<i>Praxillella</i> sp<i>.</i>线粒体全基因组序列与竹节虫科（Maldanidae）的系统发育关系

龚霄鹏; 段晨; 叶莹莹; 陈永久

doi:10.12284/hyxb2026002

Praxillella sp.线粒体全基因组序列与竹节虫科（Maldanidae）的系统发育关系

doi: 10.12284/hyxb2026002

1.
浙江海洋大学海洋科学与技术学院，浙江舟山 316022
2.
浙江海洋大学国家海洋设施养殖工程技术研究中心，浙江舟山 316022

基金项目: 浙江海洋大学2023年自主航次海洋锋面与渔业资源长期调查计划（SOPHI）；科技部基础性工作专项（2014FY110500）。

详细信息

作者简介:
龚霄鹏（2001—），男，浙江省金华市人，主要研究方向为海洋生物学。E-mail：gongxiaopeng@zjou.edu.cn

通讯作者:
陈永久，副教授，主要研究方向为海洋生物学。E-mail: yongjiuchen@zjou.edu.cn

中图分类号: Q958.8
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出版历程
- 收稿日期: 2025-07-29
- 修回日期: 2025-10-24
- 刊出日期: 2026-01-25

The complete mitochondrial genome sequence of Praxillella sp.: insights into phylogenetic relationships within Maldanidae

1.
Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China
2.
National Engineering Research Center For Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China

摘要

摘要: 竹节虫科（Maldanidae）物种广泛分布于各种海洋环境，从浅海到深海皆有分布。但由于采集过程中非常容易断裂，很难获得较为完整的样本，因此形态学研究难以充分进行。关于竹节虫的分类地位，不同的研究者存在着不同的观点和争议。为进一步确定竹节虫科的系统发育关系，本研究采用二代基因组测序数据对Praxillella sp.的线粒体基因组进行了组装与分析。结果显示Praxillella sp.基因组全长15 539 bp，碱基组成为A（33.7%）、T（32.6%）、G（13.6%）和C（20%），具有明显的AT偏向性。与大多数后生动物类似，Praxillella sp.线粒体基因含有13个蛋白编码基因（PCGs），22个tRNA，2个rRNA和一段控制区（CR）。密码子偏好性可能主要受到自然选择的影响。基于13个PCGs构建的最大似然树和贝叶斯树的扑拓结构基本一致，除了真节虫亚科（Euclymeninae）内的P. praetermissa的位置存在不确定性外，但总体上支持了竹节虫亚科（Maldaninae）的单系性；与之相比，真节虫亚科（Euclymeninae）并未形成单系群，而是一个与征节虫亚科（Nicomachinae）并系的类群，在竹节虫科的14个物种中，共鉴定出4种基因排序方式，其中3种仅为tRNA顺序的变化，通过复制−随机丢失即可完成。本研究结果为厘清Praxillella sp.在竹节虫科中的分类与系统发育地位提供了新的观点。
- Praxillella sp. /
- 竹节虫科 /
- 线粒体基因组 /
- 基因重排 /
- 系统发育关系
Abstract: Species of the family Maldanidae are widely distributed across various marine environments, ranging from shallow to deep-sea habitats. However, due to the fragility of their bodies during collection, obtaining intact specimens is often uneasy, and morphological research is difficult to conduct fully. As a result, there are differing viewpoints and ongoing debates among researchers regarding their taxonomic classification. To clarify the evolutionary relationships within Maldanidae, this study assembled and analyzed the complete mitochondrial genome (mitogenome) of Praxillella sp. using second-generation genome sequencing data. The mitogenome of Praxillella sp. is 15539 bp in length, with a base composition of A (33.7%), T (32.6%), G (13.6%), and C (20%), showing a pronounced AT bias. Similar to most metazoans, the genome contains 13 protein-coding genes (PCGs), 22 tRNA genes (including a duplicated tRNA-M), two rRNA genes, and a control region (CR). The codon usage is mainly driven by natural selection. The topological structures of the ML tree and the Bayesian tree constructed based on 13 PCGs are almost all consistent, but the position of P. praetermissa within the subfamily Euclymeninae being uncertain. Phylogeny based on the 13 PCGs overall supports the monophyly of Maldaninae, in contrast, no monophyletic clade is formed within Euclymeninae, being paraphyletic with Nicomachinae, Among the 14 analyzed Maldanid species, four types of gene order are identified, three of which involve changes in tRNA arrangements, driven by tandem duplication and random loss mechanisms. The results offer novel insights into in clarification of taxonomy and phylogenetic relationships of Praxillella sp. in Maldanidae.
- Praxillella sp. /
- Maldanidae /
- mitogenome /
- gene rearrangement /
- phylogenetic relationships

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图 1 Praxillella sp.线粒体基因组图谱

Fig. 1 Map of Praxillella sp. mitogenome

下载: 全尺寸图片幻灯片

图 2 Praxillella sp. 线粒体基因组中具有特殊的tRNA二级结构示意图

Fig. 2 Illustration of a special tRNA secondary structure in Praxillella sp. mitogenome

下载: 全尺寸图片幻灯片

图 3 Praxillella sp.线粒体基因组的同义密码子使用的相对频率

Fig. 3 The relative frequency of synonymous codon（RSCU）used in the mitogenome of Praxillella sp.

