Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence

@article{Crollius2000EstimateOH,
  title={Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence},
  author={Hugues Roest Crollius and Olivier Jaillon and Alain Bernot and Corinne Dasilva and Laurence Bouneau and C{\'e}cile Fischer and C{\'e}cile Fizames and Patrick Wincker and Philippe Brottier and Françis Qu{\'e}tier and W. Saurin and Jean Weissenbach},
  journal={Nature Genetics},
  year={2000},
  volume={25},
  pages={235-238}
}
The number of genes in the human genome is unknown, with estimates ranging from 50,000 to 90,000 (refs 1, 2), and to more than 140,000 according to unpublished sources. We have developed ‘Exofish’, a procedure based on homology searches, to identify human genes quickly and reliably. This method relies on the sequence of another vertebrate, the pufferfish Tetraodon nigroviridis, to detect conserved sequences with a very low background. Similar to Fugu rubripes , a marine pufferfish proposed by… 
Estimation of the Extent of Synteny Between Tetraodon nigroviridis and Homo sapiens Genomes
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A genomic comparison between 20 sequenced BACs from Tetraodon nigroviridis and the human genome suggests that genomic evolution by rearrangement is not uniform within the vertebrates.
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This study confirms the utility of the Fugu as a supplementary tool to uncover and confirm novel genes and putative gene regulatory regions in the human genome.
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The main populations and clusters of pseudogenes on chromosomes 21 and 22 are determined, and it is found that chromosome 22 pseudogene population is dominated by immunoglobulin segments, which have a greater rate of disablement per amino acid than the other pseudogene populations and are also substantially more diverged.
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Methods for using cross-species whole-genome shotgun sequence (WGS) for genome annotation are described in this paper and showed a 23-fold enrichment for coding regions compared with noncoding regions in the human genome.
Characterization and repeat analysis of the compact genome of the freshwater pufferfish Tetraodon nigroviridis.
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The previously uncharacterized Tetraodon genome is described here together with a detailed analysis of its repeat content and organization, and the sequencing of 46 megabases of bacterial artificial chromosome end sequences, which represents a random DNA sample equivalent to 13% of the genome.
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The near-complete sequence reported here should serve as a firm foundation for biomedical research in the decades ahead and greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death.
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes
TLDR
A two-stage procedure is developed that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods, and it is estimated that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes.
Extensive search does not identify genomic sex markers in Tetraodon nigroviridis
*Author to whom correspondence should be addressed: Tel.: +65 6872 7413; fax: +65 6872 7007; email: laszlo@tll.org.sg The green spotted pufferfish Tetraodon nigroviridis Marion de Procé has the
[Finishing the euchromatic sequence of the human genome].
  • M. Hattori
  • Medicine, Biology
    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme
  • 2005
TLDR
The near-complete sequence reported here should serve as a firm foundation for biomedical research in the decades ahead and greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death.
Selection on human genes as revealed by comparisons to chimpanzee cDNA.
TLDR
The comparison to intergenic DNA sequences indicates that about 39% of silent sites in protein-coding regions are deleterious and subject to negative selection, and there is significantly higher divergence in the 5' untranslated regions (UTRs) but not in other parts of the transcript.
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