Genomic sequence capture of Plasmodium relictum in experimentally infected birds.
Genomic sequence capture of Plasmodium relictum in experimentally infected birds.
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DOI：
10.1186/s13071-022-05373-w
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发表时间：
2022-07-29
影响因子：
3.2
通讯作者：
中科院分区：
文献类型：
--
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在宿主DNA存在的情况下对寄生虫基因组进行测序是具有挑战性的。序列捕获可以通过使用与寄生虫DNA杂交然后从溶液中去除的RNA探针来克服这个问题，从而分离寄生虫DNA用于有效测序。在这里，我们描述了一组设计用于靶向1035个基因的序列捕获探针（c. 2.5 Mbp）的全球分布的禽血孢子虫寄生虫，残余疟原虫。先前对来自血变形菌属的禽类血孢子虫的序列捕获研究表明，测序成功取决于寄生虫血症，低强度的慢性感染（野生大多数感染鸟类的典型感染）通常难以测序。我们使用实验性感染残遗疟原虫并保持在实验室条件下的鸟类来评估寄生虫血症和测序成功之间的关系。我们证实了测序成功对寄生虫血症的依赖性。对于具有低水平寄生虫血症（< 1%感染的红血细胞）的鸟，测序成功率低，而对于具有较高水平寄生虫血症的鸟，测序成功率高。残留疟原虫由线粒体DNA单倍型定义的多个谱系组成，包括三个广泛分布的谱系（SGS 1，GRW 11和GRW 4）;探针成功地从所有三个谱系中分离出DNA。此外，我们使用来自25个基因的数据来描述谱系内和谱系间的遗传变异。例如，从不同宿主物种分离的两个SGS 1样品在这25个基因中存在11个取代。我们所描述的序列捕获方法将允许产生基因组数据，这将有助于我们理解残遗疟原虫的种群遗传结构和进化历史，残遗疟原虫是一种极端的宿主通才和广泛分布的寄生虫。在线版本包含补充材料，可通过10.1186/s13071-022-05373-w获得。
Sequencing parasite genomes in the presence of host DNA is challenging. Sequence capture can overcome this problem by using RNA probes that hybridize with the parasite DNA and then are removed from solution, thus isolating the parasite DNA for efficient sequencing. Here we describe a set of sequence capture probes designed to target 1035 genes (c. 2.5 Mbp) of the globally distributed avian haemosporidian parasite, Plasmodium relictum. Previous sequence capture studies of avian haemosporidians from the genus Haemoproteus have shown that sequencing success depends on parasitemia, with low-intensity, chronic infections (typical of most infected birds in the wild) often being difficult to sequence. We evaluate the relationship between parasitemia and sequencing success using birds experimentally infected with P. relictum and kept under laboratory conditions. We confirm the dependence of sequencing success on parasitemia. Sequencing success was low for birds with low levels of parasitemia (< 1% infected red blood cells) and high for birds with higher levels of parasitemia. Plasmodium relictum is composed of multiple lineages defined by their mitochondrial DNA haplotype including three that are widespread (SGS1, GRW11, and GRW4); the probes successfully isolated DNA from all three. Furthermore, we used data from 25 genes to describe both among- and within-lineage genetic variation. For example, two samples of SGS1 isolated from different host species differed by 11 substitutions across those 25 genes. The sequence capture approach we describe will allow for the generation of genomic data that will contribute to our understanding of the population genetic structure and evolutionary history of P. relictum, an extreme host generalist and widespread parasite. The online version contains supplementary material available at 10.1186/s13071-022-05373-w.
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DOI：
10.1098/rspb.2006.3671
发表时间：
2006-12-07
影响因子：
4.7
作者：
Beadell, Jon S.;Ishtiaq, Farah;Fleischer, Robert C.
通讯作者：
Fleischer, Robert C.
影响因子：
7.7
作者：
Bensch, Staffan;Hellgren, Olof;Perez-Tris, Javier
通讯作者：
Perez-Tris, Javier
影响因子：
2.4
作者：
Ellis, Vincenzo A.;Sari, Eloisa H. R.;Ricklefs, Robert E.
通讯作者：
Ricklefs, Robert E.
影响因子：
4
作者：
Ellis, Vincenzo A.;Bensch, Staffan
通讯作者：
Bensch, Staffan
影响因子：
3
作者：
Hellgren O;Kelbskopf V;Ellis VA;Ciloglu A;Duc M;Huang X;Lopes RJ;Mata VA;Aghayan SA;Inci A;Drovetski SV
通讯作者：
Drovetski SV