阳人,硕士研究生,主要从事基于基因组的昆虫系统发生研究。E-mail:xingyulin666666@163.com
通讯作者: *宋南,E-mail:songnan@henau.edu.cn
基金资助:
国家自然科学基金(U1904104)

Mitochondrial genome and phylogenetic analysis of Nysius graminicola (Kolenati, 1845)

LIN Xingyu(), SONG Nan()

College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China

Received:2023-03-15 Online:2023-12-25 Published:2023-12-27

摘要/Abstract

摘要：

为探究茸毛小长蝽Nysius graminicola(Kolenati, 1845)的线粒体基因组结构及长蝽总科的系统发育关系,利用二代测序方法获得了茸毛小长蝽线粒体全基因组序列。在系统发育分析中,使用长蝽总科17个科52个物种作为内群,并选择缘蝽总科Coreoidea的2个物种作为外群,利用最大似然法和贝叶斯法重建长蝽总科的系统发育关系。茸毛小长蝽的线粒体基因组包含37个基因(13个蛋白质编码基因、22个转运RNA基因和2个核糖体RNA基因)和1个非编码控制区,全长为16 760 bp (GenBank 登录号: OQ553818)。茸毛小长蝽线粒体基因组的13个蛋白质编码基因的起始密码子除nad2利用GTG和cox1利用TTG作为起始,其余蛋白质编码基因都是以ATN开头,终止密码子除cox1、cox2、nad3、cob和nad1以不完整的T作为结尾,其余蛋白质编码基因都是以TAA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,其余转运RNA基因均能形成典型的三叶草结构。两个方法构建的系统发育树的结果均表明:长蝽科和地长蝽科为非单系群,梭长蝽科、室翅长蝽科、跷蝽科、杆长蝽科和束长蝽科为单系群。此外,茸毛小长蝽与N. fuscovittatus 有较近的亲缘关系。

关键词: 半翅目, 长蝽总科, 茸毛小长蝽, 线粒体基因组, 系统发育

Abstract:

To explore the mitochondrial genome of Nysius graminicola (Kolenati, 1845) and the phylogeny of Lygaeoidea, we newly sequenced the complete mitochondrial genome of N. graminicola by using the next-generation sequencing method. In phylogenetic analyses, we selected 17 family including 52 exemplars of Lygaeoidea as ingroups. Two species of Coreoidea was used as outgroup. We reconstructed the phylogenetic relationships using Maximum likelihood and Bayesian inference methods. The sequenced genome is a circular molecule of 16 760 bp in length (Genbank accession No.: OQ553818) which possesses 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and putative control regions as well. For most of the protein-coding genes the star codons were ATN except for nad2 using GTG and cox1using TTG as star codon. Most of the protein-coding genes terminated with the stop codon TAA, while cox1, cox2, nad3, cob and nad1 employed the incomplete T as the stop codon. All tRNA genes can be folded into a typical cloverleaf structure, with the except of the trnS1-AGN. The trnS1 lacks the DHU arm. Both phylogenetic inference methods showed largely identical tree topological structures. The families of Lygaeidae and Rhyparochromidae were non-monophyletic. However, the families of Pachygronthidae, Heterogastridae, Berytidae, Blissidae and Malcidae were monophyletic. In addition, N. graminicola is closely related to N. fuscovittatus.

Key words: Hemiptera, Lygaeoidea, Nysius graminicola, mitochondrial genome, phylogeny

中图分类号:

Q963

林兴雨, 宋南. 茸毛小长蝽的线粒体基因组测序和分析[J]. 浙江农业学报, 2023, 35(12): 2878-2889.

LIN Xingyu, SONG Nan. Mitochondrial genome and phylogenetic analysis of Nysius graminicola (Kolenati, 1845)[J]. Acta Agriculturae Zhejiangensis, 2023, 35(12): 2878-2889.

