Development Genes and Evolution

, Volume 222, Issue 6, pp 325–339 | Cite as

Additive multiple k-mer transcriptome of the keelworm Pomatoceros lamarckii (Annelida; Serpulidae) reveals annelid trochophore transcription factor cassette

Original Article

Abstract

Recent advances in both next-generation sequencing and assembly programmes have made the low-cost construction of transcriptome datasets for non-model species feasible, capable of yielding a raft of information even from less well-transcribed genes. Here we present the results of assemblies performed on a 51-bp paired end Illumina dataset derived from a mixed larval sample of the annelid Pomatoceros lamarckii at 24, 48 and 72 h post-fertilization. We used Oases to assemble 36.5 million paired end reads with k-mer sizes from 21 to 29, followed by amalgamation of assemblies, redundancy removal with Vmatch and TGICL and removal of contigs less than 500 bp in length. This resulted in a final assembly of 50,151 contigs, with a mean length of 1,221 bp and covering 61.3 Mbp. A total of 34,846 (69.4 %) of these returned a BlastX hit above a cutoff of 1.0e−3, and 17,967 (35.8 %) were assigned at least one GO annotation using Blast2GO. We used the assembly to identify genes belonging to the homeobox superclass and the Fox, Sox and Tbx classes, recovering 37, 16, four and three genes, respectively. This included orthologues of genes previously unidentified in lophotrochozoans and protostomes. Our study illustrates the utility of such transcriptomic assembly methods as a gene discovery tool and greatly expands our knowledge of transcription factor genes in annelids in general and in this species in particular.

Keywords

Transcriptome Pomatoceros lamarckii Annelid Hox Sox Fox T-box 

Abbreviations

bp

Base pair

Fox

Forkhead box

Hox

Homeobox

Sox

Sry-related HMG box

Supplementary material

427_2012_416_MOESM1_ESM.pdf (120 kb)
ESM 1(PDF 120 kb)
427_2012_416_MOESM2_ESM.pdf (514 kb)
ESM 2(PDF 513 kb)
427_2012_416_Fig6_ESM.jpg (571 kb)
ESM 3

(JPEG 570 kb)

427_2012_416_MOESM3_ESM.tif (6.7 mb)
High resolution image (TIFF 6818 kb)
427_2012_416_MOESM4_ESM.fasta (60.4 mb)
ESM 4(FASTA 61833 kb)
427_2012_416_MOESM5_ESM.annot (3.2 mb)
ESM 5(ANNOT 3289 kb)
427_2012_416_MOESM6_ESM.xlsx (144 kb)
ESM 6(XLSX 144 kb)

