Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
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Citations
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
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References
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
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Frequently Asked Questions (15)
Q2. What are the types of novelties in the eukaryotic cell?
Matrix metalloproteases also were invented as Type II novelties, whereasguidance cues such as netrin and semaphorin that mediate adhesion are novelties with no clearhomology to ancient eukaryotic proteins.
Q3. What are the types of novelties in the sarcolemma?
Variouscomponents of the dystrophin-associated protein complex (DPC) in the sarcolemma such asdystrophin, syntrophin, beta-dystrobrevin and beta-sarcoglycan are Type The authornovelties.
Q4. How many complete or partial protein-coding transcripts were predicted in the genome?
Combining homology-based and ab initio methodswith sequences from over 146,000 expressed sequence tags, the authors predicted ~27,000 complete orpartial protein-coding transcripts in the genome (32).
Q5. How many amino acids were required to be in the flanking regions of the splice?
the authors required that at least 5 amino acids out of 10 in the flanking regions of the splice sites be either fully conserved or have strong functional similarity among all four species.
Q6. What is the recent preference of C2H2 zinc finger genes?
In addition to olfactory and taste receptors, the human genome shows strong recent preference of C2H2 zinc finger genes with a KRAB domain, keratin, and immune defence proteins.
Q7. What are the types of proteins that appear completely novel in the eumetazoan?
Certain enzymes important in synaptic transmission (e.g.DOPA-beta monooxygenase) and some vesicular trafficking proteins (e.g. synaptophysin) appearas completely novel (Type I) eumetazoan proteins.
Q8. How can a laboratory culture be maintained?
Self-sustaining laboratory cultures can be maintained year-round in artificial seawater, with daily feedings of brine shrimp (3, 4).
Q9. How many clusters of short proteins are there?
There are 5 large clusters of short proteins (around ~100aa), each comprising 55-74 memberswith weak similarity to hypothetical short ORFs from fungi (28)•
Q10. How many families are represented in the anemone genome?
while different classes of anemone retrotransposons, including Gypsy, DIRS, Penelope, and CR1, are composed of more than 50-100 families each, different classes of autonomous DNA transposons are represented by just a few families.
Q11. What is the type of novelty of the eumetazoan gene set?
The first and largest group ("type I" novelty) comprises animal genes that have no identifiablerelatives (with BLAST) outside of animals in the available sequence datasets, and accounts for15% (1,186) of ancestral eumetazoan genes.
Q12. How many sets of scaffolds and chromosome segments were ordered?
The rows and columns of this table have been ordered to reveal 13 sets of scaffolds and chromosome segments, defined by the criterion that none can be subdivided without separating into different sets a scaffold-segment pair with significant evidence (p<0.01) for conserved synteny.
Q13. How many eumetazoan genes are in the cluster?
This clustering of scaffolds and chromosome segments defines 15 large PALs, each with descendants of more than one hundred ancestral eumetazoan genes.
Q14. How did the authors determine whether the functional categories were overrepresented among the different types of novelties?
To asses whether specific functional categories were over- or underrepresented among the different types of novelties, the authors adapted the GOstat approach of Beissbarth and Speed (44) for use with the Panther ontologies, and computed p-values for enrichment and dearth relative the hypergeometric distribution.
Q15. How many predicted gene models were built using the JGI Annotation Pipeline?
The genome of Nematostella vectensis includes 27,273 predicted gene models built using the JGI Annotation Pipeline, described below.