Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing.
Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing.
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DOI：
10.1093/gbe/evr043
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发表时间：
2011
影响因子：
3.3
通讯作者：
Pollock DD
中科院分区：
文献类型：
--
作者：
Castoe TA;Hall KT;Guibotsy Mboulas ML;Gu W;de Koning AP;Fox SE;Poole AW;Vemulapalli V;Daza JM;Mockler T;Smith EN;Feschotte C;Pollock DD
我们进行了一个全面的评估，在两个蛇的基因组，有毒的铜斑蛇（蝮蛇）和缅甸蟒蛇（蟒蛇molurus bivittatus）的基因组重复内容。这两个基因组都相对较小（约1.4 Gb），但在重复元件的丰度和扩展历史方面存在令人惊讶的广泛差异。在蟒蛇中，容易识别的重复元件含量很低（21%），与鸟类基因组相似，而铜头蛇的重复元件含量较高（45%），与哺乳动物基因组相似。铜头蛇的更大的重复内容来自于最近许多不同的微卫星和转座因子（TE）家族的扩展，铜头蛇的TE相关转录本水平比蟒蛇高23倍。这表明铜头蛇中更大的TE活动正在进行的可能性。CR 1 LINE在铜斑蛇基因组中的扩增导致TE介导的微卫星扩增（“微卫星播种”），其规模比先前在脊椎动物中观察到的大几个数量级。蛇似乎也倾向于横向转移的TE，特别是在铜头蛇的血统。尽管与极端代谢性能相关的选择压力是一个明显的候选者，但铜头蛇在面对如此多的最近重复元件扩增时具有如此小的基因组的原因仍然是一个悬而未决的问题。TE活动可以影响基因调控以及重组和基因复制的速率，因此TE活动可能在蛇的主要适应性进化中发挥作用;一些证据表明这可能包括毒液库的进化。
We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus). These two genomes are both relatively small (∼1.4 Gb) but have surprisingly extensive differences in the abundance and expansion histories of their repeat elements. In the python, the readily identifiable repeat element content is low (21%), similar to bird genomes, whereas that of the copperhead is higher (45%), similar to mammalian genomes. The copperhead's greater repeat content arises from the recent expansion of many different microsatellites and transposable element (TE) families, and the copperhead had 23-fold greater levels of TE-related transcripts than the python. This suggests the possibility that greater TE activity in the copperhead is ongoing. Expansion of CR1 LINEs in the copperhead genome has resulted in TE-mediated microsatellite expansion (“microsatellite seeding”) at a scale several orders of magnitude greater than previously observed in vertebrates. Snakes also appear to be prone to horizontal transfer of TEs, particularly in the copperhead lineage. The reason that the copperhead has such a small genome in the face of so much recent expansion of repeat elements remains an open question, although selective pressure related to extreme metabolic performance is an obvious candidate. TE activity can affect gene regulation as well as rates of recombination and gene duplication, and it is therefore possible that TE activity played a role in the evolution of major adaptations in snakes; some evidence suggests this may include the evolution of venom repertoires.
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影响因子：
7.7
作者：
Castoe TA;Poole AW;Gu W;Jason de Koning AP;Daza JM;Smith EN;Pollock DD
通讯作者：
Pollock DD
影响因子：
4.1
作者：
Guiher, Timothy J.;Burbrink, Frank T.
通讯作者：
Burbrink, Frank T.
影响因子：
3.4
作者：
Jiang ZJ;Castoe TA;Austin CC;Burbrink FT;Herron MD;McGuire JA;Parkinson CL;Pollock DD
通讯作者：
Pollock DD
影响因子：
3.7
作者：
Castoe TA;Jiang ZJ;Gu W;Wang ZO;Pollock DD
通讯作者：
Pollock DD
影响因子：
64.8
作者：
Fry, BG;Vidal, N;Kochva, E
通讯作者：
Kochva, E