References

  1. Andrews S (2011) FastQC—a quality control tool for high throughput sequence data. Babraham Bioinformatics. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/
  2. Arenas-Mena C (2008) The transcription factors HeBlimp and HeT-brain of an indirectly developing polychaete suggest ancestral endodermal, gastrulation, and sensory cell-type specification roles. J Exp Zool B 310B(7):567–576CrossRefGoogle Scholar
  3. Arendt D, Technau U, Wittbrodt J (2001) Evolution of the bilaterian larval foregut. Nature 409:81–85CrossRefPubMedGoogle Scholar
  4. Arendt D, Denes AS, Jekely G, Tessmar-Raible K (2008) The evolution of nervous system centralization. Philos T Roy Soc B 363(1496):1523–1528CrossRefGoogle Scholar
  5. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Statist Soc Ser B (Methodol) 57(1):289–300Google Scholar
  6. Bowles J, Schepers G, Koopman P (2000) Phylogeny of the Sox family of developmental transcription factors based on sequence and structural indicators. Dev Biol 227(2):239–255CrossRefPubMedGoogle Scholar
  7. Brusca R, Brusca G (2002) Invertebrates, 2nd edn. Sinauer, SunderlandGoogle Scholar
  8. Burglin TR, Cassata G (2002) Loss and gain of domains during evolution of cut superclass homeobox genes. Int J Dev Biol 46(1):115–123PubMedGoogle Scholar
  9. Carlsson P, Mahlapuu M (2002) Forkhead transcription factors: key players in development and metabolism. Dev Biol 250(1):1–23CrossRefPubMedGoogle Scholar
  10. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552CrossRefPubMedGoogle Scholar
  11. Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor. Bioinformatics 20(3):426–427CrossRefPubMedGoogle Scholar
  12. Conesa A, Gotz S, Garcia-Gomez J, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676CrossRefPubMedGoogle Scholar
  13. Denes A, Jekely G, Steinmetz P, Raible F, Snyman H, Prud'homme B, Ferrier D, Balavoine G, Arendt D (2007) Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell 129:277–288CrossRefPubMedGoogle Scholar
  14. Emrich S, Barbazuk W, Li L, Schnable P (2007) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res 17(1):69–73CrossRefPubMedGoogle Scholar
  15. Feldmeyer B, Wheat C, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics 12(1):317CrossRefPubMedGoogle Scholar
  16. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer ELL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38(Suppl 1):D211–D222CrossRefPubMedGoogle Scholar
  17. Fischer A, Henrich T, Arendt D (2010) The normal development of Platynereis dumerilii (Nereididae, Annelida). Front Zool 7(1):31CrossRefPubMedGoogle Scholar
  18. Gehring WJ (1992) The homeobox in perspective. Trends Biochem Sci 17(8):277–280CrossRefPubMedGoogle Scholar
  19. Gotz S, Garcia-Gomez J, Terol J, Williams T, Nagaraj S, Nueda M, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435CrossRefPubMedGoogle Scholar
  20. Gotz S, Arnold R, Sebastian-Leon P, Martin-Rodriguez S, Tischler P, Jehl M, Dopazo J, Rattei T, Conesa A (2011) B2G-FAR, a species-centered GO annotation repository. Bioinformatics 27(7):919–924CrossRefPubMedGoogle Scholar
  21. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech 29(7):644–652CrossRefGoogle Scholar
  22. Hansen KD, Brenner SE, Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38(12):e131CrossRefPubMedGoogle Scholar
  23. Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9(9):868–877CrossRefPubMedGoogle Scholar
  24. Hui JHL, McDougall C, Monteiro AS, Holland PWH, Arendt D, Balavoine G, Ferrier DEK (2012) Extensive chordate and annelid macrosynteny reveals ancestral homeobox gene organization. Mol Biol Evol 29:157–165CrossRefPubMedGoogle Scholar
  25. Jager M, Queinnec E, Houliston E, Manuel M (2006) Expansion of the Sox gene family predated the emergence of the Bilateria. Mol Phylogenet Evol 39(2):468–477CrossRefPubMedGoogle Scholar
  26. JGI genome website http://genome.jgi-psf.org/
  27. Kaestner KH, Knochel W, Martinez DE (2000) Unified nomenclature for the winged helix/forkhead transcription factors. Gene Dev 14(2):142–146PubMedGoogle Scholar
  28. Katoh K, Misawa K, Kuma KÄ, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30(14):3059–3066CrossRefPubMedGoogle Scholar
  29. Kerner P, Simionato E, Le Gouar M, Vervoort M (2009) Orthologs of key vertebrate neural genes are expressed during neurogenesis in the annelid Platynereis dumerilii. Evol Dev 11(5):513–524CrossRefPubMedGoogle Scholar
  30. Koopman P, Schepers G, Brenner S, Venkatesh B (2004) Origin and diversity of the Sox transcription factor gene family: genome-wide analysis in Fugu rubripes. Gene 328:177–186CrossRefPubMedGoogle Scholar
  31. Kumar S, Blaxter M (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11:571CrossRefPubMedGoogle Scholar
  32. Kurtz S (2011) The Vmatch large scale sequence analysis software. http://www.vmatch.de/
  33. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25CrossRefPubMedGoogle Scholar
  34. Lartillot N, Lespinet O, Vervoort M, Adoutte A (2002) Expression pattern of Brachyury in the mollusc Patella vulgata suggests a conserved role in the establishments of the AP axis in Bilateria. Development 129(6):1411–1421PubMedGoogle Scholar
  35. Lesch BJ, Bargmann CI (2010) The homeodomain protein hmbx-1 maintains asymmetric gene expression in adult C. elegans olfactory neurons. Genes Dev 24(16):1802–1815CrossRefPubMedGoogle Scholar
  36. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12(10):671–682CrossRefPubMedGoogle Scholar
  37. Martin J, Bruno V, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z (2010) Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC Genomics 11(1):663CrossRefPubMedGoogle Scholar
  38. McDougall C, Chen W-C, Shimeld S, Ferrier D (2006) The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes. Front Zool 3(1):16CrossRefPubMedGoogle Scholar
