Characterization and Evolution of Germ1, an Element that Undergoes Diminution in Lampreys (Cyclostomata: Petromyzontidae)

  • Rex Meade StrangeEmail author
  • Landon L. Moore
Original Article


The sea lamprey (Petromyzon marinus) undergoes substantial genomic alterations during embryogenesis in which specific sequences are deleted from the genome of somatic cells yet retained in cells of the germ line. One element that undergoes diminution in P. marinus is Germ1, which consists of a somatically rare (SR) region and a fragment of 28S rDNA. Although the SR-region has been used as a marker for genomic alterations in lampreys, the evolutionary significance of its diminution is unknown. We examined the Germ1 element in five additional species of lamprey to better understand its evolutionary significance. Each representative species contained sequences similar enough to the Germ1 element of P. marinus to be detected via PCR and Southern hybridizations, although the SR-regions of Lampetra aepyptera and Lethenteron appendix are quite divergent from the homologous sequences of Petromyzon and three species of Ichthyomyzon. Lamprey Germ1 sequences have a number of features characteristic of the R2 retrotransposon, a mobile element that specifically targets 28S rDNA. Phylogenetic analyses of the SR-regions revealed patterns generally consistent with relationships among the species included in our study, although the 28S-fragments of each species/genus were most closely related to its own functional rDNA, suggesting that the two components of Germ1 were assembled independently in each lineage. Southern hybridizations showed evidence of genomic alterations involving Germ1 in each species. Our results suggest that Germ1 is a R2 retroelement that occurs in the genome of P. marinus and other petromyzontid lampreys, and that its diminution is incidental to the reduction in rDNA copies during embryogenesis.


Genome evolution Genome rearrangement Retroelement rDNA 



We would like to thank our friends and colleagues who either contributed specimens (T. Buchinger and S. Miehls), assisted with collections (G. Adams), or provided locality information from their personal collection notes (D. Eisenhour, B. Fisher, and G. Weddle). We also thank K. Delany for many insightful discussions. This work was partially funded by an internal Grant to RMS and resources supplied by the Department of Biology, University of Southern Indiana.

Compliance with Ethical Standards

Conflict of interest

The authors declare they have no conflict of interest to disclose.


