入侵害虫长林小蠹线粒体全基因组的测定与分析

doi:10.11707/j.1001-7488.LYKX20230077

摘要/Abstract

摘要：

目的: 首次解析入侵害虫长林小蠹Hylurgus ligniperda线粒体基因组的序列和特征，在线粒体基因组学水平探讨长林小蠹与近缘物种的亲缘关系，丰富了象甲科昆虫线粒体基因组学数据的多样性，为推进我国重大林业检疫性害虫长林小蠹的分子鉴定、种群监测和管理提供数据支持。方法: 利用Illumina Novaseq 6000平台进行高通量测序，参考已发表的鞘翅目昆虫线粒体基因组数据，对组装好的长林小蠹线粒体基因组进行注释和特征分析；运用tRNA Scan-SE 2.0网络平台预测tRNA的二级结构；联合鞘翅目的23个物种，基于最大似然法重建长林小蠹及象甲科其他近缘物种的进化关系。结果: 1）长林小蠹线粒体基因组全长为15912 bp，共编码37个基因：13个蛋白质编码基因、22个tRNA基因和2个rRNA基因，以及1个控制区。线粒体基因组全部37个基因的排序与昆虫祖先的线粒体基因排序一致。2）碱基构成表现为明显的AT碱基偏向性，其中A + T碱基的含量为74.50%，G + C碱基的含量23.80%；AT偏斜值为0.06，GC偏斜值为-0.24。3）除nad5基因外，所有蛋白质编码基因均具有标准的起始密码子ATN；全部蛋白质编码基因终止密码子为TAA或T。除trnS1外，长林小蠹线粒体基因组中tRNA的二级结构均为典型的三叶草形。4）基于线粒体基因组和最大似然法以及贝叶斯混合异质性模型构建的系统发育关系支持本研究中象甲科4个亚科的单系性，其亲缘关系为 [粗喙象亚科Entiminae + （隐喙象亚科Cryptorhynchinae + 魔喙象亚科Molytinae） + 小蠹亚科Scolytinae）]。结论: 长林小蠹线粒体基因组结构保守，具有明显的AT碱基偏向性，蛋白质编码基因的起始子和终止子组成稳定。基于线粒体基因组重建的长林小蠹及象甲科其他近缘物种间的系统发育关系与形态学研究结果相互支持。

关键词: 象甲科, 长林小蠹, 入侵害虫, 线粒体基因组, 系统发育分析

Abstract:

Objective: In this study, the complete mitochondrial genome of Hylurgus ligniperda was characterized and analyzed for the first time, and the phylogenetic relationships between H. ligniperda and closely related coleopteran species was reconstructed at mitochondrial genomic level. This study aims to enrich the mitochondrial genome diversity of curculionids, and facilitate molecular identification, population monitoring and control of the invasive pest species H. ligniperda. Method: The mitochondrial genome of H. ligniperda was sequenced using Illumina Novaseq 6000 platform, and was annotated and characterized based on published mitochondrial genomes of other Coleoptera species. The secondary structures of the tRNA genes were predicted using online tRNA Scan-SE 2.0 search server. Phylogenetic relationships between H. ligniperda and close related coleopterans were reconstructed using the maximum likelihood method based on mitochondrial genomes from a total of 23 species. Result: 1) The complete mitochondrial genome of H. ligniperda is a circular structure, which is 15912 bp in size and contains 37 genes, including 13 protein coding genes (PCGs), 22 tRNA genes and 2 rRNA genes, and a control region. The arrangement of all the 37 genes retains the same order and direction as the ancestral insect mitochondrial genome. 2) Nucleotide composition exhibits distinct AT-bias, with A + T content of 74.50%, G + C content of 23.80%; and the AT-skew value is 0.06, and GC-skew value is -0.24. 3) Except for the gene nad5, the other PCGs have the standard start codon ATN; and the stop codon of all PCGs is TAA or T. Except for trnS1, all tRNA genes display the secondary structures as classic clover-leaf shape. 4) Phylogenetic analysis based on mitochondrial genomes support that all the four subfamilies chosen from Curculionidae in present study are monophyletic, and they are branched as (Entiminae + ((Cryptorhynchinae + Molytinae) + Scolytinae)). Conclusion: Mitochondrial genome of H. ligniperda is conserved in structure and codon usage, and shows distinct A + T biased nucleotide composition. Phylogenetic relationships of H. ligniperda and the close relatives yielded by mitochondrial genomes are consistent with previous morphological investigations.

