Loss of LINE-1 activity in the megabats

Abstract

LINE-1 (L1) retrotransposons are the most abundant type of mammalian retroelement. They have profound effects on genome plasticity and have been proposed to fulfill essential host functions, yet it remains unclear where they lie on the spectrum from parasitism to mutualism. Their ubiquity makes it difficult to determine the extent of their effects on genome evolution and gene expression because of the relative dearth of animal models lacking L1 activity. We have isolated L1 sequences from 11 megabat species by a method that enriches for recently inserted L1s and have done a bioinformatic examination of L1 sequences from a 12th species whose genome was recently shotgun sequenced. An L1 extinction event appears to have occurred at least 24 million years ago (MYA) in an ancestor of the megabats. The ancestor was unusual in having maintained two highly divergent long-term L1 lineages with different levels of activity, which appear, on an evolutionary scale, to have simultaneously lost that activity. These megabat species can serve as new animal models to ask what effect loss of L1 activity has on mammalian genome evolution and gene expression.

Figure 1.—

–Phylogenies of selected bat species (A) and rodent species (B). The phylogenies are adapted from Teeling et al. (2005) and from Steppan et al. (2004), respectively. The asterisk on each tree shows the branch on which L1 activity ceased. Branch lengths indicate the molecular time scale, and the numbers at nodes are the estimated times since divergence (millions of years ago, MYA). The megabats (family Pteropodidae) and the microbat genus Rhinopoma are within the suborder Yinpterochiroptera, while the genera Tonatia and Artibeus are microbat genera within the suborder Yangochiroptera. The four megabat species shown represent a broad phylogenetic range of that group. The rodent divergence times are the estimates Steppan et al. obtained using nonparametric rate smoothing. The sigmodontine rodents are indicated within the bracket.

Figure 2.—

–Southern hybridization of genomic DNA digested with RsaI and probed with a dog L1. The four left lanes contain DNA from megabat species: (A) Cynopterus sphinx, (B) Nyctimene albiventer, (C) Pteropus hypomelanus, and (D) Rousettus amplexicaudatus. The two right lanes contain DNA from two microbat species: (E) Artibeus jamaicensis and (F) Tonatia saurophila bakeri. Numbers at the left show positions of size markers (kb).

Figure 3.—

–Maximum a posteriori probability phylogeny of 218 megabat L1 sequences from 11 megabat species. Three recently transposed L1 sequences from Notiosorex crawfordi (Ncra) were used as the outgroup. Posterior probabilities are given above relevant branches to show the two supported long-term lineages (1 and 2) and significantly older elements. Names of individual elements have been removed, and terminal branches for megabat species have been color coded. The tree is rooted with the N. crawfordi elements. The small tree is of 20 Rattus norvegicus L1 sequences with two recently transposed Peromyscus maniculatus (Pman) elements used as the outgroup. The small tree was constructed using rat sequences from 10 blue colonies and 10 white colonies obtained by PCR as for the megabat sequences but with no subsequent removal of older elements. The large tree contains only the more recently transposed subset of megabat sequences from each species.

Figure 4.—

–Distance distribution of megabat lineage-1 elements (A) and sigmodontine elements (B) to ancestor. The adjusted pairwise sequence distance from each megabat lineage-1 (L1) element to the megabat lineage-1 ancestor and from each sigmodontine L1 element to the sigmodontine ancestor was determined. For each data set, the percentage of the total elements that were within each indicated distance range is shown.