图/表 10

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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
trnI trnQ	64 69	128 257	191 189	—	—	H H
trnM	69	259	327	—	—	L
nad2	990	328	1 317	GTG	TAA	H
trnW	64	1 316	1 379	—	—	H
trnC	61	1 451	1 391	—	—	L
trnY	66	1 522	1 457	—	—	L
cox1	1 534	1 523	3 056	TTG	T	H
trnL2	65	3 057	3 121	—	—	H
cox2	676	3 122	3 797	ATA	T	H
trnK	73	3 798	3 870	—	—	H
trnD	62	3 873	3 934	—	—	H
atp8	156	3 935	4 090	ATA	TAA	H
atp6	663	4 084	4 746	ATG	TAA	H
cox3	789	4 746	5 534	ATG	TAA	H
trnG	62	5 534	5 595	—	—	H
nad3	352	5 596	5 947	ATA	T	H
trnA	61	5 948	6 008	—	—	H
trnR	68	6 010	6 077	—	—	H
trnN	67	6 081	6 147	—	—	H
trnS1	67	6 147	6 213	—	—	H
trnE	64	6 213	6 276	—	—	H
trnF	66	6 342	6 277	—	—	L
nad5	1 707	8 048	6 342	ATT	TAA	L
trnH	65	8 113	8 049	—	—	L
nad4	1 311	9 491	8 181	ATA	TAA	L
nad4l	282	9 769	9 488	ATT	TAA	L
trnT	64	9 772	9 835	—	—	H
trnP	64	9 899	9 836	—	—	L
nad6	471	9 902	10 372	ATT	TAA	H
cob	1 132	10 372	11 503	ATG	T	H
trnS2	70	11 504	11 573	—	—	H
nad1	919	12 507	11 589	ATT	T	L
trnL1	65	12 572	12 508	—	—	L
rrnL	1 256	13 805	12 550	—	—	L
trnV	67	13 902	13 836	—	—	L
rrnS Control region	765 2 011	14 668 14 877	13 904 127	—	—	L Non-coding sequence

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
trnI trnQ	64 69	128 257	191 189	—	—	H H
trnM	69	259	327	—	—	L
nad2	990	328	1 317	GTG	TAA	H
trnW	64	1 316	1 379	—	—	H
trnC	61	1 451	1 391	—	—	L
trnY	66	1 522	1 457	—	—	L
cox1	1 534	1 523	3 056	TTG	T	H
trnL2	65	3 057	3 121	—	—	H
cox2	676	3 122	3 797	ATA	T	H
trnK	73	3 798	3 870	—	—	H
trnD	62	3 873	3 934	—	—	H
atp8	156	3 935	4 090	ATA	TAA	H
atp6	663	4 084	4 746	ATG	TAA	H
cox3	789	4 746	5 534	ATG	TAA	H
trnG	62	5 534	5 595	—	—	H
nad3	352	5 596	5 947	ATA	T	H
trnA	61	5 948	6 008	—	—	H
trnR	68	6 010	6 077	—	—	H
trnN	67	6 081	6 147	—	—	H
trnS1	67	6 147	6 213	—	—	H
trnE	64	6 213	6 276	—	—	H
trnF	66	6 342	6 277	—	—	L
nad5	1 707	8 048	6 342	ATT	TAA	L
trnH	65	8 113	8 049	—	—	L
nad4	1 311	9 491	8 181	ATA	TAA	L
nad4l	282	9 769	9 488	ATT	TAA	L
trnT	64	9 772	9 835	—	—	H
trnP	64	9 899	9 836	—	—	L
nad6	471	9 902	10 372	ATT	TAA	H
cob	1 132	10 372	11 503	ATG	T	H
trnS2	70	11 504	11 573	—	—	H
nad1	919	12 507	11 589	ATT	T	L
trnL1	65	12 572	12 508	—	—	L
rrnL	1 256	13 805	12 550	—	—	L
trnV	67	13 902	13 836	—	—	L
rrnS Control region	765 2 011	14 668 14 877	13 904 127	—	—	L Non-coding sequence