  1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Control 19:716–723CrossRefGoogle Scholar
  2. Biederman MK, Nelson MM, Asalone KC, Pederson AL, Saldanha CJ, Bracht JR (2018) Discovery of the first germline-restricted gene by subtractive transcriptomic analysis in the zebra finch, Taeniopygia guttata. Curr Biol 28:1620–1627CrossRefGoogle Scholar
  3. Bryant SA, Herdy JR, Amemiya CT, Smith JJ (2016) Characterization of somatically-eliminated gene during development of the sea lamprey (Petromyzon marinus). Mol Biol Evol 33:2337–2344CrossRefGoogle Scholar
  4. Burke WD, Malik HS, Jones JP, Eickbush TH (1999) The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Mol Biol Evol 16:502–511CrossRefGoogle Scholar
  5. Caputo V, Giovannotti M, Cerioni PN, Splendiani A, Tagliavini J, Olmo E (2011) Chromosomal study of a lamprey (Lampetra zanandreai Vladykov 1955) (Petromyzontida: Petromyzontiformes): conventional and FISH analysis. Chromosome Res 19:481–491CrossRefGoogle Scholar
  6. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1666CrossRefGoogle Scholar
  7. Covelo-Soto L, Moran P, Passantes JJ, Perez-Garcia C (2014) Cytogenetic evidences of genome rearrangement and differential epigenetic chromatin modification in the sea lamprey (Petromyzon marinus). Genetica 142:545–554CrossRefGoogle Scholar
  8. Eickbush DG, Eickbush TH (1995) Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Genetics 139:671–684Google Scholar
  9. Eickbush TH, Eickbush DG (2007) Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175:477–485CrossRefGoogle Scholar
  10. Eickbush TH, Eickbush DG (2015) Integration, regulation, and long-term stability of R2 retrotransposons. Microbiol Spectrum 3(2):2014. Google Scholar
  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  12. Goday C, Estaban MR (2001) Chromosome elimination in sciarid flies. BioEssays 23:242–250CrossRefGoogle Scholar
  13. Goto Y, Kubota S, Kohno S (1998) Highly repetitive DNA sequences that are restricted to the germ line in the hagfish Eptatretus cirrhatus: a mosaic of eliminated elements. Chromosoma 107:17–32CrossRefGoogle Scholar
  14. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321CrossRefGoogle Scholar
  15. Hall TA (1999) BioEdit: a user-friendly biological sequence editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  16. Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453CrossRefGoogle Scholar
  17. Hufton AL, Groth D, Vingron M, Lehrach H, Poustka AJ, Panopoulou G (2008) Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. Genome Res 18:1582–1591CrossRefGoogle Scholar
  18. Ishijima J, Uno Y, Nunome M, Nishida C, Kuraku S, Matsuda Y (2017) Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae). DNA Res 24:93–101Google Scholar
  19. Jakubczak JL, Zenni MK, Woodruff RC, Eickbush TH (1992) Turnover of R1 (Type I) and R2 (Type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Genetics 131:129–142Google Scholar
  20. Jamburuthugoda VK, Eickbush TH (2011) The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error prone as that encoded by HIV-1. J Mol Biol 407:661–672CrossRefGoogle Scholar
  21. Kocher TD, Thomas W, Meyer A, Edwards SV, Pallablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. PNAS USA 86:6196–6200CrossRefGoogle Scholar
  22. Kojima KK, Fujiwara H (2005) Long-term inheritance of the 28S rDNA specific retrotransposon R2. Mol Biol Evol 22:2157–2165CrossRefGoogle Scholar
  23. Kojima FN, Kojima KK, Kobayakawa S, Higaside N, Hamanaka C, Nitta A, Koeda I, Yamaguchi T, Shichiri M, Kohno S, Kubota S (2010) Whole chromosome elimination and chromosome terminus elimination both contribute to somatic differentiation in Taiwanese hagfish Paramyxine sheni. Chromosome Res 18:383–400CrossRefGoogle Scholar
  24. Kojima KK, Seto Y, Fujiwara H (2016) The Wide distribution and change of target specificity of R2 non-LTR retrotransposons in animals. PLoS ONE 11(9):e0163496. CrossRefGoogle Scholar
  25. Kubota S, Takano J, Tsuneishi R, Kobayakawa S, Fujikawa N, Nabeyama M, Kohno S (2001) Highly repetitive DNA families restricted to germ cells in a Japanese hagfish (Eptatretus burger): a hierarchical and mosaic structure in eliminated chromosomes. Genetica 111:319–328CrossRefGoogle Scholar
  26. Kuraku S, Meyer A, Kuratani S (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol 26:47–59CrossRefGoogle Scholar
