Population Genomics of Transposable Elements in Drosophila melanogaster
Population Genomics of Transposable Elements in Drosophila melanogaster
复制标题
DOI：
10.1093/molbev/msq337
复制
发表时间：
2011-05-01
影响因子：
10.7
通讯作者：
Gonzalez, Josefa
中科院分区：
文献类型：
--
作者：
Petrov, Dmitri A.;Fiston-Lavier, Anna-Sophie;Gonzalez, Josefa
转座元件（TE）是许多生物体基因组体积的主要贡献者，并且是基因组进化的主要参与者。因此，清晰、透彻地了解 TE 的群体动态对于全面理解真核基因组进化和功能至关重要。尽管果蝇的 TE 受到了广泛关注，但该物种中大多数 TE 家族的种群动态仍然完全未被探索。目前尚不清楚相同的种群过程是否可以解释果蝇中所有 TE 的种群行为，或者是否如之前所建议的那样，不同的目根据非常不同的规则进行行为。在这项工作中，我们分析了 5 个北美黑腹果蝇种群和 1 个撒哈拉以南非洲黑腹果蝇种群（总共 75 个品系）中大量个体 TE（755 个 TE）的种群频率。这些 TE 已在参考黑腹果蝇常染色质基因组中进行注释，并从所有三个主要目（非 LTR、LTR 和 TIR）以及具有超过 20 个 TE 拷贝的所有科（总共 55 个科）中采样。我们发现强有力的证据表明，果蝇所有目和科中的 TE 都受到异位重组水平的纯化选择。我们表明，这种选择的强度可预测地随重组率、单个 TE 的长度以及同一家族中其他 TE 的拷贝数和长度而变化。重要的是，这些规则似乎并没有因订单而异。最后，我们建立了一个统计模型，仅考虑个体 TE 水平（例如 TE 长度）和家族水平属性（例如拷贝数），并且能够解释黑腹果蝇 TE 频率变异的 40% 以上。
Transposable elements (TEs) are the primary contributors to the genome bulk in many organisms and are major players in genome evolution. A clear and thorough understanding of the population dynamics of TEs is therefore essential for full comprehension of the eukaryotic genome evolution and function. Although TEs in Drosophila melanogaster have received much attention, population dynamics of most TE families in this species remains entirely unexplored. It is not clear whether the same population processes can account for the population behaviors of all TEs in Drosophila or whether, as has been suggested previously, different orders behave according to very different rules. In this work, we analyzed population frequencies for a large number of individual TEs (755 TEs) in five North American and one sub-Saharan African D. melanogaster populations (75 strains in total). These TEs have been annotated in the reference D. melanogaster euchromatic genome and have been sampled from all three major orders (non-LTR, LTR, and TIR) and from all families with more than 20 TE copies (55 families in total). We find strong evidence that TEs in Drosophila across all orders and families are subject to purifying selection at the level of ectopic recombination. We showed that strength of this selection varies predictably with recombination rate, length of individual TEs, and copy number and length of other TEs in the same family. Importantly, these rules do not appear to vary across orders. Finally, we built a statistical model that considered only individual TE-level (such as the TE length) and family-level properties (such as the copy number) and were able to explain more than 40% of the variation in TE frequencies in D. melanogaster.