Transposable Elements (TEs) in Chromosomal DNA – Irina Arkhipova
Research in the Arkhipova lab is focused on transposable elements (TEs) in chromosomal DNA. As part of the A. vaga genome sequencing consortium, we have analyzed repetitive DNA content in the genome of the bdelloid rotifer, Adineta vaga (pictured), a microscopic freshwater invertebrate that reproduces asexually. This is the first representative of the Phylum Rotifera for which a complete genome sequence has been determined. We found that TEs and TE-related sequences occupy an unusually small proportion of the A. vaga genome assembly (ca. 3% of genomic DNA). This is in contrast with other aquatic metazoans such as Hydra or Nematostella, where TEs make up 57% and 26% of the genome, respectively. Another surprising feature is the high diversity of TE families and the extremely low number of copies for each family, which indicates that the incoming TEs do not proliferate efficiently in A. vaga. Out of 254 families, the overwhelming majority (208) is represented by only one or two full-length copies (for 24 families, no full-length copies could be identified), and for each full-length copy there is, on average, only about ten times as many TE fragments. In many cases, fragmented copies were formed through microhomology-mediated deletions. Excision of LTR (long terminal repeat) retrotransposons also occurs through LTR-LTR recombination, leaving behind numerous solo LTRs. The prevalence of intact copies over decayed ones, in particular of LTR retrotransposons with identical or nearly-identical LTRs, suggests that most low-copy-number families represent recent arrivals. Efficient suppression of incoming TEs in A. vaga is likely to be associated with expansion and diversification of the RNA-mediated silencing machinery. Its major components, such as the Argonaute/Piwi proteins and RdRPs (RNA-directed RNA polymerases), are represented by 23 and 15 different proteins, respectively. Finally, a conservative estimate of foreign gene content indicates that at least 8% of A. vaga genes were acquired horizontally. On balance, bdelloid genomes, despite being relatively open to assimilation of foreign DNA, are apparently able to control proliferation of incoming TEs through a multi-layered system of genome defense, including RNA-mediated silencing, mutation, and deletion via homologous recombination and non-homologous end-joining.