MicroRNAs support the monophyly of enteropneust hemichordates

Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Volumn 320, Issue 6, 2013, Pages 368-374

  Peterson, Kevin J ^a   Su, Yi Hsien ^b   Arnone, Maria Ina ^c   Swalla, Billie ^d,e,f   King, Benjamin L ^g  

^a Dartmouth College   (United States)

^b INSTITUTE OF CELLULAR AND ORGANISMIC BIOLOGY   (Taiwan)

^c STAZIONE ZOOLOGICA ANTON DOHRN   (Italy)

^d UNIVERSITY OF WASHINGTON   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

^f UNIVERSITY OF HAWAII   (United States)

^g MOUNT DESERT ISLAND BIOLOGICAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ANTEDON MEDITERRANEA; ASTERINA MINIATA; ASTEROIDEA; CEPHALODISCUS; CEPHALODISCUS HODGSONI; CHORDATA; CRINOIDEA; DEUTEROSTOMIA; ECHINODERMATA; ECHINOIDEA; ENTEROPNEUSTA; HARRIMANIIDAE; HEMICHORDATA; METAZOA; PTEROBRANCHIA; PTYCHODERA (ACORN WORM); PTYCHODERA FLAVA; PTYCHODERIDAE; SACCOGLOSSUS; SACCOGLOSSUS KOWALEVSKII; STRONGYLOCENTROTUS PURPURATUS;

EID: 84881547306     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.22510     Document Type: Article

References (45)

