Article open access publication

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

PLOS Biology, Public Library of Science (PLoS), ISSN 1544-9173

Volume 12, 11, 2014

DOI:10.1371/journal.pbio.1002005, Dimensions: pub.1008491596, PMC: PMC4244043, PMID: 25423365,

Authors

Brites, Daniela (12) (13)
Erikson, Galina (16) (17)
Gabaldón, Toni (14) (20) (21)
Guigó, Roderic (14) (21)
Han, Yi (4)
Kraus, F. Bernhard (27) (31)
Lv, Jie (26)
Mariotti, Marco (14) (21)
Neumann, Tobias (30) (33)
Stief, Anna (3) (37)

Affiliations

Organisations

  1. (1) Hebrew University of Jerusalem, grid.9619.7
  2. (2) University of St Andrews, grid.11914.3c
  3. (3) University of Cambridge, grid.5335.0
  4. (4) Baylor College of Medicine, grid.39382.33
  5. (5) European Bioinformatics Institute, grid.225360.0
  6. (6) University of Rostock, grid.10493.3f
  7. (7) National University of Tucumán, grid.108162.c
  8. (8) University of Barcelona, grid.5841.8
  9. (9) University of Sussex, grid.12082.39
  10. (10) Foundation for Research and Technology Hellas, grid.4834.b
  11. (11) National University of Ireland, Galway, grid.6142.1
  12. (12) Swiss Tropical and Public Health Institute, grid.416786.a
  13. (13) University of Basel, grid.6612.3
  14. (14) Centre for Genomic Regulation, grid.11478.3b
  15. (15) University of Otago, grid.29980.3a
  16. (16) Scripps Health, grid.419722.b
  17. (17) Salk Institute for Biological Studies, grid.250671.7
  18. (18) Babraham Institute, grid.418195.0
  19. (19) Harvard University, grid.38142.3c
  20. (20) Catalan Institution for Research and Advanced Studies, grid.425902.8
  21. (21) Pompeu Fabra University, grid.5612.0
  22. (22) Stony Brook University, grid.36425.36
  23. (23) Hendrix College, grid.256928.2
  24. (24) University of Manchester, grid.5379.8
  25. (25) University of Copenhagen, grid.5254.6, KU
  26. (26) Rice University, grid.21940.3e
  27. (27) Martin Luther University Halle-Wittenberg, grid.9018.0
  28. (28) Chinese University of Hong Kong, grid.10784.3a
  29. (29) Utrecht University, grid.5477.1
  30. (30) University of Vienna, grid.10420.37
  31. (31) University Hospital in Halle, grid.461820.9
  32. (32) University College London, grid.83440.3b
  33. (33) Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
  34. (34) Hubrecht Institute for Developmental Biology and Stem Cell Research, grid.419927.0
  35. (35) Texas A&M University – Corpus Christi, grid.264759.b
  36. (36) University of Illinois at Urbana Champaign, grid.35403.31
  37. (37) University of Potsdam, grid.11348.3f
  38. (38) Research Platform “Marine Rhythms of Life”, Vienna, Austria
  39. (39) Leiden University, grid.5132.5
  40. (40) University of Georgia, grid.213876.9

Description

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.

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Times Cited: 164

Field Citation Ratio (FCR): 28.2

Relative Citation ratio (RCR): 6.3

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