Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes.
Evolutionary dynamics of retrotransposable elements Rex1, Rex3 and Rex6 in neotropical cichlid genomes.
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DOI：
10.1186/1471-2148-13-152
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发表时间：
2013-07-16
影响因子：
3.4
通讯作者：
Feldberg E
中科院分区：
文献类型：
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作者：
Schneider CH;Gross MC;Terencio ML;do Carmo EJ;Martins C;Feldberg E
转座因子（Transposable elements，TE）有可能在宿主基因组中产生广泛的变化，充当一种进化工具箱，产生一系列新的调控和编码序列。几个TE类已在新热带慈鲷进行了研究，然而，从这些研究中获得的信息仅限于物理染色体作图，而TE的遗传多样性仍然未知。因此，非LTR反转录转座子Rex 1，Rex 3和Rex 6在五个亚马逊慈鲷物种的基因组组织进行了评估，使用物理染色体定位和DNA测序，以提供有关TE在慈鲷基因组进化中的作用的信息。物理作图显示大量的TE簇分散在整个染色体。此外，几个物种显示出明显的集群积累在着丝粒和染色体的末端部分。这些TE染色体位点与异染色质和常染色质区域都相关。在衍生物种中观察到更多的Rex 1簇。Rex 1和Rex 3的核苷酸序列在基础物种中比在衍生物种中更保守;然而，在Rex 6中没有观察到这种模式。此外，可以观察到与Rex 1和Rex 3克隆的逆转录酶片段和Rex 6的内切核酸酶对应的保守区块。我们的数据显示，没有一致的贝叶斯树之间产生的Rex 1，Rex 3和Rex 6的慈鲷物种和系统发育假说所描述的组。Rex 1和Rex 3核苷酸序列在基础物种中更为保守，而Rex 6在基础物种和衍生物种中均表现出高取代率。雷克斯元素在慈鲷基因组中的分布表明，这些元素是在进化机制的作用下，导致其积累在特定的染色体区域，主要是在异染色质。
Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins.
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影响因子：
1.7
作者：
Jurka, J;Kapitonov, VV;Walichiewicz, J
通讯作者：
Walichiewicz, J
影响因子：
1.7
作者：
Gross, M. C.;Schneider, C. H.;Feldberg, E.
通讯作者：
Feldberg, E.
影响因子：
1.7
作者：
da Silva, M.;Matoso, D. A.;Artoni, R. F.
通讯作者：
Artoni, R. F.
影响因子：
4.1
作者：
López-Fernández, H;Honeycutt, RL;Winemiller, KO
通讯作者：
Winemiller, KO
DOI：
10.1038/nrg3030
发表时间：
2011-08-18
期刊：
Nature reviews. Genetics
影响因子：
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作者：
通讯作者：
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