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Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (pufferfish) Presented by Charu Gupta Kumar

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (pufferfish) Presented by Charu Gupta Kumar. Aparicio et al and Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Aug 23;297(5585):1301-10. .

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Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (pufferfish) Presented by Charu Gupta Kumar

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  1. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes (pufferfish)Presented by Charu Gupta Kumar • Aparicio et al and Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Aug 23;297(5585):1301-10.

  2. Classification of bony vertebrates…. • Euteleostomi (bony vertebrates) • Actinopterygii (ray-finned fishes) • Actinopteri • Chondrostei • NeopterygiiTeleosts  Tetraodonts Fugu Rubripes • Polypteriformes • Polypteridae (bichirs) • Sarcopterygii (lobe-finned fishes) • Coelacanthimorpha • Coelacanthiformes • Dipnoi (lungfishes) • Ceratodontimorpha • Tetrapoda (tetrapods) • Amniota (amniotes) MammaliaHumans • Amphibia (amphibians) 450 million years since their last common ancestor

  3. 365 Mbp genome 31,059 predicted gene loci 33,609 predicted peptides Intron size is 79 bp modal, with 75% < 425bp 1/6 of genome is repetitive elements Fugu has reduced intergenic regions Number of introns is comparable in both Fugu and Human 2.91 Gbp genome ~29,181 predicted gene loci 31,780 nonredundant peptides Intron size is 87 bp modal, with 75% < 2605bp ~43% of genome is repetitive elements Fugu Genome Human Genome

  4. Preliminary Annotation • 33,609 predicted Fugu peptides • Gene containing fraction of genome is a mere 108 Mb of the euchromatic 320Mb • Intron-exon structure of most genes is preserved between Fugu and Human • Conservation of synteny between Fugu and Human. Allows one to identify chromosomal elements from the common ancestor • 75% of Fugu loci have Tblastx hits against human genome

  5. Identification of novel putative gene loci in Hs…. Fugu Proteins Blast against Ensembl Hs peptides 8,761 Fugu proteins have hits > 10-3 (27,779 have hits < 10-3) Tblastn against masked Hs genomic sequence 1800 match Used these as input to build Hs genes through an EnsEMBL Hs pipeline 1260 remain as apparent Novels Filter for low-complexity peptides, search NCBI again 961 Fugu proteins that are novel gene loci in Humans

  6. Genome Analysis…. • RepeatMasker analysis showed 2.7% of genome matches interspersed repeats (LINEs, SINEs, MIR, etc) • Total number of introns about the same in Fugu and Humans. • Majority of Fugu gene loci are scaled in proportion to the compact genome size. • Observed intronless Fugu orthologs in Humans. But some genes were 1.3X or greater in size compared to Human

  7. Distribution of ratios for gene locus sizes of putative Fugu-human orthologous pairs.

  8. Conservation of synteny…. • Orthologous gene loci are linked in two species, regardless of gene order or presence of intervening genes.

  9. Location of conserved Fugu segments in the human genome.

  10. Duplications in Fugu Genome • Compared Fugu to itself using windows of 1 kb and 500bp. • ~0.15 % and 1.3% respectively of the Fugu genome contained duplicated segments. • In Humans, ~ 5% of the genome was duplicated in segments of > 1 kb. • More evidence comes from existence of ancient paralogous segments. When occur after speciation event, called in-paralogs.

  11. Comparison of Fugu and Human predicted proteomes…. • 3/4 of predicted human proteins have a strong match to Fugu. • Remaining 1/4 (8109) appear to have no pufferfish homologs. • Reciprocally, ~6000 (19%) Fugu predicted proteins lack significant homology in human. • A significant part of this 8109 set could represent • evolution of proteins between two vertebrates so that they are no longer mutually recognizable at the sequence level, or • Loss of genes common to other vertebrates in Fugu, or • Gain of sequences specific to tetrapod or mammalian orders, or • Erroneous human gene predictions

  12. Distribution of protein similarities between Fugu and Human proteomes.

  13. In conclusion…… • Compact Fugu genome, and low abundance of repeats. Easy to characterize regulatory elements in noncoding sequence • More similarities than differences between Fugu and Human Rapid evolution of proteins may account for most of the observable differences. • Often gene order and orientation preserved in vertebrates. • Comparative Analysis with Fugu genome powerful for discovering vertebrate homologs, and discovering synteny.

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