Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

Abstract

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.

Coexistence of diploid, triploid and tetraploid crucian carp (Carassius auratus) in natural waters

“…It seems difficult to understand how the chromosomes of 3nCC performed pairing during meiosis. Considering the fish-specific genome duplication that was regarded as having happened in the history of teleosts evolution [17-20], 3nCC could actually be regarded as an ancient hexaploid which could certainly perform pairing of homologous chromosomes during meiosis. Therefore, the results supported the occurrence of genome duplication in fish evolution.…”

“…Recent studies on comparative genomics have further suggested that the third round of fish-specific genome duplication might have occurred in ray-finned (actinopterygian) fishes about 350 million years ago during the divergence between teleost fish and basal actinopterygian lineages. Polyploidy induces redundant genes, increasing the possibility of gene loss, gene silencing, subfunctionalization of genes, and evolution to new genes [17-21]. These variations provide polyploids with more possibilities for new characteristics and adaptations than diploids.…”

Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications

“…A whole-genome shotgun assembly of the genome of Takifugu rubripes was published recently [2]. Blast searches of the known Hox-A proteins from other species against version 3.0 of the Fugu database [34] leave little doubt that there are two Hox-A clusters.…”

Expanding the organismal scope of proteomics: Cross‐species protein identification by mass spectrometry and its implications

“…With the complete sequencing of the pufferfish genome, we can predict that studies into the proteomes of other fishes will capitalize on these sequence resources by using sequence similarity search methods [59]. Once a bird's or reptile's genome is sequenced, we can expect to see developments in the proteomics of related organisms.…”