Linking micro-and macro-evolution at the cell type level: A view from the lophotrochozoan Platynereis dumerilii

Briefings in Functional Genomics

Volumn 12, Issue 5, 2013, Pages 430-439

  Simakov, Oleg ^a   Larsson, Tomas A ^a,b   Arendt, Detlev ^c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UPPSALA UNIVERSITY   (Sweden)

^c UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Cell type; Comparative genomics; Lophotrochozoan; Macro evolution; Micro evolution; Platynereis

Indexed keywords

ARTICLE; BREEDING; CELL TYPE; CHROMOSOME; DNA POLYMORPHISM; ECOLOGICAL GENETICS; EUKARYOTE EVOLUTION; EXPRESSED SEQUENCE TAG; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENOTYPE; GEOGRAPHIC DISTRIBUTION; LOPHOTROCHOZOA; MODEL; NONHUMAN; PHENOTYPE; PHYLOGENY; PLATYNEREIS DUMERILII; PROTIST LIFE CYCLE STAGE; SPECIES DIVERSITY;

CELL TYPE; COMPARATIVE GENOMICS; LOPHOTROCHOZOAN; MACRO-EVOLUTION; MICRO-EVOLUTION; PLATYNEREIS;

ANIMALS; BIOLOGICAL EVOLUTION; GENETIC VARIATION; MODELS, BIOLOGICAL; POLYCHAETA;

EID: 84884507915     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/els049     Document Type: Article

References (80)

