鼠蚤印度客蚤的完整线粒体基因组：基因组描述、比较分析和系统发育意义。
The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications.
机构信息
Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, 410013, Hunan, China.
Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
出版信息
Parasit Vectors. 2024 Jun 11;17(1):253. doi: 10.1186/s13071-024-06329-y.
BACKGROUND
Fleas are one of the most common and pervasive ectoparasites worldwide, comprising at least 2500 valid species. They are vectors of several disease-causing agents, such as Yersinia pestis. Despite their significance, however, the molecular genetics, biology, and phylogenetics of fleas remain poorly understood.
METHODS
We sequenced, assembled, and annotated the complete mitochondrial (mt) genome of the rodent flea Nosopsyllus laeviceps using next-generation sequencing technology. Then we combined the new mitogenome generated here with mt genomic data available for 23 other flea species to perform comparative mitogenomics, nucleotide diversity, and evolutionary rate analysis. Subsequently, the phylogenetic relationship within the order Siphonaptera was explored using the Bayesian inference (BI) and maximum likelihood (ML) methods based on concentrated data for 13 mt protein-coding genes.
RESULTS
The complete mt genome of the rodent flea N. laeviceps was 16,533 base pairs (bp) in a circular DNA molecule, containing 37 typical genes (13 protein-coding genes, 22 transfer RNA [tRNA] genes, and two ribosomal RNA [rRNA] genes) with one large non-coding region (NCR). Comparative analysis among the order Siphonaptera showed a stable gene order with no gene arrangement, and high AT content (76.71-83.21%) with an apparent negative AT and GC skew except in three fleas Aviostivalius klossi bispiniformis, Leptopsylla segnis, and Neopsylla specialis. Moreover, we found robust evidence that the cytochrome c oxidase subunit 1 (cox1) gene was the most conserved protein-coding gene (Pi = 0.15, non-synonymous/synonymous [Ka/Ks] ratio = 0.13) of fleas. Phylogenomic analysis conducted using two methods revealed different topologies, but both results strongly indicated that (i) the families Ceratophyllidae and Leptopsyllidae were paraphyletic and were the closest to each other, and (ii) the family Ctenophthalmidae was paraphyletic.
CONCLUSIONS
In this study, we obtained a high-quality mt genome of the rodent flea N. laeviceps and performed comparative mitogenomics and phylogeny of the order Siphonaptera using the mt database. The results will enrich the mt genome data for fleas, lay a foundation for the phylogenetic analysis of fleas, and promote the evolutionary analysis of Siphonaptera.
背景
跳蚤是全球最常见和普遍的外寄生虫之一，至少包含 2500 种有效物种。它们是多种致病因子的载体，如鼠疫耶尔森氏菌。然而，尽管它们意义重大，但跳蚤的分子遗传学、生物学和系统发生学仍然知之甚少。
方法
我们使用下一代测序技术对啮齿动物跳蚤印鼠客蚤的完整线粒体（mt）基因组进行测序、组装和注释。然后，我们将在这里生成的新线粒体基因组与 23 种其他跳蚤的 mt 基因组数据相结合，进行比较线粒体基因组学、核苷酸多样性和进化率分析。随后，使用贝叶斯推断（BI）和最大似然（ML）方法，基于 13 个 mt 蛋白编码基因的集中数据，探索了在鳞翅目目内的系统发生关系。
结果
啮齿动物跳蚤印鼠客蚤的完整 mt 基因组是一个圆形 DNA 分子，大小为 16533 个碱基对（bp），包含 37 个典型基因（13 个蛋白编码基因、22 个转移 RNA [tRNA] 基因和两个核糖体 RNA [rRNA] 基因）和一个大型非编码区（NCR）。鳞翅目目内的比较分析显示，基因排列稳定，没有基因排列，高 AT 含量（76.71-83.21%），除了三种跳蚤（Aviostivalius klossi bispiniformis、Leptopsylla segnis 和 Neopsylla specialis）外，明显存在负 AT 和 GC 倾斜。此外，我们发现强有力的证据表明，细胞色素 c 氧化酶亚基 1（cox1）基因是跳蚤中最保守的蛋白编码基因（Pi=0.15，非同义/同义[Ka/Ks]比值=0.13）。使用两种方法进行的基因组分析揭示了不同的拓扑结构，但两种结果都强烈表明：（i）Ceratophyllidae 和 Leptopsyllidae 科是并系的，彼此最为接近，（ii）Ctenophthalmidae 科是并系的。
结论
在这项研究中，我们获得了啮齿动物跳蚤印鼠客蚤的高质量 mt 基因组，并使用 mt 数据库对鳞翅目目内的比较线粒体基因组学和系统发生进行了研究。结果将丰富跳蚤的 mt 基因组数据，为跳蚤的系统发育分析奠定基础，并促进鳞翅目目内的进化分析。
Zotero 插件