Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes.
Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes.
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DOI：
10.1098/rspb.2017.2732
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发表时间：
2018-02-14
期刊：
影响因子：
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通讯作者：
Taylor MI
中科院分区：
文献类型：
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作者：
Marburger S;Alexandrou MA;Taggart JB;Creer S;Carvalho G;Oliveira C;Taylor MI
真核生物类群的基因组大小差异很大，最大的变化通常是由宏突变驱动的，例如全基因组复制（WGD）和重复元件的增殖。这两个过程可能通过增加遗传变异和改变基因表达来影响谱系的进化潜力。在这里，我们阐明了物种丰富的新热带鲶鱼（Corydoradinae）基因组大小变异的进化历史和机制，这些鲶鱼的基因组大小存在极大差异——每个单倍体细胞为 0.6 至 4.4 pg。首先，对 65 个物种的基因组大小进行了量化，并将其映射到新的化石校准系统发育上。在整个树中发现了基因组大小的两个进化转变——第一个在 43 到 49 Ma 之间（95% 最高后验密度 (HPD) 36.2–68.1 Ma），第二个在大约 19 Ma 之间（95% HPD 15.3–30.14 Ma）。其次，使用限制性位点相关 DNA (RAD) 测序来识别潜在的 WGD 事件并量化不同谱系中的转座元件 (TE) 丰度。在整个系统发育过程中确定了两个谱系规模 WGD 的证据，第一个事件发生在 54 到 66 Ma（95% HPD 42.56–99.5 Ma）之间，第二个事件发生在 20–30 Ma（95% HPD 15.3–45 Ma）之间，基于每个重叠群的单倍型数量，以及在 35 到 44 Ma 之间（95% HPD） 30.29–64.51 Ma) 和 20–30 Ma (95% HPD 15.3–45 Ma) 基于 SNP 读取比率。 TE丰度随着基因组大小的增加而显着增加，单个TE家族（TC1-IS630-Pogo）在整个Corydoradinae中显示出几次增加，最近一次发生在20-30 Ma（95% HPD 15.3-45 Ma），而较早的事件发生在35-44 Ma（95% HPD 30.29-64.51 Ma）。我们确定了与两个 WGD 重复事件一致的信号，以及不同谱系中 TE 丰度的增加，使 Corydoradinae 成为研究 WGD 和 TE 对基因组和生物体进化影响的优秀模型系统。
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.