Characterization and evolution of LAVA elements in gibbons. M. K. Konkel1, J. A. Walker1, B. Ullmer2, T. J. Meyer3, A. Damert4, R. Hubley5, A. F. A. Smit5, L. Carbone3, M. A. Batzer1 for the Gibbon Genome Sequencing and Analysis Consortium 1) Dept. of Biological Sciences, Louisiana State University, Baton Rouge, LA; 2) School of Electrical Engineering and Computer Science, Center for Computation and Technology, Louisiana State University, Baton Rouge, LA; 3) Dept. of Behavioral Neuroscience, Oregon Health & Science University, Beaverton, OR; 4) Molecular Biology Center, Babes-Bolyai University, Cluj-Napoca, Cluj, Romania; 5) Institute for Systems Biology, Seattle, WA.
We have recently discovered a novel retrotransposon called LAVA in the gibbon lineage. LAVA represents a composite element closely related to the hominoid-specific SVA element. Both share the VA part (VNTR (variable number of tandem repeat region) and Alu-like sequence). However, instead of the SVA-specific SINE-R region, LAVA elements contain unique sequence sections as well as ancient Alu and L1 sequence. In our investigations of this element, we first analyzed LAVA insertions to confirm that they harbor hallmarks of non-LTR (long terminal repeat) retrotransposons. We conclude that LAVAs most likely rely on the enzymatic machinery of L1 (long interspersed element 1) for their propagation. Next, we investigated the tempo and mode of LAVA expansion in the gibbon lineage leading to Nomascus leucogenys (NLE). Computational reconstruction followed by manual curation of the LAVA subfamily structure revealed 23 distinct full-length subfamilies in the NLE draft genome assembly [Nleu 1.1]. We identified >2500 LAVA elements since the origin of gibbons in the NLE genome. Based on the LAVA subfamily structure, activity of some subfamilies peaked prior to the radiation of gibbons, while other subfamilies show evidence for continued propagation until (at least) very recently. To better understand the expansion dynamics of LAVA elements and to investigate the still unresolved gibbon phylogeny, we selected 200 loci for our phylogenetic PCR analyses. We selected LAVA elements based on their divergence from their respective consensus sequence. PCR analyses were performed on a primate DNA panel containing 13 gibbon species from all four genera, with four great apes and green monkey as outgroups. Our wet-bench results confirmed our computational findings that several of the oldest appearing subfamilies ceased activity prior to the radiation of gibbons; while some subfamilies provide evidence for very recent retrotransposition. Even though mobile elements represent a marker system with advantages such as identity by descent and near-absence of homoplasy, we were not able to determine the radiation order of the four gibbon genera due to extended incomplete lineage sorting. This indicates rapid speciation and/or historically recurring hybridization events. Furthermore, our results show an expansion of LAVA elements in gibbons, provide evidence for ongoing LAVA propagation, and highlights that primate lineages evolve uniquely.
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