Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing

GBE Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing Todd A. Castoe1, Kathryn T. Hall1, Marcel L. Guibotsy Mboulas2, Wanjun Gu ,1, A.P. Jason de Koning1, Samuel E. Fox3, Alexander W. Poole1, Vijetha Vemulapalli1, Juan M. Daza4, Todd Mockler4, Eric N. Smith2, Cédric Feschotte2, and David D. Pollock*,1 1 Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine 2 Department of Biology, University of Texas at Arlington 3 Department of Botany and Plant Pathology, Oregon State University 4 Instituto de Biologia, Universidad de Antioquia, Medellin, Colombia Present address: Key Laboratory of Child Development and Learning Science, Southeast University, Ministry of Education, Nanjing, People’s Republic of China *Corresponding author: E-mail: . Accepted: 27 April 2011 Abstract We conducted a comprehensive assessment of genomic repeat content in two snake genomes, the venomous copperhead (Agkistrodon contortrix) and the Burmese python (Python molurus bivittatus). These two genomes are both relatively small (;1.4 Gb) but have surprisingly extensive differences in the abundance and expansion histories of their repeat elements. In the python, the readily identifiable repeat element content is low (21%), similar to bird genomes, whereas that of the copperhead is higher (45%), similar to mammalian genomes. The copperhead’s greater repeat content arises from the recent expansion of many different microsatellites and transposable element (TE) families, and the copperhead had 23-fold greater levels of TE-related transcripts than the python. This suggests the possibility that greater TE activity in the copperhead is ongoing. Expansion of CR1 LINEs in the copperhead genome has resulted in TE-mediated microsatellite expansion (‘‘microsatellite seeding’’) at a scale several orders of magnitude greater than previously observed in vertebrates. Snakes also appear to be prone to horizontal transfer of TEs, particularly in the copperhead lineage. The reason that the copperhead has such a small genome in the face of so much recent expansion of repeat elements remains an open question, although selective pressure related to extreme metabolic performance is an obvious candidate. TE activity can affect gene regulation as well as rates of recombination and gene duplication, and it is therefore possible that TE activity played a role in the evolution of major adaptations in snakes; some evidence suggests this may include the evolution of venom repertoires. Key words: Burmese python, copperhead, microsatellite seeding, non-avian reptile comparative genomics, transposable elements. Introduction Among vertebrates, the snake lineage represents an impressively speciose (;3100 sp.) and phenotypically diverse radiation, and as a result, snakes have become increasingly important model systems for diverse research areas. Snakes provide a unique model system for studying extreme physiological remodeling and metabolic cycling (Secor and Diamond 1995, 1998) and in venom-related research (Fry et al. 2006; Ikeda et al. 2010). Snakes have also become important models for developmental biology, evolutionary ecology, and molecular evolution and adaptation (Cohn and Tickle 1999; Fry et al. 2006; Castoe et al. 2008, 2009b; Vonk et al. 2008). Despite the importance of snakes as models for basic and biomedical research, there is little known about the genomes of snakes and about reptile genomes in general (Shedlock et al. 2007; Janes et al. 2010). Our aim here was thus to obtain comprehensive sequence-based comparative insight into snake genomic diversity, particularly the diversity and structure of the ª The Author(s) 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/ 2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Genome Biol. Evol. 3:641–653. doi:10.1093/gbe/evr043 Advance Access publication May 13, 2011 641 GBE Castoe et al. repetitive element landscape. Such insight is important because repetitive elements comprise major portions of vertebrate genomes and exert major influences over genome evolution. Among repetitive sequences, transposable elements (TEs) in particular have had a tremendous impact on the structural and functional evolution of genes and genomes. Numerous studies have documented how TE activity and ectopic recombination between TE copies promote small- and large-scale variation in the structure of genomes; such rearrangements provide a substrate for the emergence of new functional sequences, both coding and noncoding, including the birth of new protein-coding genes and the rewiring of regulatory networks (Feschotte 2008; Cordaux and Batzer 2009; Herpin et al. 2010). Despite a recent comprehensive review summarizing current knowledge about reptilian TEs (Kordis 2009), our understanding of vertebrate TE diversity and evolutionary dynamics remains largely dominated by perspectives from mammalian and to a lesser extent avian genomes. The speciose nature and evolutionary age of the snake radiation make it an excellent amniote lineage for comparisons to mammals. Snakes and mammals share a common ancestor ;310 Ma and snakes diverged from other squamate reptiles about ;170 Ma (Castoe et al. 2009a), which slightly predates the estimated split of eutherian (placental) and metatherian (marsupial) mammals. In this study, we chose to focus on two fairly distantly related snake species, the Burmese python (Python molurus bivittatus) and the copperhead (Agkistrodon contortrix)—these two lineages share a common ancestor at about the same time as do all eutherian mammals, around 100 Ma (Castoe et al. 2009a). In comparison to mammalian genomes, snake genomes are generally small (Gregory et al. 2007), ranging from 1.3 to 3.8 Gbp and averaging 2.1 Gbp, and the two snakes chosen both have similarly sized genomes, on the small side of this range (;1.4 Gbp). Evidence from early DNA reassociation studies suggests that there may be extensive variation in the genomic repeat landscapes among snake species, particularly between pythons and colubroid species such as the copperhead (Olmo et al. 1981; Olmo 1984). These two snakes also represent important lineages for research. The Burmese python (P. molurus bivittatus) is an important model for physiological and metabolic adaptation and the copperhead (A. contortrix) is a model for metabolic adaptation and a viperid model for studies related to venom. Although distantly related, these two lineages (pythons and viperids) have convergently evolved extremely dynamic metabolisms to facilitate the infrequent consumption of large prey (Secor and Diamond 2000). To gain insight i (...truncated)