1. Ambros V, Bartel B, Bartel DP, et al. 2003. A uniform system for microRNA annotation. RNA 9:277-279.
2. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
3. Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136:215-233.
4. Bateson W. 1885. The later stages in the development of Balanoglossus kowalevskii, with a suggestion as to the affinities of the Enteropneusta. Q J Microsc Sci 25:81-122.
5. Berezikov E. 2011. Evolution of microRNA diversity and regulation in animals. Nat Rev Genet 12:846-860.
6. Bourlat SJ, Nielsen C, Lockyer AE, Littlewood DTJ, Telford MJ. 2003. Xenoturbella is a deuterostome that eats molluscs. Nature 424:925-928.
7. Bremer K. 1994. Branch support and tree stability. Cladistics 10:295-304.
8. Brown FD, Prendergast A, Swalla BJ. 2008. Man is but a worm: chordate origins. Genesis 46:605-613.
9. Cameron CB. 2005. A phylogeny of the hemichordates based on morphological characters. Can J Zool 83:196-215.
10. Cameron CB, Garey JR, Swalla BJ. 2000. Evolution of the chordate body plan: new insights from phylogenetic analyses of deuterostome phyla. Proc Natl Acad Sci USA 97:4469-4474.
11. Campbell LI, Rota-Stabellli O, Marchioro T, et al. 2011. MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest the velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci USA 108:15920-15924.
12. Campo-Paysaa F, Sémon M, Cameron RA, Peterson KJ, Schubert M. 2011. miRNA complements in deuterostomes: origin and evolution of miRNAs. Evol Dev 13:15-27.
13. Cannon JT, Rychel AL, Eccleston H, Halanych KM, Swalla BJ. 2009. Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts. Mol Phylogenet Evol 52:17-24.
14. Carthew RW, Sontheimer EJ. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642-655.
15. Donoghue MJ. 2005. Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny. Paleobiology 31:77-93.
16. Edgecombe GD, Giribet G, Dunn CW, et al. 2011. Higher-level metazoan relationships: recent progress and remaining questions. Org Divers Evol 11:151-172.
17. Halanych KM. 1995. The phylogenetic position of the pterobranch hemichordates based on 18S rDNA sequence data. Mol Phylogenet Evol 4:72-76.
18. Heimberg AM, Cowper-Sallari R, Sémon M, Donoghue PCJ, Peterson KJ. 2010. microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proc Natl Acad Sci USA 107:19379-19383.
19. Helm C, Bernhart SH, Siederdissen CHZ, Nickel B, Bleidorn C. 2012. Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Mol Phylogenet Evol 64:198-203.
20. Huntzinger E, Izaurralde E. 2011. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12:99-110.
21. Jefferies RPS. 1986. The ancestry of the vertebrates. London: British Museum (Natural History).
22. Kadri S, Hinman VF, Benos PV. 2011. RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS ONE 6:e29217.
23. Kozomara A, Griffiths-Jones S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152-D157.
24. Li MA, He L. 2012. microRNAs as novel regulators of stem cell pluripotency and somatic cell reprogramming. BioEssays 34:670-680.
25. Luttrell S, Konikoff C, Byrne A, Bengtsson B, Swalla BJ. 2012. Ptychoderid hemichordate neurulation without a notochord. Integr Comp Biol 52:829-834.
26. Lyson TR, Sperling EA, Heimberg AM, et al. 2011. microRNAs support a Testudines-Lepidosaur clade. Biol Lett 8:104-107.
27. Maddison DR, Maddison WP. 2005. MacClade 4. Sunderland: Sinauer Associates.
28. McClay DR. 2011. Evolutionary crossroads in developmental biology: sea urchins. Development 138:2639-2648.
29. Peterson KJ, Eernisse DJ. 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol Dev 3:170-205.
30. Peterson KJ, Cameron RA, Davidson EH. 1997. Set-aside cells in maximal indirect development: evolutionary and developmental significance. BioEssays 19:623-631.
31. Philippe H, Brinkmann H, Copley RR, et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-258.
32. Rota-Stabellli O, Campbell L, Brinkmann H, et al. 2010. A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata. Proc R Soc Lond B Biol Sci 278:298-306.
33. Röttinger E, Lowe CJ. 2012. Evolutionary crossroads in developmental biology: hemichordates. Development 139:2463-2475.
34. Sato A, Bishop JDD, Holland PWH. 2008. Developmental biology of pterobranch hemichordates: history and perspectives. Genesis 46:587-591.
35. Smith AB, Peterson KJ, Wray G, Littlewood DTJ. 2004. From bilateral symmetry to pentaradiality: the phylogeny of hemichordates and echinoderms. In: Cracraft J Donoghue MJ, editors. Assembling the tree of life. Oxford: Oxford University Press. p 365-383.
36. Sperling EA, Peterson KJ. 2009. microRNAs and metazoan phylogeny: big trees from little genes. In: Telford MJ, Littlewood, DTJ, editors. Animal evolution-Genomes, trees and fossils. Oxford: Oxford University Press. p 157-170.
37. Sperling EA, Pisani D, Peterson KJ. 2007. Poriferan paraphyly and its implications for Precambrian palaeobiology. In: Vickers-Rich P Komarower P, editors. The rise and fall of the Ediacaran Biota. London: The Geological Society. p 355-368. Special Publications.
38. Sperling EA, Robinson JM, Pisani D, Peterson KJ. 2010. Where's the glass? Biomarkers, molecular clocks, and microRNAs suggest a 200-Myr missing Precambrian fossil record of siliceous-sponge spicules. Geobiology 8:24-36.
39. Starega-Roslan J, Koscianska E, Kozlowski P, Kryzyzosiak WJ. 2011. The role of the precursor structure in the biogenesis of microRNA. Cell Mol Life Sci 68:2859-2871.
40. Swalla BJ, Smith AB. 2008. Deciphering deuterostome phylogeny: molecular, morphological and paleontological perspectives. Philos Trans R Soc Lond Ser B Biol Sci 363:1557-1568.
41. Swofford DL. 2002. PAUP* Phylogenetic Analysis Using Parsimony (* and Other Methods) v.4.0b10 for Macintosh. Sunderland: Sinauer Associates.
42. Tarver JE, Donoghue PCJ, Peterson KJ. 2012. Do miRNAs have a deep evolutionary history? BioEssays 34:857-866.
43. Wheeler BM, Heimberg AM, Moy VN, et al. 2009. The deep evolution of metazoan microRNAs. Evol Dev 11:50-68.
44. Winchell CJ, Sullivan J, Cameron CB, Swalla BJ, Mallatt J. 2002. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Mol Biol Evol 19:762-776.
45. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415.