1. Stearn CW, Carroll RL. Paleontology:TheRecord of Life. New York: John Wiley, 1989.
2. Struck TH, Paul C, Hill N, et al. Phylogenomic analyses unravel annelid evolution. Nature 2011;471:95-8.
3. Gould SJ. Wonderful Life:The Burgess Shale and the Nature of History. New York: W.W. Norton, 1989.
4. Peterson KJ, Cotton JA, Gehling JG, et al. The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records. PhilosTransRSocLond BBiol Sci 2008;363:1435-43.
5. Valentine JW. Late precambrian bilaterians: grades and clades. Proc Natl Acad SciUSA 1994;91:6751-7.
6. Halanych KM, Bacheller JD, Aguinaldo AM, et al. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science 1995;267:1641-3.
7. Aguinaldo AM, Turbeville JM, Linford LS, et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997;387:489-93.
8. Fischer AH, Henrich T, Arendt D. The normal development of Platynereis dumerilii (Nereididae, Annelida). Front Zool 2010;7:31.
9. Rouse GW, Pleijel F. Polychaetes. Oxford; New York: Oxford University Press, 2001.
10. Foster N. FRESHWATER POLYCHAETES (ANNELIDA) OF NORTH AMERICA. Water Pollution Control Research Series. U.S. Environemntal Protection agency, 1972.
11. Giribet G. Assembling the lophotrochozoan (=spiralian) tree of life. Philos Trans R Soc Lond B Biol Sci 2008;363: 1513-22.
12. Berriman M, Haas BJ, LoVerde PT, et al. The genome of the blood fluke Schistosoma mansoni. Nature 2009;460:352-8.
13. Robb SM, Ross E, Sanchez Alvarado A. SmedGD: the Schmidtea mediterranea genome database. Nucleic Acids Res 2008;36:D599-606.
14. Takeuchi T, Kawashima T, Koyanagi R, etal. Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology. DNA Res 2012;19:117-30.
15. Zhang G, Fang X, Guo X, et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 2012;490:49-54.
16. Gregory TR. Animal Genome Size Database. http://www.genomesize.com, Last accessed October 2nd, 2012.
17. Gregory TR, Hebert PD, Kolasa J. Evolutionary implications of the relationship between genome size and body size in flatworms and copepods. Heredity (Edinb) 2000; 84(Pt 2):201-8.
18. Conner WG, Hinegardner R, Bachmann K. Nuclear DNA amounts in polychaete annelids. Cell Mol Life Sci 1972;28: 1502-4.
19. Hui JH, McDougall C, Monteiro AS, etal. Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization. Mol Biol Evol 2012;29:157-65.
20. Hui JH, Raible F, Korchagina N, et al. Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes. BMC Biol 2009;7:43.
21. Frobius AC, Matus DQ, Seaver EC. Genomic organization and expression demonstrate spatial and temporal Hox gene colinearity in the lophotrochozoan Capitella sp. I. PLoSOne 2008;3:e4004.
22. Cho SJ, Valles Y, Giani VC, Jr, et al. Evolutionary dynamics of the wnt gene family: a lophotrochozoan perspective. Mol Biol Evol 2010;27:1645-58.
23. Shimeld SM, Boyle MJ, Brunet T, etal. Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster. Dev Biol 2010;340:234-48.
24. Putnam NH, Srivastava M, Hellsten U, et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 2007;317:86-94.
25. Rokas A, Holland PW. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 2000;15:454-9.
26. Raible F, Tessmar-Raible K, Osoegawa K, et al. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science 2005;310:1325-6.
27. Christodoulou F, Raible F, Tomer R, et al. Ancient animal microRNAs and the evolution of tissue identity. Nature 2010;463:1084-8.
28. Fischer A, Dorresteijn A. The polychaete Platynereis dumerilii (Annelida): a laboratory animal with spiralian cleavage, lifelong segment proliferation and a mixed benthic/pelagic life cycle. Bioessays 2004;26:314-25.
29. Denes AS, Jekely G, Steinmetz PR, et al. Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell 2007;129: 277-88.
30. Arendt D, Technau U, Wittbrodt J. Evolution of the bilaterian larval foregut. Nature 2001;409:81-5.
31. Steinmetz PR, Kostyuchenko RP, Fischer A, et al. The segmental pattern of otx, gbx, and Hox genes in the annelid Platynereis dumerilii. Evol Dev 2011;13:72-9.
32. Tomer R, Denes AS, Tessmar-Raible K, et al. Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell 2010;142:800-9.
33. Tessmar-Raible K, Raible F, Christodoulou F, et al. Conserved sensory-neurosecretory cell types in annelid and fish forebrain: insights into hypothalamus evolution. Cell 2007;129:1389-1400.
34. Arendt D, Tessmar-Raible K, Snyman H, et al. Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science 2004;306:869-71.
35. Dray N, Tessmar-Raible K, Le Gouar M, et al. Hedgehog signaling regulates segment formation in the annelid Platynereis. Science 2010;329:339-42.
36. Jekely G, Colombelli J, Hausen H, et al. Mechanism of phototaxis in marine zooplankton. Nature 2008;456:395-9.
37. Conzelmann M, Offenburger SL, Asadulina A, et al. Neuropeptides regulate swimming depth of Platynereis larvae. Proc Natl Acad Sci USA 2011;108:E1174-83.
38. Jha AN, Hutchinson TH, Mackay JM, et al. The chromosomes of Platynereis dumerilii (Polychaeta: Nereidae).JMarine Biol AssocUK 1995;75:551-62.
39. Grassle JP, Gelfman CE, Mills SW. Karyotypes of Capitella sibling species, and of several species in the related genera Capitellides and Capitomastus (Polychaeta). Bull Biol Soc Wash 1987;7:77-88.
40. Cichocka J, Bielecki A. Biological diversity of leeches (Clitellata: Hirudinida) based on characteristics of the karyotype. Wiad Parazytol 2008;54:309-14.
41. Wada K. Number and gross morphology of chromosomes in the pearl oyster, Pinctada fucata (GOULD): collected from two regions of Japan. Venus 1976;35:9-14.
42. Thiriot-Quievreux C, Pogson GH, Zouros E. Genetics of growth rate variation in bivalves: aneuploidy and heterozygosity effects in a Crassostrea gigas family. Genome 1992;35:39-45.
