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Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia Pulex

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Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia Pulex GBE Insertion Polymorphisms of Mobile Genetic Elements in Sexual and Asexual Populations of Daphnia pulex Xiaoqian Jiang1,*, Haixu Tang2,*, Zhiqiang Ye1, and Michael Lynch1 1Department of Biology, Indiana University, Bloomington, Indiana 2School of Informatics and Computing, Indiana University, Bloomington, Indiana *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: December 29, 2016 Abstract Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evo- lutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D. pulex isolates. However, in general, sexual clones contain fewer fixed TE insertions but more total insertion polymorphisms than asexual clones, supporting the hypothesis that sexual repro- duction facilitates the spread and elimination of TEs. We identified nine asexual-specific fixed TE insertions, eight long terminal repeat retrotransposons, and one DNA transposon. By comparison, no sexual-specific fixed TE insertions were observed in our analysis. Furthermore, except one TE insertion located on a contig from chromosome 7, the other eight asexual-specific insertion sites are located on contigs from chromosome 9 that is known to be associated with obligate asexuality in D. pulex. We found that all nine asexual-specific fixed TE insertions can also be detected in some Daphnia pulicaria isolates, indicating that a substantial number of TE insertions in asexual D. pulex have been directly inherited from D. pulicaria during the origin of obligate asexuals. Key words: transposable elements, TE insertions, Daphnia pulex, Daphnia pulicaria, asexuality. Introduction provide an adaptive advantage (Gonza´lez and Petrov 2009; Transposable elements (TEs) are mobile DNA elements that Bie´mont 2010; de Souza et al. 2013), a premium example can replicate from one location to another within a genome being the Het-A elements that comprise the telomeric DNA or between genomes, and are believed to be a major factor in of Drosophila (Zemojtel et al. 2009). large-scale genome reorganization. TEs constitute a large por- TEs are generally divided into two major classes based on tion of many eukaryotic genomes, although the proportions their transposition mechanisms: retrotransposons or class I el- of TEs vary among species, for example, TEs constitute ~4% ements, spreading in a “copy-and-paste” manner, copying of the Drosophila genome, ~6.5% of the Caenorhabditis through an RNA template prior to inserting into the elegans genome, ~45% of the human genome, ~60% of genome, and DNA transposons or class II elements, spreading the soybean genome, and up to ~80% of the maize through a “cut-and-paste” manner, enabling movement and genome (SanMiguel et al. 1996; Duret et al. 2000; Lander integration into a new location in the genome without copy- et al. 2001; Kaminker et al. 2002). Mobilization of TEs is ca- ing the parent allele (Wicker et al. 2007). Retrotransposons pable of introducing gene inactivation or illegitimate recom- can be further subdivided into two subclasses: long terminal bination, and the insertion of TEs typically reduces the viability repeat (LTR) retrotransposons, and non-LTR retrotransposons. of the host genome (Hurst and Werren 2001). Therefore, LTR retrotransposons are composed of a coding region with a active TEs are a significant source of deleterious mutations. pair of LTRs, containing opening reading frames (ORFs) for For example, TEs cause ~10 and ~50% of deleterious muta- Gag and Pol coding regions. The Pol ORF includes four key tions in mammals and Drosophila, respectively (Finnegan protein domains required for the replication and transposition 1992; Kazazian 1998). In a few cases, TE insertions may of TEs into host genome: aspartic protease (AP), RNase H (RH), ß The Author(s) 2017. 