Transposons and the dynamic genome pdf

This volume gives an overview on mobile DNA and how such contradiction to the obligatory stability of genomes can be understood. Obviously, an understanding can only be achieved by cutting deeply into the evolutionary history of life. Plant Transposons and Genome Dynamics in Evolution. The transposable genetic elements, or transposons, as they are now known, have had a tumultuous history. Discovered in the midth century by Barbara McClintock, they were initially received with puzzlement.

Transposons and the Dynamic Genome. This volume gives an overview on mobile DNA and how such contradiction to the obligatory stability of genomes can be understood.

Obviously, an understanding can only be achieved by cutting deeply into the evolutionary history of life. Plant Transposons and Genome Dynamics in Evolution. The transposable genetic elements, or transposons, as they are now known, have had a tumultuous history.

The length and sequence of the TSDs and terminal motifs of the TIRs are highly conserved across superfamilies and are useful in categorizing elements. Following the excision of an element, the donor site may be repaired via homologous recombination.

However, the gap repair process is oftentimes interrupted resulting in shorter elements with internal deletions Engels et al. These shorter copies still possess TIRs that can be recognized by the transposase encoded by complete elements and consequently they retained their mobility Hartl et al. These nonautonomous elements compete with their progenitors for the transposase and often outnumber their autonomous relatives Yang et al.

TEs have dramatically affected the size, structure, and function of the genomes they inhabit Feschotte and Pritham ; Cordeaux and Batzer Although most TE insertions are either neutral or deleterious, the domestication by the host of TE-encoded sequences can occur and is responsible for the evolution of fundamental biological processes such as light sensing in plants Hudson et al.

However, it is likely that the impact of class 1 and class 2 elements varies among species because their abundance and diversity greatly differ among group of organisms Eickbush and Furano ; Furano et al. For instance, fish genomes contain a diversity of active DNA transposons that coexist with a multitude of retrotransposon families Duvernell et al. In contrast, mammalian genomes are dominated by class 1 elements and it was believed until recently that mammals completely lack active class 2 elements, although DNA transposons were once diverse and very active in early mammalian evolution Lander et al.

However, recent analyses have shown that vertebrate genomes, including mammalian genomes, can be recolonized by laterally transferred DNA transposons and that these transfers seem to occur relatively frequently Pace et al. Here, we present the first analysis of class 2 elements in a reptile, the North American green anole, Anolis carolinensis. The green anole is the first non-avian reptile to have its genome sequenced, bridging a large phylogenetic gap between fish and mammals.

These prolific superfamilies are represented in the anole genome by ten autonomous families, which are responsible for the amplification of a multitude of nonautonomous families that largely outnumber their autonomous counterparts.

The age distribution of DNA transposons suggests that novel insertions do reach fixation, yet the near absence of ancient elements indicates that some postinsertional mechanism s limits the accumulation of DNA transposons in the anole genome. An exhaustive search of the anole genome for class 2 transposons was completed with three different methods. From the output subgroups, only those with a minimum of ten copies were analyzed. The resulting alignments were collected to form an initial library of TEs from the anole genome.

This library was then used as the basis of a RepeatMasker search of the genome to find additional copies of the putative elements. Hits of sufficient length, typically at least bp, were extracted from the genome along with a minimum of bp of flanking sequence using custom PERL scripts.

The process was repeated until the full-length sequence of each putative element was obtained. A second search of the genome, using the Repeatscout program Price et al. Any previously identified putative elements were not processed, whereas new elements were used to create a library for use in a Repeatmasker search and the output as described above.

Lastly, we performed a BlastX search of the genome using amino acid sequences derived from a known transposon library available from Repbase v Elements were separated into superfamilies and further subdivided into families based upon size and sequence similarity.

A consensus sequence for each family was created. The pairwise divergence between elements and the average divergence from the consensus sequence were calculated using Kimura's 2-parameter method in MEGA 4.

We estimated copy number for each family by using the Blast option on NCBI; however, as many of the elements are either extremely fragmented and some families are nearly identical at their ends but differ in their central region, it is difficult to ascertain the exact copy number of each family.

Percentages for each of the four possible nucleotides were then calculated for each position. As repeat masker oftentimes did not recognize some of these novel nonautonomous elements, the sequence and length of TSDs and TIRs were used to categorize each family to its proper autonomous superfamily.

Finally, in order to identify possible events of horizontal transfer, consensus sequences from each family were submitted to the Blast option on the NCBI Web site and a multitude of sequenced organisms were screened. The genome of A. Conversely, the hAT , Mariner , Helitron , and Chapaev superfamilies were very prolific and produced 67 distinct families ten autonomous and 57 nonautonomous , yet they differ drastically in abundance and diversity.

