Amphioxus Genomics

Cross reference:   Amphioxus Hormones    Endostyle = Thyroid   
Amphioxus Gut Hormones      Lamellar Body = Pineal Gland   Amphioxus Pituitary      
Amphioxus Gonads    Amphioxus Stress Hormones     Amphioxus Oxytocin   
Lamprey Genomics   

Gene duplications and the origins of vertebrate development.    
All vertebrates possess anatomical features not seen in their closest living relatives, the protochordates (tunicates and amphioxus). Some of these features depend on developmental processes or cellular behaviours that are again unique to vertebrates. We are interested in the genetic changes that may have permitted the origin of these innovations. Gene duplication, followed by functional divergence of new genes, may be one class of mutation that permits major evolutionary change. Here we examine the hypothesis that gene duplication events occurred close to the origin and early radiation of the vertebrates. Genome size comparisons are compatible with the occurrence of duplications close to vertebrate origins; more precise insight comes from cloning and phylogenetic analysis of gene families from amphioxus, tunicates and vertebrates.  
    Comparisons of Hox gene clusters, other homeobox gene families, Wnt genes and insulin-related genes all indicate that there was a major phase of gene duplication close to vertebrate origins, after divergence from the amphioxus lineage; we suggest there was probably a second phase of duplication close to jawed vertebrate origins. From amphioxus and vertebrate homeobox gene expression patterns, we suggest that there are multiple routes by which new genes arising from gene duplication acquire new functions and permit the evolution of developmental innovations."  

Developmental Gene Expression in Amphioxus: New Insights into the Evolutionary Origin of Vertebrate Brain Regions, Neural Crest, and Rostrocaudal Segmentation 

Full 12 page PDF.    Must download to copy. 
    "SYNOPSIS. Amphioxus is widely held to be the closest invertebrate relative of the vertebrates and the best available stand-in for the proximate ancestor of the vertebrates.  The spatiotemporal expression patterns of developmental genes can help suggest body part homologies between vertebrates and amphioxus. This approach is illustrated using five homeobox genes (AmphiHoxl, AmphiHox2, AmphiOtx, AmphiDll, and AmphiEri) to provide insights into the evolutionary origins of three important vertebrate features: the major brain regions, the neural crest, and rostrocaudal segmentation. During amphioxus development, the neural expression patterns of these genes are consistent with the presence of a forebrain (detailed neuroanatomy indicates that the forebrain is all diencephalon without any telencephalon) and an extensive hindbrain; the possible presence of a midbrain requires additional study. Further, during neurulation, the expression pattern of AmphiDll as well as migratory cell behavior suggest that the epidermal cells bordering the neural plate may represent a phylogenetic precursor of the vertebrate neural crest.  Finally,  when the paraxial mesoderm begins to segment, the earliest expression of AmphiEn is detected in the posterior part of each nascent and newly formed somite.  This pattern recalls the expression of the segment-polarity gene engrailed during establishment of the segments of metameric protostomes. Thus, during animal evolution, the role of engrailed in establishing and maintaining metameric body plans may have arisen in a common segmented ancestor of both the protostomes and deuterostomes. 
    NOTE:  Searching PubMed for "amphioxus endocrine" yielded 42 hits, many of which were very interesting. 

Characterization of Amphioxus AmphiVent, an evolutionarily conserved marker for chordate ventral mesoderm.  
    Related articles   
from the Abstract:       
     "Structure and developmental expression are described for amphioxus AmphiVent, a homolog of vertebrate Vent genes. In amphioxus, AmphiVent-expressing ventral mesoderm arises at midneurula by outgrowth from the paraxial mesoderm, but in vertebrates, Vent-expressing ventral mesoderm originates earlier, at the gastrula stage. In other embryonic tissues (nascent paraxial mesoderm, neural plate, endoderm, and tailbud), AmphiVent and its vertebrate homologs are expressed in similar spatiotemporal domains, indicating conservation of many Vent gene functions during chordate evolution. The ventral mesoderm evidently develops precociously in vertebrates because their relatively large embryos probably require an early and extensive deployment of the mesoderm-derived circulatory system. The vertebrate ventral mesoderm, in spite of its strikingly early advent, still resembles the nascent ventral mesoderm of amphioxus in expressing Vent homologs. This coincidence may indicate that Vent homologs in vertebrates and amphioxus play comparable roles in ventral mesoderm specification."  

Ancient phylogenetic separation between Pacific and Atlantic cephalochordates as revealed by mitochondrial genome analysis.
Only abstract available online.   
Two maximum-likelihood trees from the COI and 16S rRNA genes showed that the Pacific and Atlantic lancelets were reciprocally clustered into different clades. Furthermore, both gene trees consistently exhibited deep phylogenetic separation between the two oceans. The estimated divergence time suggested that differentiation may have followed the migration of ancestral lancelets from the Pacific to the Atlantic Oceans via the Tethys Sea.

