Hemichordate Genomics

Cross references:    Hemichordates       Hemichordate Hormones   
Hemichordate Nerves       Hemichordate Neurotransmitters    
Hemichordate Receptors
    Genetics in General    Genomics in General    Genomic Analysis   Ediacaran Genomics    Parazoa Genomics     Coelenterata Genomics     Deuterostome Genomics  
Protochordate Genomics

Expansion of the Hox gene family and the evolution of chordates. (PubMed) - 1993 
from the abstract   
Homeobox genes encode DNA-binding transcription regulators that participate in the formation of embryonic pattern or contribute to cell-type specificity during metazoan development.  
    Homeobox genes that regulate axial patterning and segmental identity (Hox/HOM genes) share a conserved clustered genomic organization.    
    Mammals have four clusters that have likely arisen from the duplication of a single ancestral cluster. The number of Hox-type genes in other deuterostomes was estimated by using a polymerase chain reaction sampling method. Increased Hox gene complements are associated with the appearance of chordate and vertebrate characters.    
    Our data suggest the presence of one Hox cluster in the acorn worm, a hemichordate; two Hox clusters in
Amphioxus, a cephalochordate; and three in the Lamprey, a primitive vertebrate."  
My comment
    For background on the Hox genes, see: 
Genomics in General   .   

Anteroposterior patterning in hemichordates and the origins of the chordate nervous system.  (PubMed)  - 2003   
from the abstract   
we examined the hemichordate Saccoglossus kowalevskii and studied the expression of orthologs of genes that are involved in patterning the chordate central nervous system. All 22 orthologs studied are expressed in the ectoderm in an anteroposterior arrangement nearly identical to that found in chordates. Domain topography is conserved between hemichordates and chordates despite the fact that hemichordates have a diffuse nerve net, whereas chordates have a centralized system. We propose that the deuterostome ancestor may have had a diffuse nervous system, which was later centralized during the evolution of the chordate lineage.

Isolation of Hox and Parahox genes in the hemichordate Ptychodera flava and the evolution of deuterostome Hox genes.  (PubMed)  - 2004   
Only abstract available online.   
Because of their importance for proper development of the bilaterian embryo, Hox genes have taken center stage for investigations into the evolution of bilaterian metazoans.    
    Taxonomic surveys of major protostome taxa have shown that Hox genes are also excellent phylogenetic markers, as specific Hox genes are restricted to one of the two great protostome clades, the Lophotrochozoa or the Ecdysozoa, and thus support the phylogenetic relationships as originally deduced by 18S rDNA studies.  
    Deuterostomes are the third major group of bilaterians and consist of three major phyla, the echinoderms, the hemichordates, and the chordates. Most morphological studies have supported Hemichordata+Chordata, whereas molecular studies support Echinodermata+Hemichordata, a clade known as Ambulacraria.  
    To test these competing hypotheses, complete or near complete cDNAs of eight Hox genes and four Parahox genes were isolated from the enteropneust hemichordate Ptychodera flava. Only one copy of each Hox gene was isolated suggesting that the Hox genes of P. flava are arranged in a single cluster.  
    Of particular importance is the isolation of three posterior or Abd-B Hox genes; these genes are only shared with echinoderms, and thus support the monophyly of Ambulacraria.
My comment
    For background on the Hox genes, see: 
Genomics in General  .    

Hemichordates and the origin of chordates. (PubMed)  - 2005   
Only abstract available online.   
    "Hemichordates, the phylum of bilateral animals most closely related to chordates, could reveal the evolutionary origins of chordate traits such as the nerve cord, notochord, gill slits and tail.  
    The anteroposterior maps of gene expression domains for 38 genes of chordate neural patterning are highly similar for hemichordates and chordates, even though hemichordates have a diffuse nerve-net.  
    About 40% of the domains are not present in protostome maps.  
    We propose that this map, the gill slits and the tail date to the deuterostome ancestor.  
    The map of dorsoventral expression domains, centered on a Bmp-Chordin axis, differs between the two groups; hemichordates resemble protostomes more than they do chordates. The dorsoventral axis might have undergone extensive modification in the chordate line, including centralization of the nervous system, segregation of epidermis, derivation of the notochord, and an inversion of organization.

Dorsoventral patterning in hemichordates: insights into early chordate evolution.
  (PubMed)  - 2006   
HTML:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1551926/?tool=pubmed   
from the abstract       
In the hemichordate embryo, genes encoding bone morphogenetic proteins (Bmp) 2/4 and 5/8, as well as several genes for modulators of Bmp activity, are expressed in a thin stripe of ectoderm on one midline, historically called "dorsal."  
    On the opposite midline, the genes encoding Chordin and Anti-dorsalizing morphogenetic protein (Admp) are expressed.  
    Thus, we find a Bmp-Chordin developmental axis preceding and underlying the anatomical dorsoventral axis of hemichordates, adding to the evidence from Drosophila and chordates that this axis may be at least as ancient as the first bilateral animals.   
Numerous genes encoding transcription factors and signaling ligands are expressed in the three germ layers of hemichordate embryos in distinct dorsoventral domains, such as pox neuro, pituitary homeobox, distalless, and tbx2/3 on the Bmp side and netrin, mnx, mox, and single-minded on the Chordin-Admp side.
Finally, since hemichordates develop the mouth on the non-Bmp side, like arthropods but opposite to chordates, the mouth and Bmp-Chordin axis may have rearranged in the chordate line, one relative to the other.

Molecular phylogeny of hemichordata, with updated status of deep-sea enteropneusts (PubMed)  - 2009   
Only abstract available online.  I got the PDF from the library. 
from the PDF       
    "An alternate view, that the ancestral hemichordate was enteropneust-
like, has been proposed on the basis of homologies between enteropneust and cephalochordate gill slits, as well as similarities in axis specification genes in enteropneusts and chordates."   
    "In the future, comparison of the 18S dataset presented here with one constructed from genomic information—single copy nuclear genes, introns, and entire mitochondria—should provide us with a better picture of the evolutionary relationships among the solitary and colonial hemichordates." 

Sequencing the Genome of the hemichordate Saccoglossus kowalevskii (Goog) 
PDF:  http://www.genome.gov/Pages/Research/Sequencing/SeqProposals/AcornWormSEQ.pdf  
    Must download to copy-and-paste.   -  date unknown 
This appears to be the proposal for a future research project rather than the results of a completed project. 
    Genes Already Identified by Expressed Sequence Tags (see below):
opioid receptor, neuropeptide Y receptor, serotonin transporter, GABA transporter, GAD (GABA synthesis), GABA receptor, vasotocin, tyrosine hydroxylase, thyrotropin releasing hormone receptor, corticotropin-releasing hormone receptor 
My comment
    These were just the genes I recognized from a very much longer list.     
    For background information on receptors, see: 
Receptors in General  . 
        specific receptors mentioned:  
See:  Hemichordate Receptors   
            neuropeptid Y
            thyrotropin releasing hormone
            cortiotropin-releasing hormone receptor   
    For background on transporters, see:  Transmembrane Transport in General  .   
        specific transporters mentioned:  
serotonin transporter   
GABA transporter   
    For background on enzymes, see:  Enzymes                
        specific enzymes mentioned:                   
GAD (GABA synthesis)   
tyrosine hydroxylase  
    For background on hormones, see:  Hormones in General  .     
        specific hormones mentioned: 

Expressed sequence tag (Wiki)   
    "An expressed sequence tag or EST is a short sub-sequence of a cDNA sequence.[1] They may be used to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination.[2]"