马尾松毛虫线粒体全基因组的测定与分析

doi:10.11707/j.1001-7488.20191217

Abstract

Abstract:

Objectve: In this study, we sequenced the mitochondrial genome of Dendrolimus punctatus, and analyzed the mitochondrial genome characteristics and the higher-level phylogenetic relationships in moths of Lepidoptera. Method: The complete genome sequence of the mitochondrial genome of D. punctatus was determined by Hiseq X Ten sequencer. The genes were located and annotated based on the known complete mitochondrial genomes of Lepidopteran species. The tRNA Scan-SE 2.0 was used to predict the secondary structure of the tRNA genes online. Based on the whole nucleotide sequence of mitochondrial genome, the phylogenetic relationships of 50 insect species from 11 families of Lepidoptera were reconstructed. Result: The results showed that the complete mitochondrial genome of D. punctatus was a circular molecule of 15 417 bp, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region without gene rearrangement. Among the 13 protein-coding genes, amino acids of Phe, Leu, Ile, Tyr, and Asn (Count>290) were used more frequently, while Ala and Arg were uesd less frequently (Count < 50). In the use of its codon, except CGA as the starting codon of COI gene, the starting codons of the other genes were all typical ATN (ATA, ATT, ATG). The stop codon of COI、COII and ND4 was T, while that of the other genes was TAA. All tRNAs showed the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA^Ser(AGN) formed a simple loop. The (A+T)-rich region contained some conserved structure including the motif ATAGAA, 14 bp ploy (T) stretch and two repeating units with a length of 13 bp and one (AT)₇ structure. The complete mitochondrial genome sequence and the nucleotide sequence of 13 protein-coding genes of D. punctatus were compared with other species of Dendrolimus genus, and the results showed that there was high homology between D.punctatus, D.wenshanensis, and D.tabulaeformis. Phylogenetic tree results show that D. punctatus is closely related with D. tabulaeformis, and D. spectabilis is closely related with D. kikuchii. Conclusion: The mitochondrial genes structure of D. punctatus are stable, the phylogenetic relationship of some species from Lepidoptera based on mitochondrial genome is consistent with the traditional morphological classification.

Key words: Lepidoptera, Lasiocampidae, Dendrolimus punctatus, mitochondrial genome, phylogeny

CLC Number:

S718.7

Huicong Du,Yao Wang,Jiaxing Fang,Zhenyin Zhang,Sufang Zhang,Fu Liu,Zhen Zhang,Xiangbo Kong. Sequencing and Analysis of the Complete Mitochondrial Genome of Dendrolimus punctatus (Lepidoptera: Lasiocampidae)[J]. Scientia Silvae Sinicae, 2019, 55(12): 162-172.

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基因 Gene	方向 Direction	起始位置 Start position	终止位置 Stop position	长度 Length/bp	反密码子 Anticodon	起始密码子 Start codon	终止密码子 Stop codon	基因间隔 IGS/bp
trnM	F	1	67	67	CAT
trnI	F	75	135	61	GAT			7
trnQ	R	133	201	69	TTG			-3
ND2	F	260	1 267	1 008		ATT	TAA	58
trnW	F	1 266	1 334	69	TCA			-2
trnC	R	1 327	1 392	66	GCA			-8
trnY	R	1 393	1 460	68	GTA			0
COI	F	1 495	3 025	1 531		CGA	T	34
trnL2	F	3 026	3 092	67	TAA			0
COII	F	3 093	3 774	682		ATA	T	0
trnK	F	3 775	3 845	71	CTT			0
trnD	F	3 849	3 916	68	GTC			3
ATP8	F	3 917	4 078	162		ATT	TAA	0
ATP6	F	4 072	4 749	678		ATG	TAA	-7
COIII	F	4 764	5 552	789		ATG	TAA	14
trnG	F	5 555	5 620	66	TCC			2
ND3	F	5 621	5 974	354		ATG	TAA	0
trnA	F	5 974	6 040	67	TGC			-1
trnR	F	6 056	6 119	64	TCG			15
trnN	F	6 124	6 189	66	GTT			4
trnS1	F	6 201	6 268	68	GCT			11
trnE	F	6 268	6 332	65	TTC			-1
trnF	R	6 337	6 402	66	GAA			4
ND5	R	6 405	8 147	1 743		ATT	TAA	2
trnH	R	8 148	8 215	68	GTG			0
ND4	R	8 216	9 554	1 339		ATG	T	0
ND4L	R	9 579	9 872	294		ATG	TAA	24
trnT	F	9 880	9 943	64	TGT			7
trnP	R	9 944	10 008	65	TGG			0
ND6	F	10 017	10 547	531		ATA	TAA	8
CytB	F	10 552	11 700	1 149		ATG	TAA	4
trnS2	F	11 704	11 770	67	TGA			3
ND1	R	11 770	12 723	954		ATG	TAA	-1
trnL1	R	12 725	12 792	68	TAG			1
rrnL	R	12 793	14 253	1 461				0
trnV	R	14 254	14 318	65	TAC			0
rrnS	R	14 319	15 097	779				0
D-loop	F	15 098	15 417	320				0