特征 Feature	长度 Size/bp	AT含量 AT content/%	AT偏斜 AT-skew	GC偏斜 GC-skew
PCGs-H	6 762	75.3	0.036	-0.107
PCGs-L	4 218	78.3	-0.326	0.249
rRNAs-L	2 021	77.9	-0.169	0.284
tRNAs-H	920	76.2	0.070	0.023
tRNAs-L	523	73.1	-0.079	0.291
全基因组	16 760	76.3	0.130	-0.198
Whole genome

特征 Feature	长度 Size/bp	AT含量 AT content/%	AT偏斜 AT-skew	GC偏斜 GC-skew
PCGs-H	6 762	75.3	0.036	-0.107
PCGs-L	4 218	78.3	-0.326	0.249
rRNAs-L	2 021	77.9	-0.169	0.284
tRNAs-H	920	76.2	0.070	0.023
tRNAs-L	523	73.1	-0.079	0.291
全基因组	16 760	76.3	0.130	-0.198
Whole genome

密码子 Codon	数量 Count	RSCU	密码子 Codon	数量 Count	RSCU	密码子 Codon	数量 Count	RSCU	密码子 Codon	数量 Count	RSCU
UUU(F)	193	1.33	UCU(S)	54	0.86	UAU(Y)	266	1.55	UGU(C)	43	1.46
UUC(F)	97	0.67	UCC(S)	52	0.83	UAC(Y)	78	0.45	UGC(C)	16	0.54
UUA(L)	282	3.09	UCA(S)	106	1.69	UAA(*)	316	1.71	UGA(W)	90	1.44
UUG(L)	38	0.42	UCG(S)	16	0.25	UAG(*)	54	0.29	UGG(W)	35	0.56
CUU(L)	78	0.86	CCU(P)	67	1.22	CAU(H)	70	1.33	CGU(R)	16	1.33
CUC(L)	33	0.36	CCC(P)	62	1.13	CAC(H)	35	0.67	CGC(R)	4	0.33
CUA(L)	92	1.01	CCA(P)	86	1.56	CAA(Q)	118	1.70	CGA(R)	25	2.08
CUG(L)	24	0.26	CCG(P)	5	0.09	CAG(Q)	21	0.30	CGG(R)	3	0.25
AUU(I)	386	1.55	ACU(T)	73	0.99	AAU(N)	405	1.55	AGU(S)	73	1.16
AUC(I)	112	0.45	ACC(T)	66	0.89	AAC(N)	118	0.45	AGC(S)	52	0.83
AUA(M)	415	1.80	ACA(T)	138	1.86	AAA(K)	427	1.67	AGA(S)	98	1.56
AUG(M)	45	0.20	ACG(T)	19	0.26	AAG(K)	85	0.33	AGG(S)	51	0.81
GUU(V)	47	1.42	GCU(A)	30	1.15	GAU(D)	59	1.57	GGU(G)	33	1.26
GUC(V)	18	0.55	GCC(A)	22	0.85	GAC(D)	16	0.43	GGC(G)	19	0.72
GUA(V)	59	1.79	GCA(A)	50	1.92	GAA(E)	116	1.76	GGA(G)	37	1.41
GUG(V)	8	0.24	GCG(A)	2	0.08	GAG(E)	16	0.24	GGG(G)	16	0.61

茸毛小长蝽的线粒体基因组测序和分析

Mitochondrial genome and phylogenetic analysis of Nysius graminicola (Kolenati, 1845)

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种名 Species	N. cymoides	N. fuscovittatus	N. graminicola	N. plebeius
Nysius fuscovittatus	0.163
Nysius graminicola	0.159	0.143
Nysius plebeius	0.174	0.173	0.171
Nysius sp.	0.166	0.170	0.169	0.115

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