Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.
Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.
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DOI：
10.1186/1471-2164-15-687
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发表时间：
2014-08-18
期刊：
影响因子：
4.4
通讯作者：
André C
中科院分区：
文献类型：
--
作者：
Panova M;Johansson T;Canbäck B;Bentzer J;Rosenblad MA;Johannesson K;Tunlid A;André C
阵列比较基因组杂交（aCGH）通常用于筛选人类和模式物种中不同类型的遗传变异。在这里，我们进行了aCGH使用的寡核苷酸基因表达阵列的非模式物种，潮间带蜗牛石纹滨螺。首先，我们测试了什么类型的遗传变异可以通过这种方法使用直接重新测序和比较Littorina基因组草图。其次，我们对四种密切相关的滨螺属物种进行了全基因组比较：L。蚕豆L. compressa，L. arcana和L. saxatilis和L.产于西班牙、英国和瑞典。最后，我们测试了我们是否可以识别潜在的“螃蟹”和“波”生态型的L。岩藻我们可以可靠地检测拷贝数变异，缺失和高序列差异（即3%以上），但不是单核苷酸多态性。整体杂交模式和显着分歧的基因的数量与早期的系统发育重建的基础上单基因的密切一致。L.阿尔卡纳湖compressa和L. saxatilis无法解决，我们认为，这些分歧事件发生在最近和非常接近的时间。我们发现的证据表明，在Littorina基因组中存在高水平的片段性重复（10%的转录本出现在阵列上，高达23%的分析基因组片段）;在所有分析的物种中，重复的基因和区域大多相同。最后，该方法还可区分出L. saxatilis，但我们没有发现任何显着的基因组分歧与生态型L。岩藻本研究提供了新的信息的灵敏度和潜在的使用寡核苷酸阵列的非模式生物的基因分型。将此方法应用于Littorina物种，可以深入了解最近物种辐射后的基因组进化，并支持早期基于单基因的遗传学。L.的遗传分化在这项研究中没有检测到saxatilis生态型，尽管存在明显的先天表型差异。原因可能是这些差异是由于单核苷酸多态性。本文的在线版本（doi：10.1186/1471-2164-15-687）包含补充材料，可供授权用户使用。
Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
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DOI：
10.1111/evo.12329
发表时间：
2014-04
期刊：
Evolution; international journal of organic evolution
影响因子：
--
作者：
Butlin RK;Saura M;Charrier G;Jackson B;André C;Caballero A;Coyne JA;Galindo J;Grahame JW;Hollander J;Kemppainen P;Martínez-Fernández M;Panova M;Quesada H;Johannesson K;Rolán-Alvarez E
通讯作者：
Rolán-Alvarez E
影响因子：
7.7
作者：
Baker, Allan J.;Tavares, Erika Sendra;Elbourne, Rebecca F.
通讯作者：
Elbourne, Rebecca F.
影响因子：
14.9
作者：
Barrett T;Troup DB;Wilhite SE;Ledoux P;Rudnev D;Evangelista C;Kim IF;Soboleva A;Tomashevsky M;Marshall KA;Phillippy KH;Sherman PM;Muertter RN;Edgar R
通讯作者：
Edgar R
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
3.3
作者：
Flibotte, Stephane;Edgley, Mark L.;Moerman, Donald G.
通讯作者：
Moerman, Donald G.