  27. Lang NJ, Roe KJ, Renaud CB, Gill HS, Potter IC, Freyhof J, Naseka AM, Cochran P, Perez HE, Habit EM, Kahajda BR, Neely DA, Reshetnikov YS, Salnikov VB, Stoumboudi MT, Mayden RL (2009) Novel relationships among lampreys (Petromyzontiformes) revealed by a taxonomically comprehensive molecular data set. Am Fish Soc Symp 72:41–55Google Scholar
  28. Lefort V, Longueville JE, Gascuel O (2017) SMS: smart model selection in PhyML. Mol Biol Evol 34:2422–2424CrossRefGoogle Scholar
  29. Lyckegaard EMS, Clark AG (1991) Evolution of ribosomal RNA gene copy number on the sex chromosomes of Drosophila melanogaster. Mol Biol Evol 8:458–474Google Scholar
  30. Mehta TK, Ravi V, Yamasaki S, Lee AP, Lian MM, Tay BH, Tohari S, Yanai S, Tay A, Brenner S, Venkatesh B (2013) Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum). Proc Natl Acad Sci USA 110:16044–16049CrossRefGoogle Scholar
  31. Mingazzini V, Luchetti A, Mantovani B (2011) R2 dynamics in Triops cancriformes (Bosc, 1801) (Crustacea, Branchiopoda, Nostraca): turnover rate and 28S concerted evolution. Heredity 106:567–575CrossRefGoogle Scholar
  32. Muller F, Tobler H (2000) Chromatin diminution in the parasitic nematodes Ascaris suum and Parascaris univalens. Int J Parasitol 30:391–399CrossRefGoogle Scholar
  33. Osorio J, Retaux S (2008) The lamprey in evolutionary studies. Dev Genes Evol 218:221–235CrossRefGoogle Scholar
  34. Potter IC, Gill HS, Renaud CB, Hanoucher D (2015) The taxonomy, phylogeny, distribution, of lampreys. In: Docker MF (ed) Lampreys: biology, conservation and control. Springer, New York, pp 35–73CrossRefGoogle Scholar
  35. Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH (2004) Secondary structure models of the 3'unstranslated regions of diverse R2 RNAs. RNA 10:978–987CrossRefGoogle Scholar
  36. Schlotterer C, Tautz D (1994) Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Curr Biol 4:777–783CrossRefGoogle Scholar
  37. Schmidt TR, Gold JR (1993) Complete sequence of the mitochondrial cytochrome bgene in the Cherryfin Shiner, Lythrurus roseipinnis (Teleostei: Cyprinidae). Copeia 1993:880–883CrossRefGoogle Scholar
  38. Smith JJ, Antonacci F, Eichler EE, Amemiya CT (2009) Programmed loss of millions of base pairs from a vertebrate genome. Proc Natl Acad Sci USA 106:11212–11217CrossRefGoogle Scholar
  39. Smith JJ, Baker C, Eichler EE, Amemiya CT (2012) Genetic consequences of programmed genome rearrangement. Curr Biol 22:1524–1529CrossRefGoogle Scholar
  40. Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT (2018) The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet 50:270–277CrossRefGoogle Scholar
  41. Standiford DM (1988) The development of a large nucleolus during oogenesis in Acanthocyclops vernalis (Crustacea, Copepoda) and its possible relationship to chromatin diminution. Biol Cell 63:35–40CrossRefGoogle Scholar
  42. Strange RM, Delaney KJ (2018) First report of a mitochondrial pseudogene in agnathan vertebrates (Cyclostomata: petromyzontidae). J Mol Evol 86:187–189CrossRefGoogle Scholar
  43. Strange RM, Noland A (2018) Genetic identity of the least brook lamprey (Lampetra aepyptera) in Indiana. Proc Indiana Acad Sci 127:89–95Google Scholar
  44. Sun C, Wyngaard G, Walton DB, Wichman HA (2014) Mueller RL (2014) Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development. BMC Genomics 15:186CrossRefGoogle Scholar
  45. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods). version 4.0b10. Sinauer Associates, SunderlandGoogle Scholar
  46. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar
  47. Timoshevskiy VA, Lampman RT, Hess JE, Porter LL, Smith JJ (2017) Deep ancestry of programmed genome rearrangement in lampreys. Dev Biol 429:31–34CrossRefGoogle Scholar
  48. Wang J, Davis RE (2014) Programmed DNA elimination in multicellular organisms. Curr Opin Genet Dev 2014:26–34CrossRefGoogle Scholar
  49. Yang J, Malik HS, Eickbush TH (1999) Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc Natl Acad Sci USA 96:7847–7852CrossRefGoogle Scholar
  50. Zagoskin MV, Marshak TL, Mukha DV, Grishanin AK (2010) Chromatin diminution process regulates rRNA gene copy number in freshwater copepods. Acta Nat 2:52–57CrossRefGoogle Scholar
  51. Zardoya R, Meyer A (1996) Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc Natl Acad Sci USA 93:5449–5454CrossRefGoogle Scholar
  52. Zhou J, Eickbush MT, Eickbush TH (2013) A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci. PLoS Genet 9(1):e1003179. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiologyUniversity of Southern IndianaEvansvilleUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of OklahomaNormanUSA

Personalised recommendations