LTR retroelements in the genome of Daphnia pulex.
LTR retroelements in the genome of Daphnia pulex.
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DOI：
10.1186/1471-2164-11-425
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发表时间：
2010-07-09
期刊：
影响因子：
4.4
通讯作者：
Tang H
中科院分区：
文献类型：
--
作者：
Rho M;Schaack S;Gao X;Kim S;Lynch M;Tang H
长末端重复（LTR）逆转录因子是一组成功的转座因子（te），在塑造许多真核生物基因组结构中发挥了重要作用。在这里，我们对水蚤（Daphnia pulex）的LTR逆转录因子进行了全基因组分析，水蚤是一种周期性孤雌生殖动物，也是第一个完整基因组序列可用的甲壳类动物。此外，我们分析了转录数据，并对实验室培养的谱系和自然分离株进行转座子显示分析，以确定有无性别繁殖个体之间TE迁移率和LTR逆转录元件负载差异的潜在影响。我们进行了LTR逆转录因子的全面从头搜索，并在D. pulex基因组中鉴定了333个完整的LTR逆转录因子，代表142个家族。虽然近一半已确定的LTR逆转录因子属于gypsy组，但我们也发现了copia (95), BEL/Pao（66）和DIRS（19）逆转录因子。逆转录酶序列的系统发育分析表明，在D. pulex基因组中，LTR逆转录元件形成了许多不同于已知家族的谱系，表明大多数是新的。我们利用三种不同实验条件下获得的瓦片阵列数据对LTR逆转录元件的转录活性进行了研究，发现71个LTR逆转录元件是活跃转录的。突变积累系的转座子显示试验显示，两个DIRS逆转录因子家族可能存在体细胞插入。在自交谱系中观察到可能的杂合插入丢失，但在无性谱系中从未观察到，这突出了生殖模式对TE丰度和分布的潜在影响。同样的两个科也在自然分离株（周期性孤雌生殖和专性无性生殖）中进行了分析，并且在两个科中的一个能够有性繁殖的群体中存在更多的逆转录因子。考虑到LTR逆转录因子活性在其他基因组进化中的重要性，这项全面的调查提供了LTR逆转录因子对D. pulex基因组的潜在影响，D. pulex是一种循环孤雌生殖的微甲壳类动物，一个多世纪以来一直作为生态模型。
Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex. We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed. Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.
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影响因子：
7
作者：
Malik, HS;Eickbush, TH
通讯作者：
Eickbush, TH
影响因子：
3.5
作者：
Frame, IG;Cutfield, JF;Poulter, RTM
通讯作者：
Poulter, RTM
影响因子：
10.7
作者：
Goodwin, TJD;Poulter, RTM
通讯作者：
Poulter, RTM
DOI：
10.1073/pnas.97.26.14473
发表时间：
2000-12-19
影响因子：
11.1
作者：
Arkhipova, I;Meselson, M
通讯作者：
Meselson, M
影响因子：
14.9
作者：
Chenna, R;Sugawara, H;Thompson, JD
通讯作者：
Thompson, JD