Tethys Ocean (Wiki)   


The Tethys Ocean (Greek: Τηθύς) was an ocean that existed between the
continents of Gondwana and Laurasia during the Mesozoic era before the opening of the Indian Ocean.

Gene Catalogue of the Amphioxus Nervous System (Wiki) 

Full length HTML available online for free. 
    "During the last decade, increasing information on the molecular aspects of amphioxus development has revealed a number of previously hidden features. One prominent example is the molecular regionalisation of the amphioxus nervous system ...
    In contrast with the anatomically non-regionalised central nervous system and the apparently disorganised peripheral nervous system, ... Most of the neural genes characterised to date reveal ... a well-controlled pre-patterning that defines distinct territories, not only within the neural ectoderm but also within the epidermis of amphioxus embryos.
    "Figure 1

    Morphological features of an adult amphioxus. Lateral view showing the internal anatomy and part of the overlying segmented muscle blocks (myomeres).
Int J Biol Sci ijbsv02p0149g01.jpg (Click on the image to enlarge.)
    "The cryptic internal segmentation of the amphioxus neural tube has been visualized by iterative gene expression patterns. As illustrative examples, AmphiKrox, shox, islet and AmphiMnx share a one somite-wide periodicity of expression throughout the neural tube. "

Phylogenetic position of a whale-fall lancelet (PubMed) 
Full length article available online for free.   
Our phylogenetic analyses showed that extant lancelets are clustered into two major clades, the Asymmetron clade and the Epigonichthys + Branchiostoma clade.  A. inferum was in the former and placed in the sister group to A. lucayanum complex. The divergence time between A. inferum and A. lucayanum complex was estimated to be 115 Mya using the penalized likelihood (PL) method or 97 Mya using the nonparametric rate smoothing (NPRS) method (the middle Cretaceous).

The amphioxus genome illuminates vertebrate origins and
cephalochordate biology 

Full length HTML available online for free. 
    "Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cephalochordate Branchiostoma floridae, commonly called amphioxus or lancelets. ... 
    The amphioxus genome contains a basic set of chordate genes involved in development and cell signaling, including a fifteenth Hox gene. This set includes many genes that were co-opted in vertebrates for new roles in neural crest development and adaptive immunity. However, where amphioxus has a single gene, vertebrates often have two, three, or four paralogs derived from two whole-genome duplication events. ...  
    The amphioxus genome also exhibits derived features, including duplications of opsins and genes proposed to function in innate immunity and endocrine systems.

    "There are many other homeobox genes beside Hox genes, and most have roles in development and cell differentiation... We identified a total of 133 homeobox genes in the draft genome sequence of B. floridae. ... a recent survey of the human genome, which revealed 235 human homeobox genes

    "The primary vertebrate endocrine organs (pineal gland, ovary, testis, endostyle/thyroid, brain, gut, and pituitary) have structurally simpler homologs in amphioxus.

Amphioxus has two genes for steroid receptors, one more closely related to vertebrate estrogen receptors (ER) and one closer to steroid receptors (SR), plus a complete set of genes for sex steroid-synthesizing enzymes: StAR, CYP11, CYP17, CYP19, 17βHSD, 3βHSD, and 5α-reductase (Supplemental Table S4)."  
Thus, except for the pituitary hormones, amphioxus has a relatively complete endocrine pathway for control of reproduction. It may be that neuroendocrine GnRH activates the gonads without pituitary amplification. Indirect support for this hypothesis is that in vertebrates, GnRH, when synthesized locally, can act directly on the gonads (Leung et al. 2003)."  
In summary, the cortisol pathway most likely did not exist in the ancestor of chordates, but an epinephrine stress response did."  
It is much more likely that the ancestral deuterostome was a free-living, bilateral, worm-like animal with a series of pharyngeal gill slits. Enteropneust hemichordates, amphioxus, and even vertebrates retain body plans comparable to this inferred ancestral deuterostome, albeit each with its own specializations, while the body plans of echinoderms and tunicates are considerably more derived."  
Also considered in:
Amphioxus Hormones Endostyle = Thyroid , Amphioxus Gut Hormones  . 

Gene duplication, co-option and recruitment during the origin of the vertebrate brain from the invertebrate chordate brain.   
    "The brain of the basal chordate amphioxus has been compared to the vertebrate diencephalic forebrain, midbrain, hindbrain and spinal cord on the basis of the cell architecture from serial electron micrographs and patterns of developmental gene expression. In addition, genes specifying the neural plate and neural plate border as well as Gbx and Otx, that position the midbrain/hindbrain boundary (MHB), are expressed in comparable patterns in amphioxus and vertebrates.
    However, migratory neural crest is lacking in amphioxus, and although it has homologs of the genes that specify neural crest, they are not expressed at the edges of the amphioxus neural plate. Similarly, amphioxus has the genes that specify organizer properties of the MHB, but they are not expressed at the Gbx/Otx boundary as in vertebrates. Thus, the genetic machinery that created migratory neural crest and an MHB organizer was present in the ancestral chordate, but only co-opted for these new roles in vertebrates. Analyses with the amphioxus genome project strongly support the idea of two rounds of whole genome duplication with subsequent gene losses in the vertebrate lineage. Duplicates of developmental genes were preferentially retained. Although some genes apparently acquired roles in neural crest prior to these genome duplications, other key genes (e.g., FoxD3 in neural crest and Wnt1 at the MHB) were recruited into the respective gene networks after one or both genome duplications, suggesting that such an expansion of the genetic toolkit was critical for the evolution of these structures. The toolkit has also increased by alternative splicing. ... The creation of new splice forms typically changes protein structure more than evolution of the protein after gene duplication.

