Genomic Landscape of Long Terminal Repeat Retrotransposons (LTR-RTs) and Solo LTRs as Shaped by Ectopic Recombination in Chicken and Zebra Finch
Genomic Landscape of Long Terminal Repeat Retrotransposons (LTR-RTs) and Solo LTRs as Shaped by Ectopic Recombination in Chicken and Zebra Finch
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鸡和斑胸草雀异位重组形成的长末端重复反转录转座子 (LTR-RT) 和单独 LTR 的基因组景观
DOI：
10.1007/s00239-016-9741-0
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发表时间：
2016
影响因子：
3.9
通讯作者：
bullet J Andrew Dewoody
中科院分区：
文献类型：
--
作者：
Yanzhu Ji;bullet J Andrew Dewoody
转座元件(TES)在真核生物基因组中几乎无处不在，但其含量在不同的系统发育谱系中差异很大。已经提出了几种机制来驱动基因组中的TE动态，包括通过选择或漂移来固定/丢失特定的TE插入，以及由于突变(例如，重组)导致的基因组结构变化。特别是，重组可以对基因组TE格局产生显著的方向性影响。例如，异位重组去除了长末端重复反转录转座子(LTR-RTS)的内部区域以及一个长末端重复序列(LTR)，导致了单独的LTR。在这项研究中，我们重点研究了鸟类基因组中LTR-RTS和单链LTRS的种内动态。LTR-RTS和单链LTRS在鸟类中的分布很有趣，因为在给定的基因组中，鸟类的重组率差异很大。我们使用已发表的连锁图谱和全基因组组合来研究鸡和斑马雀的重组率和LTR去除事件之间的关系。我们假设重组率低的区域会比重组率高的区域拥有更多的全长LTR-RTS(而更少的单个LRT)。我们通过比较跨染色体、跨非重叠的巨型数据库窗口和跨物理特征(即着丝粒和端粒)的全长LTR-RTS和单个LTRS的比率来检验这一假设。鸡的数据在统计上支持了这样的假设，即重组率与染色体水平和1-Mb非重叠窗口中全长与单个LTRS的比率成反比。我们还发现，鸡端粒附近的全长与单链转录因子的比率显著低于着丝粒附近的比率。我们的结果表明，异位重组在塑造鸡LTR-RT基因组图谱中具有潜在的作用。
Transposable elements (TEs) are nearly ubiquitous among eukaryotic genomes, but TE contents vary dramatically among phylogenetic lineages. Several mechanisms have been proposed as drivers of TE dynamics in genomes, including the fixation/loss of a particular TE insertion by selection or drift as well as structural changes in the genome due to mutation (e.g., recombination). In particular, recombination can have a significant and directional effect on the genomic TE landscape. For example, ectopic recombination removes internal regions of long terminal repeat retrotransposons (LTR-RTs) as well as one long terminal repeat (LTR), resulting in a solo LTR. In this study, we focus on the intra-species dynamics of LTR-RTs and solo LTRs in bird genomes. The distribution of LTR-RTs and solo LTRs in birds is intriguing because avian recombination rates vary widely within a given genome. We used published linkage maps and whole genome assemblies to study the relationship between recombination rates and LTR-removal events in the chicken and zebra finch. We hypothesized that regions with low recombination rates would harbor more full-length LTR-RTs (and fewer solo LTRs) than regions with high recombination rates. We tested this hypothesis by comparing the ratio of full-length LTR-RTs and solo LTRs across chromosomes, across non-overlapping megabase windows, and across physical features (i.e., centromeres and telomeres). The chicken data statistically supported the hypothesis that recombination rates are inversely correlated with the ratio of full-length to solo LTRs at both the chromosome level and in 1-Mb non-overlapping windows. We also found that the ratio of full-length to solo LTRs near chicken telomeres was significantly lower than those ratios near centromeres. Our results suggest a potential role of ectopic recombination in shaping the chicken LTR-RT genomic landscape.
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影响因子：
3.3
作者：
M. Lichten;R. Borts;James E. Haber
通讯作者：
M. Lichten;R. Borts;James E. Haber
DOI：
10.1007/978-1-61779-582-4_13
发表时间：
2012-01-01
期刊：
EVOLUTIONARY GENOMICS: STATISICAL AND COMPUTATIONAL METHODS, VOL 1
影响因子：
--
作者：
Gonzalez, Josefa;Petrov, Dmitri A.
通讯作者：
Petrov, Dmitri A.
果蝇自然群体的世界性反转中的转座元件数量。
影响因子：
3.3
作者：
Sniegowski,PD;Charlesworth,B
通讯作者：
Charlesworth,B
影响因子：
1.5
作者：
LANGLEY, CH;MONTGOMERY, E;CHARLESWORTH, B
通讯作者：
CHARLESWORTH, B