下载: 全尺寸图片幻灯片

图 4 密码子偏好性分析

a. 中性绘图分析；b. ENC-plot分析；c. PR2-plot分析

Fig. 4 Analysis of codon preference

a. Neutrality plot analysis; b. ENC-plot analysis; c. PR2-plot analysis

下载: 全尺寸图片幻灯片

图 5 基于 13 个蛋白质编码基因序列构建的最大似然树（右）和贝叶斯树（左）及线粒体基因组基因排序

O. 沙蠋科的线粒体基因排序模式；Ⅰ～Ⅳ. 竹节虫科的线粒体基因排序模式

Fig. 5 Maximum Likelihood tree (right) and Bayesian tree (left) constructed based on the seuqences of 13 PCGs, along with their order on mitogenome

O. Mitochondrial arrangement patterns in Arenicolidae; Ⅰ−Ⅳ. Mitochondrial arrangement patterns in Maldanidae

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图 6 线粒体基因组共线性分析

O. 沙蠋科的线粒体基因组排序模式；Ⅰ～Ⅳ. 竹节虫科各物种线粒体基因组排序模式

Fig. 6 Collinearity analysis of mitogenomes

O. Mitochondrial genome arrangement patterns of the order Arenicolidae; Ⅰ−Ⅳ. Mitochondrial genome arrangements of the species in the family Maldanidae

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表 1 用于线粒体基因组系统发育分析的物种列表

Tab. 1 List of species for phylogenetic analysis of mitogenomes

科	亚科	种	长度/bp	登录号
Maldanidae 竹节虫科	Maldaninae 竹节虫亚科	Metasychis gotoi	15 819	OP605751.1
		Asychis amphiglyptus	15 918	NC_069297.1
		Sabaco sinicus	15 678	OM047258.1
		Maldane sarsi antarctica	17 230	OM237314.1
		Maldane sarsi	15 958	OP694172.1
	Lumbriclymeninae 索节虫亚科	Lumbriclymenella robusta	15 436	OP787079.1
	Nicomachinae 征节虫亚科	Nicomache sp.	15 443	OP605754.1
	Euclymeninae 真节虫亚科	Clymenella torquata	15 538	NC_006321.1
		Clymenella sp.	16 080	OP605752.1
		Euclymene annandalei	15 552	OM273170.1
		Euclymene sp.	16 624	OP627014.1
		Praxillella sp.	15 539	PV243576.1 (本研究)
		Praxillella affinis	15 524	OL804287.1
		Praxillella praetermissa	17 115	OP605753.1
Arenicolidae 沙蠋科		Abarenicola claparedi oceanica	15 524	LC707921.1
Capitellidae 小头虫科		Notomastus sp.	15 776	LC661358.1

下载: 导出CSV

表 2 Praxillella sp.线粒体基因组特征

Tab. 2 Features of the mitochondrial genome of Praxillella sp.

基因	位点		长度/bp	氨基酸	起始密码子	终止密码子	反密码子	基因间隔	编码链
基因	起始	终止	长度/bp	氨基酸	起始密码子	终止密码子	反密码子	基因间隔	编码链
COX1	1	1 542	1 542	513	ATG	TAA		4	H
trnN	1 547	1 607	61				GTT	0	H
COX2	1 608	2 291	684	227	ATG	TAA		1	H
trnD	2 293	2 356	64				GTC	1	H
ATP8	2 358	2 522	165	54	ATG	TAA		3	H
trnY	2 526	2 587	62				GTA	−1	H
trnG	2 587	2 649	63				TCC	0	H
COX3	2 650	3 432	783	260	ATG	TAG		−5	H
trnQ	3 428	3 494	67				TTG	−1	H
ND6	3 494	3 988	495	164	ATT	TAG		−8	H
CYTB	3 981	5 123	1 143	380	ATG	TAG		−2	H
trnW	5 122	5 184	63				TCA	1	H
ATP6	5 186	5 884	699	232	ATG	TAA		−3	H
trnR	5 882	5 948	67				TCG	0	H
CR	5 949	6 797	849					0	H
trnK	6 798	6 858	61				TTT	0	H
trnH	6 859	6 919	61				GTG	108	H
ND5	7 028	8 686	1 659	552	ATT	TAA		−41	H
trnF	8 646	8 706	61				GAA	1	H
trnE	8 708	8 771	64				TTC	−1	H
trnP	8 771	8 833	63				TGG	−1	H
trnT	8 833	895	63				TGT	54	H
ND4L	8 950	9 195	246	81	ATA	TAA		32	H
ND4	9 228	10 562	1 335	444	ATT	TAG		−1	H
trnC	10 562	10 624	63				GCA	1	H
trnM	10 626	10 687	62				CAT	147	H
rrnS	10 835	11 499	665					2	H
trnV	11 502	11 569	68				TAC	118	H
rrnL	11 688	12 820	1 133					21	H
trnL	12 842	12 904	63				TAG	−1	H
trnA	12 904	12 967	64				TGC	−1	H
trnS	12 967	13 030	64					0	H
trnL2	13 031	13 091	61				TAG	0	H
ND1	13 092	14 024	933	310	ATG	TAA		0	H
trnI	14 025	14 091	67				GAT	11	H
ND3	14 103	14 453	351	116	ATG	TAG		−2	H
trnS2	14 452	14 518	67				TCT	0	H
ND2	14 519	15 538	1 020	339	ATG	TAA	TCT	1	H

下载: 导出CSV

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