Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control
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DOI：
10.1101/gr.103911.109
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发表时间：
2010-07-01
期刊：
影响因子：
7
通讯作者：
Rounsley, Steven D.
中科院分区：
文献类型：
--
作者：
Neafsey, Daniel E.;Barker, Bridget M.;Rounsley, Steven D.
我们已经测序了18株密切相关的人类致病真菌粗球孢子菌和球孢子菌posadasii的基因组，以更清楚地阐明人口基因组结构，使每个物种的测序基因组总数为10。我们的数据证实了早期基于微卫星的研究结果，即这些物种在遗传上是有差异的，但我们的种群基因组学方法显示，这两个物种之间最近发生了杂交和遗传渐渗。渗入的方向性主要来自C. posadasii到C. immitis，我们发现超过800个基因在一个或多个测序的分离株中表现出强有力的基因渗入证据。我们对一个在40 ℃下表现出基因渗入的区域进行了基于PCR的测序。immitis分离株，以确认和更好地确定物种之间的基因流动的程度。我们发现更多的编码序列比预期的机会，在基因渗入的地区，这表明自然选择可能发挥作用，在观察到的遗传交换。我们发现显着的异质性重复序列组成之间的测序基因组，并提出了第一个详细的全基因组范围内的重复诱导的点突变（RIP）过程明显不同于已观察到的脉孢菌。我们确定混杂的HLA-I和HLA-II表位在这两个蛋白质组，并讨论了可能的影响，基因渗入和人口基因组数据的公共卫生和疫苗候选人的优先级。这项研究强调了群体基因组数据在检测基因渗入等微妙但潜在的重要现象方面的重要性。
We have sequenced the genomes of 18 isolates of the closely related human pathogenic fungi Coccidioides immitis and Coccidioides posadasii to more clearly elucidate population genomic structure, bringing the total number of sequenced genomes for each species to 10. Our data confirm earlier microsatellite-based findings that these species are genetically differentiated, but our population genomics approach reveals that hybridization and genetic introgression have recently occurred between the two species. The directionality of introgression is primarily from C. posadasii to C. immitis, and we find more than 800 genes exhibiting strong evidence of introgression in one or more sequenced isolates. We performed PCR-based sequencing of one region exhibiting introgression in 40 degrees C. immitis isolates to confirm and better define the extent of gene flow between the species. We find more coding sequence than expected by chance in the introgressed regions, suggesting that natural selection may play a role in the observed genetic exchange. We find notable heterogeneity in repetitive sequence composition among the sequenced genomes and present the first detailed genome-wide profile of a repeat-induced point mutation (RIP) process distinctly different from what has been observed in Neurospora. We identify promiscuous HLA-I and HLA-II epitopes in both proteomes and discuss the possible implications of introgression and population genomic data for public health and vaccine candidate prioritization. This study highlights the importance of population genomic data for detecting subtle but potentially important phenomena such as introgression.