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PMID: 9539755 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Gene number in an invertebrate chordate, Ciona intestinalis.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 95 ·No. 8 ·1998-04-14 ·Pages 4437-40

Simmen MW, Leitgeb S, Clark VH, Jones SJ, Bird A

Abstract

Gene number can be considered a pragmatic measure of biological complexity, but reliable data is scarce. Estimates for vertebrates are 50-100,000 genes per haploid genome, whereas invertebrate estimates fall below 25,000. We wished to test the hypothesis that the origin of vertebrates coincided with extensive gene creation. A prediction is that gene number will differ sharply between invertebrate and vertebrate members of the chordate phylum. A gene number estimation method requiring limited sequence sampling of genomic DNA was developed and validated by using data for Caenorhabditis elegans. Using the method, we estimated that the invertebrate chordate Ciona intestinalis has 15,500 protein-coding genes (+/-3,700). This number is significantly lower than gene numbers of vertebrate chordates, but similar to those of invertebrates in distantly related phyla. The data indicate that evolution of vertebrates was accompanied by a dramatic increase in protein-coding capacity of the genome.

MeSH Terms
Animals Chromosome Mapping Ciona intestinalis/genetics DNA/chemistry DNA, Complementary Genome Models, Genetic Models, Statistical Molecular Sequence Data Reproducibility of Results Vertebrates
Chemicals
DNA, Complementary DNA
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Simmen M W
Institute of Cell and Molecular Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3JR, United Kingdom. [email protected]
Leitgeb S
Clark V H
Jones S J
Bird A
References (22)
22 references, click to expand
  1. Number of CpG islands and genes in human and mouse.
    Proc Natl Acad Sci U S A. 1993 Dec 15;90(24):11995-9 PMID: 7505451
  2. Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome.
    Nature. 1993 Nov 18;366(6452):265-8 PMID: 8232585
  3. A workbench for large-scale sequence homology analysis.
    Comput Appl Biosci. 1994 Jun;10(3):301-7 PMID: 7922687
  4. Gene number, noise reduction and biological complexity.
    Trends Genet. 1995 Mar;11(3):94-100 PMID: 7732579
  5. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
    Science. 1995 Jul 28;269(5223):496-512 PMID: 7542800
  6. Chasing tails in ascidians: developmental insights into the origin and evolution of chordates.
    Trends Genet. 1995 Sep;11(9):354-9 PMID: 7482787
  7. The genome of Caenorhabditis elegans.
    Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):10836-40 PMID: 7479894
  8. Gene duplications and the origins of vertebrate development.
    Dev Suppl. 1994;:125-33 PMID: 7579513
  9. Transcriptional noise and the evolution of gene number.
    Philos Trans R Soc Lond B Biol Sci. 1995 Sep 29;349(1329):249-53 PMID: 8577835
  10. The SWISS-PROT protein sequence data bank and its new supplement TREMBL.
    Nucleic Acids Res. 1996 Jan 1;24(1):21-5 PMID: 8594581
  11. The role of the genome project in determining gene function: insights from model organisms.
    Cell. 1996 Aug 23;86(4):521-9 PMID: 8752207
  12. A gene map of the human genome.
    Science. 1996 Oct 25;274(5287):540-6 PMID: 8849440
  13. Life with 6000 genes.
    Science. 1996 Oct 25;274(5287):546, 563-7 PMID: 8849441
  14. Databases of mRNA untranslated regions for metazoa.
    Comput Chem. 1996 Mar;20(1):141-4 PMID: 8867845
  15. Quality not quantity: the pufferfish genome.
    Hum Mol Genet. 1996;5 Spec No:1437-42 PMID: 8875249
  16. Recombination of protein domains facilitated by co-translational folding in eukaryotes.
    Nature. 1997 Jul 24;388(6640):343-9 PMID: 9237751
  17. The complete genome sequence of Escherichia coli K-12.
    Science. 1997 Sep 5;277(5331):1453-62 PMID: 9278503
  18. Chromatid structure: relationship between DNA content and nucleotide sequence diversity.
    Chromosoma. 1971 Mar 16;32(4):378-406 PMID: 4995642
  19. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction.
    Anal Biochem. 1987 Apr;162(1):156-9 PMID: 2440339
  20. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  21. A survey of expressed genes in Caenorhabditis elegans.
    Nat Genet. 1992 May;1(2):114-23 PMID: 1302004
  22. How many genes in the human genome?
    Nat Genet. 1994 Jul;7(3):345-6 PMID: 7920649
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.95.8.4437
Email
[email protected]
Published
1998-04-14
Pages
4437-40
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC22507
Subset
IM
Grants
Wellcome Trust · United Kingdom
Databases
GENBANK
AJ226133, AJ227619, AJ227620, AJ227621, AJ227622, AJ227623, AJ227624, AJ227625, AJ227626, AJ227627, AJ227628, AJ227629, AJ227630, AJ227631, AJ227632, AJ227633, AJ227634, AJ227635, AJ227636, AJ227637, AJ227638, AJ227639, AJ227640, AJ227641, AJ227642, AJ227643, AJ227644, AJ227645, AJ227646, AJ227647
External Links
PubMed source DOI: 10.1073/pnas.95.8.4437 PMC Full Text View journal details
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