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Abstract：
UNASSIGNED: Kinetoplastids are a flagellated group of protists, including some parasites, such as Trypanosoma and Leishmania species, that can cause diseases in humans and other animals. The genomes of these species enclose a fraction of retrotransposons including VIPER and TATE, two poorly studied transposable elements that encode a tyrosine recombinase (YR) and were previously classified as DIRS elements. This study investigated the distribution and evolution of VIPER and TATE in kinetoplastids to understand the relationships of these elements with other retrotransposons.
UNASSIGNED: We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER. We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like. The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus, whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton. Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF.
UNASSIGNED: Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like.
UNASSIGNED: We observed that VIPER and TATE have a discontinuous distribution among Trypanosomatidae, with several events of loss and degeneration occurring during a vertical transfer evolution. We were able to identify the terminal repeats of these elements for the first time, and we showed that these elements are potentially active in some species, including T. cruzi copies of VIPER. We found that VIPER and TATE are strictly related elements, which were named in this study as VIPER-like. The reverse transcriptase (RT) tree presented a low resolution, and the origin and relationships among YR groups remain uncertain. Conversely, for RH, VIPER-like grouped with Hepadnavirus, whereas for YR, VIPER-like sequences constituted two different clades that are closely allied to Crypton. Distinct topologies among RT, RH and YR trees suggest ancient rearrangements/exchanges in domains and a modular pattern of evolution with putative independent origins for each ORF.
UNASSIGNED: Due to the presence of both elements in Bodo saltans, a nontrypanosomatid species, we suggested that VIPER and TATE have survived and remained active for more than 400 million years or were reactivated during the evolution of the host species. We did not find clear evidence of independent origins of VIPER-like from the other YR retroelements, supporting the maintenance of the DIRS group of retrotransposons. Nevertheless, according to phylogenetic findings and sequence structure obtained by this study and other works, we proposed separating DIRS elements into four subgroups: DIRS-like, PAT-like, Ngaro-like, and VIPER-like.
摘要：
■动植体是一群鞭毛的原生生物，包括一些寄生虫,例如锥虫和利什曼原虫，会导致人类和其他动物的疾病。这些物种的基因组包含一部分逆转录转座子，包括VIPER和TATE，两种编码酪氨酸重组酶(YR)且先前被分类为DIRS元件的转座元件研究得很少。这项研究调查了VIPER和TATE在动体中的分布和进化，以了解这些元素与其他反转录转座子的关系。
■我们观察到VIPER和TATE在锥虫科中具有不连续的分布，在垂直转移进化过程中发生了几个丢失和变性事件。我们第一次能够识别这些元素的末端重复，我们发现这些元素在某些物种中具有潜在的活性，包括T.Cruzi的VIPER副本。我们发现VIPER和TATE是严格相关的元素，在这项研究中被命名为VIPER样。逆转录酶（RT）树呈现低分辨率，YR群体之间的起源和关系仍不确定。相反，对于RH,VIPER样与Hepadnavirus成组，而对于YR,类似VIPER的序列构成了与Crypton密切相关的两个不同的进化枝。RT之间的独特拓扑，RH和YR树暗示了区域中的古老重排/交换，以及每个ORF的假定独立起源的模块化进化模式。
■由于Bodo盐中存在两种元素，一种非锥虫属物种，我们建议VIPER和TATE存活并保持活跃超过4亿年，或者在宿主物种的进化过程中被重新激活。我们没有从其他YR追溯元素中找到VIPER-like的独立起源的明确证据，支持DIRS组的反转录转座子的维持。然而，根据本研究和其他工作获得的系统发育发现和序列结构，我们建议将DIRS元素分为四个子组：类DIRS，PAT-like,像恩加罗一样，和VIPER一样。
■我们观察到VIPER和TATE在锥虫科中具有不连续的分布，在垂直转移进化过程中发生了几个丢失和变性事件。我们第一次能够识别这些元素的末端重复，我们发现这些元素在某些物种中具有潜在的活性，包括T.Cruzi的VIPER副本。我们发现VIPER和TATE是严格相关的元素，在这项研究中被命名为VIPER样。逆转录酶（RT）树呈现低分辨率，YR群体之间的起源和关系仍不确定。相反，对于RH,VIPER样与Hepadnavirus成组，而对于YR,类似VIPER的序列构成了与Crypton密切相关的两个不同的进化枝。RT之间的独特拓扑，RH和YR树暗示了区域中的古老重排/交换，以及每个ORF的假定独立起源的模块化进化模式。
■由于Bodo盐中存在两种元素，一种非锥虫属物种，我们建议VIPER和TATE存活并保持活跃超过4亿年，或者在宿主物种的进化过程中被重新激活。我们没有从其他YR追溯元素中找到VIPER-like的独立起源的明确证据，支持DIRS组的反转录转座子的维持。然而，根据本研究和其他工作获得的系统发育发现和序列结构，我们建议将DIRS元素分为四个子组：类DIRS，PAT-like,像恩加罗一样，和VIPER一样。
