Bergman Casey M, Han Shunhua, Nelson Michael G, Bondarenko Vladyslav, Kozeretska Iryna
Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America.
PeerJ. 2017 Sep 15;5:e3824. doi: 10.7717/peerj.3824. eCollection 2017.
The transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their element composition mate and produce offspring. Despite extensive research on many aspects of element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomic element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of to illuminate the molecular basis of natural variation in cytotype status. We show that element abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find that element content varies significantly across populations, with strains from a North American population having fewer elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in element abundance and structure, neither the number of elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure of elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of , and informs future efforts to decode the genomic basis of geographic and temporal differences in element induced phenotypes.
转座元件提供了真核生物中移动DNA序列水平转移的最佳案例之一。该元件对自然种群的入侵导致了一种称为P-M杂种不育的表型综合征，当元件组成不同的品系交配并产生后代时就会出现这种综合征。尽管对该元件生物学的许多方面进行了广泛研究，但关于P-M不育表型在不同种群间变异的基因组基础仍存在许多问题。在这里，我们比较了从三个全球种群获得的同雌系菌株的基因组元件含量估计值与性腺发育不全表型，以阐明细胞型状态自然变异的分子基础。我们表明，通过不同生物信息学方法从同雌系菌株基因组序列估计的元件丰度高度相关，但丰度估计对方法、过滤策略以及同雌系菌株的不完全近亲繁殖敏感。我们发现元件含量在不同种群间有显著差异，北美种群的菌株元件数量较少，但全长元件的比例高于欧洲或非洲采样种群的菌株。尽管元件丰度和结构存在这些地理差异，但元件数量以及全长与内部截短拷贝的比例均与同雌系菌株表现出的性腺发育不全程度没有强烈相关性。因此，不同种群间元件丰度和结构的变异不一定导致性腺发育不全表型相应的地理差异。最后，我们证实从同雌系品系观察到的元件丰度和结构的种群差异也可以在来自相同种群的混合测序样本中观察到。我们的工作支持这样一种观点，即仅基因组元件含量不足以解释不同品系间性腺发育不全的变异，并为未来解码元件诱导表型的地理和时间差异的基因组基础的努力提供了信息。
