Bertocchi Natasha Avila, Torres Fabiano Pimentel, Garnero Analía Del Valle, Gunski Ricardo José, Wallau Gabriel Luz
Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil.
Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa (Unipampa), São Gabriel, Rio Grande do sul 97300-000 Brazil.
Mob DNA. 2017 Aug 14;8:11. doi: 10.1186/s13100-017-0094-z. eCollection 2017.
Transposable elements (TEs) are highly abundant genomic parasites in eukaryote genomes. Although several genomes have been screened for TEs, so far very limited information is available regarding avian TEs and their evolutionary histories. Taking advantage of the rich genomic data available for birds, we characterized the evolutionary history of the element, originally described in , through the use of several bioinformatic analyses.
homologous sequences were found in 6 of 72 genomes analyzed: 5 species of Galliformes (, , , , ) and one Buceritiformes (). The copy number ranged from 5 to 10,158, in the genomes of and respectively. All 6 species possessed short elements, suggesting the presence of Miniature Inverted repeats Transposable Elements (MITEs), which underwent an ancient massive amplification in the and genomes. Only 4 species showed potential MITE full-length partners, although no potential coding copies were detected. Phylogenetic analysis of reconstructed coding sequences showed that homolog sequences form a new subfamily, which we termed . Inter-species and intragenomic distance analyses indicated a high identity between the consensus of and the other 5 related species, and different emergence ages of the element between the Galliformes species and , suggesting that horizontal transfer took place from Galliformes to a Buceritiformes ancestor, probably through an intermediate species.
Overall, our results showed that elements have amplified to high copy numbers in some avian species, and that this transposition burst probably occurred in the common ancestor of and In addition, although no coding sequences could be found currently, they probably existed, allowing an ancient massive MITE amplification in these 2 species. The other 4 species also have MITEs, suggesting that this new family is prone to give rise to such non-autonomous derivatives. Last, our results suggest that a horizontal transfer event of a element occurred between Galliformes and Buceritiformes.
转座元件（TEs）是真核生物基因组中高度丰富的基因组寄生虫。尽管已经对多个基因组进行了TEs筛查，但迄今为止，关于鸟类TEs及其进化历史的信息非常有限。利用现有的丰富鸟类基因组数据，我们通过多种生物信息学分析方法，对最初在[具体文献]中描述的[元件名称]的进化历史进行了表征。
在分析的72个基因组中的6个中发现了同源序列：5种鸡形目鸟类（[具体物种1]、[具体物种2]、[具体物种3]、[具体物种4]、[具体物种5]）和1种犀鸟目鸟类（[具体物种6]）。拷贝数在[具体物种1]和[具体物种2]的基因组中分别为5至10,158个。所有6个物种都拥有短元件，这表明存在微型反向重复转座元件（MITEs），它们在[具体物种1]和[具体物种2]的基因组中经历了一次古老的大规模扩增。虽然未检测到潜在的编码拷贝，但只有4个物种显示出潜在的MITE全长伙伴。对重建的编码序列进行系统发育分析表明，[元件名称]同源序列形成了一个新的[元件所属家族名称]亚家族，我们将其命名为[新亚家族名称]。种间和基因组内的[元件名称]距离分析表明，[具体物种1]的共有序列与其他5个相关物种之间具有高度同一性，并且鸡形目物种与[具体物种6]之间[元件名称]的出现年龄不同，这表明水平转移可能从鸡形目发生到犀鸟目祖先，可能是通过一个中间物种。
总体而言，我们的结果表明，[元件名称]元件在一些鸟类物种中扩增到了高拷贝数，并且这种转座爆发可能发生在[具体物种1]和[具体物种2]的共同祖先中。此外，尽管目前未发现编码序列，但它们可能曾经存在，从而在这两个物种中引发了一次古老的大规模MITE扩增。其他4个物种也有MITEs，这表明这个新的[元件所属家族名称]家族易于产生这种非自主衍生物。最后，我们的结果表明，[元件名称]元件在鸡形目和犀鸟目之间发生了一次水平转移事件。
