A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
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DOI：
10.1186/s12915-020-00802-7
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发表时间：
2020-06-19
期刊：
影响因子：
5.4
通讯作者：
Azad, Abdu F.
中科院分区：
文献类型：
--
作者：
Driscoll, Timothy P.;Verhoeve, Victoria, I;Azad, Abdu F.
背景：跳蚤是鸟类和哺乳动物的小型无飞行寄生虫（昆虫亚目：管翅目）；它们的吸血可传播许多严重的病原体（即黑死病、地方性斑疹伤寒和鼠斑疹伤寒的病原）。缺乏跳蚤基因组组合阻碍了研究，特别是与其他疾病媒介的比较。因此，我们对猫蚤（Ctenocephalides felis）的基因组进行了测序，猫蚤是一种在全球范围内对人类健康和兽医具有重要意义的昆虫。结果：利用Hi-C支架技术，结合Illumina和PacBio对来自多个近交雌性跳蚤的DNA测序，我们获得了染色体水平的c基因组组装。猫属。出乎意料的是，我们的组装揭示了整个基因组中广泛的基因复制，例如大约38%的蛋白质编码基因具有两个或更多拷贝和超过4000个tRNA基因。对不同种群取样的单个跳蚤进行了广泛的基因组大小测定（433-551 Mb），支持了波动拷贝数变异（CNV）的广泛存在。同样，研究人员还计算了非洲鼠蚤（xenopsylla cheopis，东方鼠蚤）个体的基因组大小，表明这种显著的“基因组通量”现象可能是siphonaptera的普遍特征。最后，从c。felissequence reads显示，我们还生成了两种新的沃尔巴克氏体菌株的封闭基因组，一种是寄生的，一种是共生的，发现它们会共同感染单个跳蚤。结论：猖獗的CNV inC.对基因靶向害虫控制措施具有可怕的影响，并且会使比较转录组学分析中使用的标准规范化程序复杂化。再加上新型沃尔巴克氏菌内共生体的共同感染——阻止病原体传播的潜在工具——这些奇怪的现象突出了一种独特的、未被重视的疾病媒介。
Background: Fleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e., the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea,Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe.Results: By combining Illumina and PacBio sequencing of DNA derived from multiple inbred female fleas with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly forC. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by similar to 38% of protein-coding genes with two or more copies and over 4000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) inC. felis. Similarly, broad genome sizes were also calculated for individuals ofXenopsylla cheopis(Oriental rat flea), indicating that this remarkable "genome-in-flux" phenomenon could be a siphonapteran-wide trait. Finally, from theC. felissequence reads, we also generated closed genomes for two novel strains ofWolbachia, one parasitic and one symbiotic, found to co-infect individual fleas.Conclusion: Rampant CNV inC. felishas dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novelWolbachiaendosymbionts-potential tools for blocking pathogen transmission-these oddities highlight a unique and underappreciated disease vector.