43. Baguna J, Carranza S, Pala M, et al. From morphology and karyology to molecules. New methods for taxonomical identification of asexual populations of freshwater planarians. A tribute to Professor Mario Benazzi. Italian J Zool 1999;66:207-14.
44. Short RB, Grossman AI. Conventional giemsa and C-banded karyotypes of Schistosoma mansoni and S. rodhaini. J Parasitol 1981;67:661-71.
45. Ackermann C, Dorresteijn A, Fischer A. Clonal domains in postlarval Platynereis dumerilii (Annelida: Polychaeta). JMorphol 2005;266:258-80.
46. Dorresteijn AWC. Quantitative analysis of cellular differentiation during early embryogenesis of Platynereis dumerilii. Roux Arch Dev Biol 1990;199:14-30.
47. Meyer NP, Boyle MJ, Martindale MQ, etal. A comprehensive fate map by intracellular injection of identified blastomeres in the marine polychaete Capitella teleta. Evodevo 2010;1:8.
48. Zhang SO, Weisblat DA. Applications of mRNA injections for analyzing cell lineage and asymmetric cell divisions during segmentation in the leech Helobdella robusta. Development 2005;132:2103-13.
49. Gline SE, Kuo DH, Stolfi A, et al. High resolution cell lineage tracing reveals developmental variability in leech. DevDyn 2009;238:3139-51.
50. Song MH, Huang FZ, Chang GY, et al. Expression and function of an even-skipped homolog in the leech Helobdella robusta. Development 2002;129:3681-92.
51. Huvet A, Fleury E, Corporeau C, et al. In vivo RNA interference of a gonad-specific transforming growth factor-beta in the Pacific oyster Crassostrea gigas. Mar Biotechnol (NY) 2012;14:402-10.
52. Sanchez Alvarado A, Newmark PA. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. ProcNatl Acad SciUSA 1999;96:5049-54.
53. Stefanic S, Dvorak J, Horn M, et al. RNA interference in Schistosoma mansoni schistosomula: selectivity, sensitivity and operation for larger-scale screening. PLoS Negl Trop Dis 2010;4:e850.
54. Kines KJ, Morales ME, Mann VH, et al. Integration of reporter transgenes into Schistosoma mansoni chromosomes mediated by pseudotyped murine leukemia virus. FASEB J 2008;22:2936-48.
55. Jekely G, Arendt D. Cellular resolution expression profiling using confocal detection of NBT/BCIP precipitate by reflection microscopy. Biotechniques 2007;42:751-5.
56. Tomer R, Khairy K, Amat F, et al. Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods 2012;9: 755-63.
57. Soldi R, Ramella L, Gambi MC, et al. Genome size in polychaetes: relationship with body length and life habit. In: Dauvin J-C, et al (ed). Actes de la 4e'meConférence internationale des Polyche'tes, Angers, France. Vol. 162. Mémoires du Muséum national d'histoire naturelle. Série A, Zoologie, 1994, 129-35.
58. Li R, Fan W, Tian G, et al. The sequence and de novo assembly of the giant panda genome. Nature 2010;463: 311-7.
59. UNESCO IOCIo. The Ocean Biogeographic Information System. http://www.iobis.org.
60. Cram A, Evans SM. Stability and lability in the evolution of behaviour in nereid polychaetes. Animal Behav 1980;28: 483-90.
61. Bellan Gr. Relationship of pollution to rocky substratum polychaetes on the French Mediterranean coast. Marine Pollution Bull 1980;11:318-21.
62. Hutchinson TH, Jha AN, Dixon DR. The polychaete Platynereis dumerilii (Audouin and Milne-Edwards): a new species for assessing the hazardous potential of chemicals in the marine environment. Ecotoxicol Environ Saf 1995;31: 271-81.
63. Hardege JD. Nereidid polychaetes as model organisms for marine chemical ecology. Hydrobiologia 1999;402:145-61.
64. Jacobs RPWM, Pierson ES. Zostera marina spathes as a habitat for Platynereis dumerilii (Audouin and Milne-Edwards, 1834). Aquat Bot 1979;6:403-6.
65. ASSEMBLE. Association of European Marine Biological Laboratories. http://www.assemblemarine.org.
66. Karsenti E, Acinas SG, Bork P, et al. A holistic approach to marine eco-systems biology. PLoS Biol 2011;9:e1001177.
67. Schneider S, Fischer A, Dorresteijn AWC. A morphometric comparison of dissimilar early development in sibling species of Platynereis (Annelida, Polychaeta). Roux Arch Dev Biol 1992;201:243-56.
68. Rhode B. Development and differentiation of the eye in Platynereis dumerilii (Annelida, Polychaeta). J Morphol 1992; 212:71-85.
69. Gambi MC, Ramella L, Sella G, et al. Variation in genome size in benthic polychaetes: systematic and ecological relationships. JMarine BiolAssocUK 1997;77:1045-57.
70. Hui JHL, Kortchagina N, Arendt D, etal. Duplication of the ribosomal gene cluster in the marine polychaete Platynereis dumerilii correlates with ITS polymorphism. J Marine Biol AssocUK 2007;87:443-9.
71. Weinberg JR, Starczak VR, Mueller C, et al. Divergence between populations of a monogamous polychaete with male parental care: premating isolation and chromosome variation. Marine Biol 1990;107:205-13.
72. McIntyre LM, Lopiano KK, Morse AM, et al. RNA-seq: technical variability and sampling. BMC Genomics 2011;12: 293.
73. OLiGO. A Tool for Automated Confocal Registration and Expression Profiling. http://4dx.embl.de/arendt/oligo/.
74. Arendt D. The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet 2008;9: 868-82.
75. Arendt D, Hausen H, Purschke G. The 'division of labour' model of eye evolution. PhilosTrans R Soc Lond B Biol Sci 2009;364:2809-17.
76. Ohta T. Evolution by gene duplication and compensatory advantageous mutations. Genetics 1988;120:841-7.
77. Ohta T. Role of gene duplication in evolution. Genome 1989;31:304-10.
78. Jones FC, Grabherr MG, Chan YF, et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 2012;484:55-61.
79. Lynch VJ, Tanzer A, Wang Y, et al. Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. ProcNatlAcad SciUSA 2008;105: 14928-33.
80. Hinman VF, Nguyen A, Davidson EH. Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins. Dev Biol 2007;312:584-95.