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/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] 362 Genome Biol. Evol. 9(2):362–374. doi:10.1093/gbe/evw302 Advance Access publication February 1, 2017 Insertion Polymorphisms of Mobile Genetic Elements GBE reverse transcriptase (RT), and integrase (INT), among which et al. 1996). Although the ancient bdelloid rotifers are not RT is the most conserved protein domain. Intact non-LTR ret- strictly asexual due to the presence of some gene exchanges rotransposons contain a protein region encoding an RT between individuals (Debortoli et al. 2016), they have fewer domain, which has been used as the main signal to identify DNA transposons and lack several classes of retrotransposons and classify these elements (RhoandTang2009). Most au- compared to their sexual relatives (Arkhipova and Meselson tonomous DNA transposons are composed of a transposase 2000, 2005; Flot et al. 2013). Moreover, the selfing plant coding region flanked by terminal inverted repeats (TIRs), Arabidopsis thaliana experienced a recent reduction in TE except for the newly identified clade of helitrons (Jiang abundance compared to its outcrossing relative Arabidopsis 2013a). Retrotransposons outnumber DNA transposons in lyrata (De La Chaux et al. 2012). Finally, a recent study com- most species partially due to their intrinsically higher prolifer- pared the whole-genome TE loads of five asexual arthropod ative potential. DNA transposons and a small subset of LTR lineages and their sexual relatives, including crustaceans, in- retrotransposons are capable of horizontal transmission sects, and mites, suggesting that there is no evidence of excess (Arkhipova and Meselson 2005). In contrast, non-LTR retro- TE accumulation in genomes of asexuals as compared to transposons can only be transmitted vertically, and phyloge- sexual lineages (Bast et al. 2016). netic analysis of RT and RH protein domains indicates that The Daphnia pulex species complex, a group of freshwater non-LTR retrotransposons are much more ancient than LTR microcrustaceans, where obligate parthenogenetic (asexual) retrotransposons (Eickbush and Malik 2002; Arkhipova and lineages and cyclically parthenogenetic (sexual) lineages coex- Meselson 2005). The evolutionary factors that affect TE abun- ist, is one of the best-documented systems of contagious asex- dances have been studied extensively (Wright et al. 2003; Le uality in animals (Lynch et al. 2008). Sexual D. pulex lineages Rouzic and Capy 2005; Le Rouzic et al. 2007), including the typically reproduce offspring by females directly developing intrinsic mechanisms of mobilization, population structure, embryos through parthenogenesis; however, they still may and the interaction between TEs and their host, among produce males capable of meiosis in unfavorable conditions. which the reproductive manner of the host is thought to In contrast, asexual D. pulex lineages lose the ability to engage play an important role in determining the fate of TEs in sexual reproduction and reproduce strictly by obligate par- (Charlesworth 1994; Wright and Finnegan 2001; Lynch thenogenesis in any environment. Interestingly, the lack of 2007). sexual reproduction in asexual lineages is limited to females, Although rare, asexual lineages arise from sexual ones in- and males produced by some asexual females are still capable dependently in some species. Whether loss of sex will cause an of haploid gamete production, providing a way for transfer- increase or decrease in TE abundance remains undetermined. ring asexuality elements to sexual populations via backcrossing On the one hand, theoretical models predict that meiosis and (Innes and Hebert 1988; Xu et al. 2015). Previous studies recombination in sexual lineages facilitate the spread of TEs to showed that the estimated age of obligately asexual new individuals in a population even if TEs are (mildly) delete- D. pulex ranges from as young as ~1,000 years (Lynch et al. rious (Hickey 1982). In contrast, in asexual lineages lacking 2008) to as old as ~172,000 years (Paland et al. 2005). Recent recombination, within-lineage transmission of genes in asex- genome-wide association studies also suggested that the ual isolates is expected to limit the spread of TEs (Charlesworth spread of asexuality in D. pulex is perhaps as recent as and Langley 1986). On the other hand, in the absence of sex, 1,250 years, although the origin of the meiosis-suppressing TEs may become less virulent because the interests of TEs are elements could be substantially older (Tucker et al. 2013). The consistent with the interests of their host. Regulatory mecha- authors observed that all asexual clones share the same hap- nisms in asexuals may also play more important roles in re- lotypes in several genomic regions, including almost the en- ducing the rate of transposition than in sexuals to defend tirety of chromosomes 8 and 9, both of which are thought to deleterious
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