Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively ...small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ancient Noncoding Elements Conserved in the Human Genome Venkatesh, Byrappa; Kirkness, Ewen F; Loh, Yong-Hwee ...
Science (American Association for the Advancement of Science),
12/2006, Letnik:
314, Številka:
5807
Journal Article
Recenzirano
Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated approximately ...1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.
Tetrodotoxin (TTX) is a highly potent neurotoxin that selectively binds to the outer vestibule of voltage-gated sodium channels. Pufferfishes accumulate extremely high concentrations of TTX without ...any adverse effect. A nonaromatic amino acid (Asn) residue present in domain I of the pufferfish,
Takifugu pardalis, Na
v1.4 channel has been implicated in the TTX resistance of pufferfishes
1. However, the effect of this residue on TTX sensitivity has not been investigated, and it is not known if this residue is conserved in all pufferfishes. We have investigated the genetic basis of TTX resistance in pufferfishes by comparing the sodium channels from two pufferfishes (
Takifugu rubripes fugu and
Tetraodon nigroviridis) and the TTX-sensitive zebrafish. Although all three fishes contain duplicate copies of Na
v1.4 channels (Na
v1.4a and Na
v1.4b), several substitutions were found in the TTX binding outer vestibule of the two pufferfish channels. Electrophysiological studies showed that the nonaromatic residue (Asn in fugu and Cys in
Tetraodon) in domain I of Na
v1.4a channels confers TTX resistance. The Glu-to-Asp mutation in domain II of
Tetraodon channel Na
v1.4b is similar to that in the saxitoxin- and TTX-resistant Na
+ channels of softshell clams
2. Besides helping to deter predators, TTX resistance enables pufferfishes to selectively feed on TTX-bearing organisms.
The genomes of several vertebrates, including six mammals, the chicken, Xenopus and four ray-finned fishes have been sequenced or are currently being sequenced to provide a better understanding of ...the human genome through comparative analysis. However, this list does not include cartilaginous fishes, which are the most basal living jawed vertebrates 1. The genomes of the current ‘popular’ cartilaginous fishes such as the nurse shark, dogfish, and horn shark are larger than the human genome (∼3800 Mb to 7000 Mb) 2, and are not attractive for whole-genome sequencing. Here, we report the characterization of the relatively small genome (1200 Mb) of a cartilaginous fish, the elephant fish (Callorhinchus milii), and propose it as a model for whole-genome sequencing.
Contrary to previous observations that fish genomes are devoid of nuclear mitochondrial pseudogenes, a genome-wide survey identified a large number of “recent” and “ancient” nuclear mitochondrial DNA ...fragments (Numts) in the whole-genome sequences of the fugu (
Takifugu rubripes),
Tetraodon nigroviridis, and zebrafish (
Danio rerio). We have analyzed the latest assembly (v4.0) of the fugu genome and show that, like the
Anopheles genome, the fugu nuclear genome does not contain mitochondrial pseudogenes. Fugu assembly v4.0 contains a single scaffold representing the near complete sequence of the fugu mitochondria. The “recent” Numts identified by the previous study in fugu assembly v2.0 are in fact shotgun sequences of mitochondrial DNA that were misassembled with the nuclear sequences, whereas the “ancient” Numts appear to be the result of spurious matches. It is likely that the Numts identified in the genomes of
Tetraodon and zebrafish are also similar artifacts. Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification.
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