基因序列 Gene sequences	T (%)	C (%)	A (%)	G (%)	A+T (%)	C+G (%)	AT偏斜 AT-skew	GC偏斜 GC-skew
全基因组Whole genome	38.6	12.5	41.0	7.9	79.6	20.4	0.030	-0.223
蛋白质编码基因Protein-coding genes	44.1	10.8	33.7	11.4	77.8	22.2	-0.134	-0.027
密码子第1位1^st codon site	45.7	9.1	35.6	9.6	81.3	18.7	-0.124	-0.024
密码子第2位2^nd codon site	41.9	11.2	34.0	12.9	75.9	24.1	-0.105	-0.070
密码子第3位3^rd codon site	44.8	12.1	31.4	11.7	76.2	23.8	-0.176	-0.028
tRNA基因tRNA genes	39.1	8.5	41.8	10.6	80.9	19.1	0.033	0.110
rRNA基因rRNA genes	43.7	4.3	41.2	10.8	84.9	15.1	-0.029	0.430
控制区Control region	49.4	5.0	42.8	2.8	92.2	7.8	-0.072	-0.282

物种Species	全基因组 Whole genome		PCG		tRNA		A+T-rich region		登录号 GenBank Accession No.
物种Species	大小 Size/bp	A+T (%)	大小 Size/bp	A+T (%)	大小 Size/bp	A+T (%)	大小 Size/bp	A+T (%)	登录号 GenBank Accession No.
马尾松毛虫D. punctatus	15 417	79.6	11 214	77.8	1 465	80.9	320	92.2	MK886799
文山松毛虫D. punctatus wenshanensis	15 418	79.4	11 214	77.6	1 468	81.0	320	92.5	KJ_913812
油松毛虫D. tabulaeformis	15 411	79.5	11 211	77.7	1 468	81.0	320	92.8	KJ_913817
思茅松毛虫D. kikuchii	15 370	78.8	11 211	77.0	1 473	80.7	319	92.5	KY_000412
落叶松毛虫D. superans	15 417	80.1	11 217	78.5	1 475	81.2	316	90.2	KY_000413
云南松毛虫D. houi	15 381	80.0	11 219	78.3	1 477	81.2	319	92.2	KJ_913817
赤松毛虫D. spectabilis	15 410	79.4	11 211	77.5	1 468	81.2	320	93.4	KJ_913816

物种 Species	马尾松毛虫 D. punctatus	文山松毛虫 D. punctatus wenshanensis	油松毛虫 D. tabulaeformis	思茅松毛虫 D. kikuchii	落叶松毛虫 D. superans	云南松毛虫 D. houi	赤松毛虫 D. spectabilis
马尾松毛虫D. punctatus	100.00	98.84	98.89	90.85	91.31	93.45	95.12
文山松毛虫D. punctatus wenshanensis	98.99	100.00	99.46	90.78	91.14	93.29	95.00
油松毛虫D. tabulaeformis	98.99	99.55	100.00	90.78	91.23	93.34	95.09
思茅松毛虫D. kikuchii	91.49	91.48	91.49	100.00	91.28	91.11	90.78
落叶松毛虫D. superans	91.75	91.66	91.71	91.85	100.00	91.86	91.41
云南松毛虫D. houi	93.84	93.76	93.79	91.73	92.36	100.00	93.38
赤松毛虫D. spectabilis	95.64	95.59	95.64	91.53	91.87	93.83	100.00

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Sequencing and Analysis of the Complete Mitochondrial Genome of Dendrolimus punctatus (Lepidoptera: Lasiocampidae)

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