  39. McDougall C, Korchagina N, Tobin J, Ferrier D (2011) Annelid Distal-less/Dlx duplications reveal varied post-duplication fates. BMC Evol Biol 11(1):241CrossRefPubMedGoogle Scholar
  40. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35(Web Server issue):W182–185. doi:10.1093/nar/gkm321 CrossRefPubMedGoogle Scholar
  41. Papaioannou VE, Silver LM (1998) The T-box gene family. Bioessays 20(1):9–19CrossRefPubMedGoogle Scholar
  42. Paps J, Holland PWH, Shimeld SM (2012) A genome-wide view of transcription factor gene diversity in chordate evolution: less gene loss in amphioxus? Brief Funct Genom 11(2):177–186CrossRefGoogle Scholar
  43. Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B (2003) TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652CrossRefPubMedGoogle Scholar
  44. Putnam N, Butts T, Ferrier D, Furlong R, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu J (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453:1064–1071CrossRefPubMedGoogle Scholar
  45. Raible F, Tessmar-Raible K, Osoegawa K, Wincker P, Jubin C, Balavoine G, Ferrier D, Benes V, De Jong P, Weissenbach J (2005) Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science 310:1325–1326CrossRefPubMedGoogle Scholar
  46. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu A-L, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJM, Hoodless PA, Birol I (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7(11):909–912CrossRefGoogle Scholar
  47. Schmerer M, Savage RM, Shankland M (2009) Paxβ: a novel family of lophotrochozoan Pax genes. Evol Dev 11(6):689–696CrossRefPubMedGoogle Scholar
  48. Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. doi:10.1093/bioinformatics/bts094
  49. Schuster S (2008) Next-generation sequencing transforms today's biology. Nat Meth 5:16–18CrossRefGoogle Scholar
  50. Segrove F (1941) The development of the Serpulid Pomatoceros triqueter L. Q J Microsc Sci 82:467–540Google Scholar
  51. Shimeld SM, Boyle MJ, Brunet T, Luke GN, Seaver EC (2010a) Clustered Fox genes in lophotrochozoans and the evolution of the bilaterian Fox gene cluster. Dev Biol 340(2):234–248CrossRefPubMedGoogle Scholar
  52. Shimeld SM, Degnan B, Luke GN (2010b) Evolutionary genomics of the Fox genes: origin of gene families and the ancestry of gene clusters. Genomics 95(5):256–260CrossRefPubMedGoogle Scholar
  53. Small K, Brudno M, Hill M, Sidow A (2007) A haplome alignment and reference sequence of the highly polymorphic Ciona savignyi genome. Genome Biol 8(3):R41CrossRefPubMedGoogle Scholar
  54. Sodergren E, Weinstock GM, Davidson EH et al (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science 314(5801):941–952CrossRefPubMedGoogle Scholar
  55. Struck TH, Paul C, Hill N, Hartmann S, Hosel C, Kube M, Lieb B, Meyer A, Tiedemann R, Purschke G, Bleidorn C (2011) Phylogenomic analyses unravel annelid evolution. Nature 471(7336):95–98CrossRefPubMedGoogle Scholar
  56. Surget-Groba Y, Montoya-Burgos JI (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20(10):1432–1440CrossRefPubMedGoogle Scholar
  57. Tagawa K, Humphreys T, Satoh N (2000) T-brain expression in the apical organ of hemichordate tornaria larvae suggests its evolutionary link to the vertebrate forebrain. J Exp Zool 288(1):23–31CrossRefPubMedGoogle Scholar
  58. Takahashi T, Holland PWH (2004) Amphioxus and ascidian Dmbx homeobox genes give clues to the vertebrate origins of midbrain development. Development 131(14):3285–3294CrossRefPubMedGoogle Scholar
  59. Takahashi T, McDougall C, Troscianko J, Chen W-C, Jayaraman-Nagarajan A, Shimeld S, Ferrier D (2009) An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals. BMC Evol Biol 9(1):240CrossRefPubMedGoogle Scholar
  60. Takatori N, Butts T, Candiani S, Pestarino M, Ferrier D, Saiga H, Holland P (2008) Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae. Dev Genes Evol 218(11):579–590CrossRefPubMedGoogle Scholar
  61. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739CrossRefPubMedGoogle Scholar
  62. Tessmar-Raible K, Arendt D (2003) Emerging systems: between vertebrates and arthropods, the Lophotrochozoa. Curr Opin Genetics Dev 13:331–340CrossRefGoogle Scholar
  63. Tessmar-Raible K, Raible F, Christodoulou F, Guy K, Rembold M, Hausen H, Arendt D (2007) Conserved sensory-neurosecretory cell types in annelid and fish forebrain: insights into hypothalamus evolution. Cell 129:1389–1400CrossRefPubMedGoogle Scholar
  64. Vera J, Wheat C, Fescemyer H, Frilander M, Crawford D, Hanski I, Marden J (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17(7):1636–1647CrossRefPubMedGoogle Scholar
  65. Wang X-W, Luan J-B, Li J-M, Bao Y-Y, Zhang C-X, Liu S-S (2010) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11(1):400CrossRefPubMedGoogle Scholar
  66. Waterhouse AM, Procter JB, Martin DMA, Ml C, Barton GJ (2009) Jalview Version 2‚ A multiple sequence alignment editor and analysis workbench. Bioinformatics 25(9):1189–1191CrossRefPubMedGoogle Scholar
  67. Winchell C, Valencia J, Jacobs D (2010) Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria. Dev Genes Evol 220(9):275–295CrossRefPubMedGoogle Scholar
  68. Zerbino DR (2010) Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics Chapter 11:Unit 11 15Google Scholar
  69. Zerbino D, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829CrossRefPubMedGoogle Scholar
  70. Zhao Q-Y, Wang Y, Kong Y-M, Luo D, Li X, Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinforma 12(Suppl 14):S2CrossRefGoogle Scholar
  71. Zhong YF, Holland PW (2011) HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology. Evol Dev 13:567–568CrossRefPubMedGoogle Scholar
  72. Zhong YF, Butts T, Holland PW (2008) HomeoDB: a database of homeobox gene diversity. Evol Dev 10(5):516–518CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Department of ZoologyUniversity of OxfordOxfordUK

Personalised recommendations