Nocturnal Behavior and Rhythmic Period Gene Expression in a Lancelet, Branchiostoma lanceolatum  

    "The authors here present the first anatomical, molecular biological, and ethological data on the organization of the circadian system of a lancelet, Branchiostoma lanceolatum, a close invertebrate relative of vertebrates. B. lanceolatum was found to be a nocturnal animal and, since its rhythmic activity persisted under constant darkness, it also appears to possess an endogenous, circadian oscillator. The authors cloned a homolog of the clock gene Period (Per), which plays a central (inhibitory) role in the biochemical machinery of the circadian oscillators of both vertebrates and protostomians. This gene from B. lanceolatum was designated as amphiPer. Both the sequence of its cDNA and that of the predicted protein are more similar to those of the Per paralogs of vertebrates than to those of the single protostomian Per gene. A strong expression of amphiPer was found in a small cell group in the anterior neural tube. The amphiPer mRNA levels fluctuated in a rhythmic manner, being high early in the day and low late at night. The authors' data suggest a homology of the amphiPer expessing cells to the suprachiasmatic nucleus of vertebrates." 

The cholinergic gene locus in amphioxus: Molecular characterization and developmental expression patterns    
 Related articles         Free article
Free PDF on line.  Also discussed in Amphioxus Neurotransmitters , Ventral Motor Neurons and Dorsal Motor Neurons.   
    "... amphioxus homologs of two alternatively spliced transcripts of the cholinergic gene locus (CGL) termed VAChT (vesicular acetylcholine transporter) and ChAT (choline acetyltransferase)" 

The amphioxus genome and the evolution of the chordate karyotype (Goog)
Long, full length article available online for free. 
Here we report the draft genome sequence of the Florida lancelet and compare its structure with the genomes of other animals.

Nuclear hormone receptor signaling in amphioxus.     
Only abstract available online. 
there is usually one amphioxus nuclear hormone receptor (NR) or NR signaling coregulator for each paralogous group of two, three, or four human receptors suggesting that the ancestral chordate had a set of 22 different NRs plus one copy of each NR coregulator
    NOTE:  Searching PubMed for "amphioxus endocrine" yielded 42 hits, many of which were very interesting. 

2010    25<72   
"Insights of early chordate genomics: endocrinology and development in amphioxus, tunicates and lampreys": introduction to the symposium.  
This symposium focused on the evolution of chordate genomes, in particular, those events that occurred before the appearance of jawed vertebrates. The aim was to highlight insights that have come from the genome sequences of jawless chordates (lampreys, tunicates, and amphioxus) not only into evolution of chordate genomes, but also into the evolution of the organism."  
    Full-length text:   
The three subphyla of the phylum Chordata: Cephalochordata (amphioxus or lancelets), Tunicata (ascidians, appendicularians and thaliaceans), and Vertebrata (agnathans plus gnathostomes) radiated over 500 mya."  
Sequencing of the genome of the sea lamprey began in 2005 and that of the amphioxus genome in 2003. Both are essentially completed (; [Holland et al. 2008; Putnam et al. 2008])."  


A study of neural-related microRNAs in the developing amphioxus    
from the Abstract:       
MicroRNAs are small noncoding RNAs regulating expression of protein coding genes at post-transcriptional level and controlling several biological processes. At present microRNAs have been identified in various metazoans and seem also to be involved in brain development, neuronal differentiation and subtypes specification. An approach to better understand the role of microRNAs in animal gene expression is to determine temporal and tissue-specific expression patterns of microRNAs in different model organisms. Therefore, we have investigated the expression of six neural related microRNAs in amphioxus, an organism having an important phylogenetic position in terms of understanding the origin and evolution of chordates."  
In amphioxus, all the microRNAs we examined are expressed in specific regions of the CNS, and some of them are correlated with specific cell types. In addition, miR-7, miR-137 and miR-184 are also expressed in endodermal and mesodermal tissues. Several potential targets expressed in the nervous system of amphioxus have been identified by computational prediction and some of them are coexpressed with one or more miRNAs."  
We identified six miRNAs that are expressed in the nervous system of amphioxus in a variety of patterns. miR-124 is found in both differentiating and mature neurons, miR-9 in differentiated neurons, miR-7, miR-137 and miR-184 in restricted CNS regions, and miR-183 in cells of sensory organs. Therefore, such amphioxus miRNAs may play important roles in regional patterning and/or specification of neuronal cell types.