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A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity.
BMC Biology ( IF 5.4 ) Pub Date : 2020-06-19 , DOI: 10.1186/s12915-020-00802-7
Timothy P Driscoll 1 , Victoria I Verhoeve 2 , Joseph J Gillespie 2 , J Spencer Johnston 3 , Mark L Guillotte 2 , Kristen E Rennoll-Bankert 2 , M Sayeedur Rahman 2 , Darren Hagen 4 , Christine G Elsik 5, 6, 7 , Kevin R Macaluso 8 , Abdu F Azad 2
Affiliation  

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. 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 for C. felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ~ 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) in C. felis. Similarly, broad genome sizes were also calculated for individuals of Xenopsylla cheopis (Oriental rat flea), indicating that this remarkable “genome-in-flux” phenomenon could be a siphonapteran-wide trait. Finally, from the C. felis sequence reads, we also generated closed genomes for two novel strains of Wolbachia, one parasitic and one symbiotic, found to co-infect individual fleas. Rampant CNV in C. felis has 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 novel Wolbachia endosymbionts—potential tools for blocking pathogen transmission—these oddities highlight a unique and underappreciated disease vector.

中文翻译:

猫跳蚤基因组的染色体级组装揭示了猖gene的基因重复和基因组大小的可塑性。

跳蚤(Insecta:Siphonaptera)是鸟类和哺乳动物的小型不会飞的寄生虫;它们的采血可以传播许多严重的病原体(例如,鼠疫,地方性和鼠类斑疹伤寒的病原体)。缺乏跳蚤基因组装配阻碍了研究,尤其是与其他疾病载体的比较。因此,我们对猫跳蚤Ctenocephalides felis的基因组进行了测序,Ctenocephalides felis是一种对人类健康和兽医意义重大的昆虫。通过结合Hi-C支架技术对来自多个近交雌性跳蚤的DNA进行Illumina和PacBio测序,我们生成了C. felis的染色体级基因组装配体。出乎意料的是,我们的装配揭示了整个基因组中广泛的基因重复,例如〜38%的蛋白质编码基因具有两个或多个拷贝以及4000多个tRNA基因。对跨不同种群采样的单个跳蚤进行的广泛的基因组大小测定(433-551 Mb),支持了猫屎肠球菌波动拷贝数变异(CNV)的广泛存在。同样,还为Xenopsylla cheopis(东方鼠蚤)的个体计算了宽泛的基因组大小,这表明这种显着的“基因组-通量”现象可能是整个虹吸体的特征。最后,从C. felis序列读取的数据中,我们还生成了两个Wolbachia新型菌株(一种寄生虫和一种共生菌)的闭合基因组,发现它们共同感染了跳蚤。C. felis中猖amp的CNV对于以基因为目标的害虫控制措施具有可怕的意义,并使比较转录组学分析中使用的标准归一化程序复杂化。
更新日期:2020-06-22
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