Key words: Curculionidae, Hylurgus ligniperda, invasive pest, mitochondrial genome, phylogenetic analysis

中图分类号:

S718.7

李心钰,钱铖,陶静,宗世祥. 入侵害虫长林小蠹线粒体全基因组的测定与分析[J]. 林业科学, 2024, 60(8): 164-173.

Xinyu Li,Cheng Qian,Jing Tao,Shixiang Zong. Analysis of the Complete Mitochondrial Genome of an Invasive Bark Beetle Species, Hylurgus ligniperda (Coleoptera: Curculionidae, Scolytinae)[J]. Scientia Silvae Sinicae, 2024, 60(8): 164-173.

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科 Family	亚科 Subfamily	物种名 Species name	GenBank序列号 GenBank accession number
卷象科Attelabidae		芒果切叶象 Deporaus marginatus	MT740322
三锥象甲科 Brentidae		甘薯蚁象 Cylas formicarius	MK421358
天牛科 Cerambycidae		大麻多节天牛 Agapanthia daurica	MN473114
象甲科 Curculionidae	隐喙象亚科 Cryptorhynchinae	芒果果肉象Sternochetus gravis	MW836140
		芒果果核象 Sternochetus mangiferae	NC_068213
		- Trigonopterus carinirostris	MT653608
		- Trigonopterus daun	MT653610
	粗喙象亚科 Entiminae	金足绿象 Chlorophanus auripes	OM112264
		茶丽纹象甲 Myllocerinus aurolineatus	MH197100
		根瘤象属 Sitona obsoletus	MH814932
	魔喙象亚科 Molytinae	萧氏松茎象 Hylobitelus xiaoi	OQ161263
		板栗雪片象 Niphades castanea	MT232762
		白松木蠹象 Pissodes strobi	MW452482
		云南木蠹象 Pissodes yunnanensis	OK135167
	小蠹亚科 Scolytinae	肾点毛小蠹 Dryocoetes autographus	KX035207
		根小蠹属 Hylastes attenuatus	KX035212
		长林小蠹 Hylurgus ligniperda*	OQ469318*
		六齿小蠹 Ips acuminatus	MK988441
		粗齿小蠹 Ips calligraphus	MW589547
		瘤小蠹属 Orthotomicus laricis	KX035213
		星坑小蠹属 Pityogenes bidentatus	KX035211
		细小蠹属 Pityophthorus pubescens	KX035209
		四眼小蠹 Polygraphus poligraphus	OK110248

基因 Gene	长度 Length/bp	位置 Position/bp	起始密码子 Start codon	终止密码子 Stop codon	反密码子 Anticodon	编码链 Coding strand
trnI	65	1－65	—	—	GAT	J
trnQ	69	704－636	—	—	CAA	N
trnM	70	711－780	—	—	ATG	J
nad2	972	802－1773	ATA	TAA	—	J
trnW	65	1790－1854	—	—	TGA	J
trnC	64	1917－1854	—	—	TGC	N
trnY	65	1987－1923	—	—	TAC	N
cox1	1521	1980－3500	ATC	TAA	—	J
trnL2	65	3523－3587	—	—	TTA	J
cox2	657	3609－4265	ATA	TAA	—	J
trnK	67	4279－4345	—	—	AAG	J
trnD	63	4346－4408	—	—	GAC	J
atp8	156	4409－4564	ATT	TAA	—	J
atp6	666	4558－5235	ATG	TAA	—	J
cox3	783	5235－6017	ATG	TAA	—	J
trnG	66	6021－6086	—	—	GGA	J
nad3	345	6087－6431	ATA	TAA	—	J
trnA	63	6440－6502	—	—	GCA	J
trnR	65	6503－6567	—	—	CGA	J
trnN	65	6567－6631	—	—	AAC	J
trnS1	66	6632－6697	—	—	AGA	J
trnE	66	6703－6768	—	—	GAA	J
trnF	64	6832－6769	—	—	TTC	N
nad5	1669	8507－6839	TTG	T	—	N
trnH	64	8607－8544	—	—	CAC	N
nad4	1317	9931－8615	ATA	TAA	—	N
nad4L	268	10213－9946	ATT	T	—	N
trnT	65	10240－10304	—	—	ACA	J
trnP	66	10370－10305	—	—	CCA	N
nad6	507	10373－10879	ATT	TAA	—	J
cob	1129	10879－12007	ATG	T	—	J
trnS2	69	12018－12086	—	—	TCA	J
nad1	886	13036－12151	ATT	T	—	N
trnL1	64	13116－13053	—	—	CTA	N
rrnL	1286	14416－13131	—	—	—	N
trnV	66	14478－14413	—	—	GTA	N
rrnS	770	15246－14477	—	—	—	N

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