The hAT superfamily is the most abundant and diverse in the anole genome. It is represented by five autonomous and 32 nonautonomous families table 1. These four laterally transferred hAT elements are more closely related to mammalian Charlie elements fig. As its name indicates, it belongs to the hobo clade of hATs fig. Most nonautonomous families correspond to deleted versions of autonomous elements; consequently their evolutionary affinities are relatively easy to determine.

Yet, we identified eight nonautonomous families that did not show any similarity with a known autonomous family beyond the TIR. The transposase of one of the autonomous copies could be mobilizing these elements despite their lack of similarity in the TIR. Alternatively, we cannot exclude that another autonomous hAT family exists in anole and either was missed by our search if its copy number is extremely low or is so new in anole that it is polymorphic in populations and absent from the individual used for the genome sequencing or has never reached fixation in the more distant past.

The tree is based on an amino acid alignment of the transposase domain. It was inferred using the neighbor joining method, and the robustness of the nodes was assessed by bootstrap 1, runs.

Although autonomous hAT elements in anole are typical members of their superfamily length and sequence of TIRs and TSDs , they differ considerably in length. Autonomous hobo elements are very similar in this 3 kb region, as suggested by the short length of the branches, yet they cluster in several distinct lineages that differ significantly in structure due to the frequent insertion or loss of DNA sequence fig.

Additionally, we found that some elements were composites of other autonomous copies. The boxed sequences indicate elements that are complete in the genome assembly we used. Seven different patterns of nested elements were recovered and are schematically presented on the right of each sequence structure 3 corresponds to elements 93, 13, 10, and Though all 45 elements are very similar to each other, they differ in their length and structure.

The arrows on the right indicate the recombination of elements 3 and 4 resulting in element 1. Within group A and B, elements have similar ends but differ drastically in structure due to insertions, deletions, and the incorporation of genomic DNA of other origin, often containing TE from other classes or superfamilies.

Using the presence of TE fragments embedded within nonautonomous families as markers, we were able to decipher the evolutionary history of these families depicted on fig. A partial deletion bp of the Penelope element occurred yielding families hobo-N2 , 3 , and 5. A recombination event between an element containing the deleted version of Penelope and one containing the deleted SINE resulted in family hobo-N4.

Ancestral group B elements contain a CR1 and a Chapaev insertion and are represented in the anole genome by families hobo-N7 , 8 , and 9. A fourth recombination event between family hobo-N15 and a group B element produced three families hobo-N10 , 11 , and 12 with termini typical of group B but a central portion similar to group A. The TIRs are boxed.

At least three elements from each family are included. Diagram depicting the evolution of the 15 nonautonomous hobo families see text for explanation. As expected, there is a relatively good concordance between the age of autonomous families and their nonautonomous counterparts. Autonomous hAT-HT2 elements are extremely young and in fact their mean divergence from consensus is 0.

In contrast, their nonautonomous counterparts have divergence ranging from 0. It is plausible that these nonautonomous copies resulted from a previous wave of lateral transfer of the hAT-HT2 family that would have produced nonautonomous families but failed to establish a resident population of autonomous copies.

Alternatively, this suggests that autonomous and nonautonomous copies have different dynamics in Anolis populations, possibly because they are differently affected by purifying selection.

If autonomous copies are more deleterious to the host than nonautonomous ones, it is plausible that they fail to reach fixation and that their very young age reflects a high rate of turnover where the transposition of new copies is countered by the selective loss of deleterious copies.

Neutral or nearly neutral elements, such as nonautonomous ones could reach fixation and accumulate more readily in the genome of the host. Values were calculated using Kimura's 2-parameter method in Mega 4. Autonomous families are emphasized with darker bars. This suggests that other Mariner families are or have been active in the anole genome. Despite numerous attempts to identify such autonomous families, we failed to find any other autonomous families.

However, several nonautonomous families show some significant similarity with Mariner -like elements from other organisms, in particular at their extremities. It is plausible that these elements never reached high copy numbers and, because of the fast decay of TEs in anole Novick et al.

Unlike hAT elements, most Mariner -like families are relatively ancient and no longer active. The rarity of autonomous copies and the age distribution of Mariner -like families suggest that mariner elements could be frequently invading the anole genome, produce abundant nonautonomous families but fail to become stable residents of this genome.

It was built using the neighbor joining method and the robustness of the nodes was assessed by bootstrap 1, runs. The third category of DNA transposon found in anole is the Helitron subclass table 2. As previously noted by Piskurek et al. Family Helitron-2N3 contains fragments of Poseidon and SINE elements, yet this seems to be a rare occurrence as this is the only Helitron family to show a composite structure.