Abstract Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions. date view level documentation methods review ones apply solutions

Abstract The mobilome, portion of the genome composed of transposable elements (TEs), of Anopheles darlingi was described together with the genome of this species. Here, this mobilome was revised using similarity and de novo search approaches. A total of 5.6% of the A. darlingi genome is derived of TEs. Class I gypsy and copia were the most abundant superfamilies, corresponding to 22.36% of the mobilome. Non-LTR elements of the R1 and Jockey superfamilies account for 11% of the TEs. Among Class II TEs, the mariner superfamily is the most abundant (16.01%). Approximately 87% of the A. darlingi mobilome consist of short, truncated and/or degenerated copies of TEs. Only three retrotransposons, two belonging to gypsy and one to copia superfamilies, are putatively active elements. Only one Class II element, belonging to the mariner superfamily, is putatively active, having 12 copies in the genome. The TE landscape of A. darlingi is formed primarily by degenerated elements and, therefore, somewhat stable. Future applications of TE-based vectors for genetic transformation of A. darlingi should take into consideration mariner and piggyBac transposons, because full length and putatively active copies of these elements are present in its genome.

Abstract Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans.

Drosophila willistoni (Sturtevant, 1916) é uma espécie do grupo willistoni de Drosophila que apresenta ampla distribuição geográfica desde o sul dos Estados Unidos (Flórida) e México até o norte da Argentina. Esta espécie tem sido alvo de muitos estudos evolutivos dentro do grupo devido à sua considerável capacidade de explorar de forma bem sucedida diversos tipos de ambientes e também por sua grande variabilidade genética expressa através de diferentes marcadores. A linhagem 17A2 de D. willistoni foi coletada em 1991 no Estado do Rio Grande do Sul, Brasil (30°05'S, 51°39'W), e vem sendo mantida desde então no laboratório de Drosophila da Universidade Federal do Rio Grande do Sul. Diferentemente das demais linhagens de D. willistoni mantidas no laboratório, a linhagem 17A2 já produziu espontaneamente machos do tipo white (olhos brancos) e do tipo sepia (olhos marrons) em estoques mantidos a 17ºC. A fim de avaliar se esta linhagem é potencialmente hipermutável, nós submetemo-la a experimentos de estresse por temperatura. Dezoito isolinhagens foram utilizadas e, após a primeira geração, todos os indivíduos de cada isolinhagem foram mantidos a 29°C. Diferentes alterações foram observadas nas gerações seguintes, similares com mutações já bem caracterizadas em D. melanogaster (white, sépia, blistered e curly). Além destas, uma alteração com aparente fusão nas antenas foi encontrada, mas somente em indivíduos da isolinhagem nº 31. Esta última alteração não foi previamente descrita como uma mutação na espécie D. melanogaster. Nossos resultados indicam que a linhagem 17A2 de D. willistoni é uma candidata a hipermutabilidade, além de apresentar uma variabilidade genética importante. Diferentes fatores podem estar atuando para a formação deste panorama observado, tais como mobilização de elementos transponíveis, seleção por endocruzamento e alteração na função de proteínas de choque térmico (heat-shock proteins).

Drosophila willistoni (Sturtevant, 1916) is a species of the willistoni group of Drosophila having wide distribution from the South of USA (Florida) and Mexico to the North of Argentina. It has been subject of many evolutionary studies within the group, due to its considerable ability to successfully occupy a wide range of environments and also because of its great genetic variability expressed by different markers. The D. willistoni 17A2 strain was collected in 1991 in the state of Rio Grande do Sul, Brazil (30°05'S, 51°39'W), and has been maintained since then at the Drosophila laboratory of UFRGS. Different to the other D. willistoni strains maintained in the laboratory, the 17A2 strain spontaneously produced mutant males white-like (white eyes) and sepia-like (brown eyes) in stocks held at 17°C. In order to discover if this strain is potentially hypermutable, we submitted it to temperature stress tests. Eighteen isofemale strains were used in our tests and, after the first generation, all the individuals produced in each strain were maintained at 29°C. Different phenotype alterations were observed in subsequent generations, similar to mutations already well characterized in D. melanogaster (white, sepia, blistered and curly). In addition, an uncommon phenotype alteration with an apparent fusion of the antennae was observed, but only in the isofemale line nº 31. This last alteration has not been previously described as a mutation in the D. melanogaster species. Our results indicate that the D. willistoni 17A2 strain is a candidate for hypermutability, which presents considerable cryptic genetic variability. Different factors may be operating for the formation of this effect, such as the mobilization of transposable elements, effect of inbreeding and alteration of the heat-shock proteins functions.