Chordate genomics is the study of the evolution of the

chordate A chordate () is an animal of the phylum Chordata (). All chordates possess, at some point during their larval or adult stages, five synapomorphies, or primary physical characteristics, that distinguish them from all the other taxa. These fiv ...

clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...

based on a comparison of the

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...

s of several

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

within the clade. The field depends on whole genome data (the entire

DNA sequence DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...

) of organisms. It uses comparisons of

synteny In genetics, the term synteny refers to two related concepts: * In classical genetics, ''synteny'' describes the physical co-localization of genetic loci on the same chromosome within an individual or species. * In current biology, ''synteny'' mo ...

blocks, chromosome translocation, and other genomic rearrangements to determine the evolutionary history of the clade, and to reconstruct the genome of the founding species.

Results

Phylogeny

The deep branching of chordate

phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

has been clarified by chordate genomics. Chordate genomics demonstrates that the

Lancelet The lancelets ( or ), also known as amphioxi (singular: amphioxus ), consist of some 30 to 35 species of "fish-like" benthic filter feeding chordates in the order Amphioxiformes. They are the modern representatives of the subphylum Cephalochorda ...

s are the most basal living clade within the chordates, while the

Tunicates A tunicate is a marine invertebrate animal, a member of the subphylum Tunicata (). It is part of the Chordata, a phylum which includes all animals with dorsal nerve cords and notochords (including vertebrates). The subphylum was at one time ca ...

are the sister clade to the

Craniata A craniate is a member of the Craniata (sometimes called the Craniota), a proposed clade of chordate animals with a skull of hard bone or cartilage. Living representatives are the Myxini (hagfishes), Hyperoartia (including lampreys), and the muc ...

Synteny

A comparison of the genomes of the Lancelet ''Branchiostoma floridae'', a

fish Fish are aquatic, craniate, gill-bearing animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish as well as various extinct related groups. Approximately 95% of li ...

, the

chicken The chicken (''Gallus gallus domesticus'') is a domesticated junglefowl species, with attributes of wild species such as the grey and the Ceylon junglefowl that are originally from Southeastern Asia. Rooster or cock is a term for an adult m ...

''Gallus gallus'', and

humans Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

''Homo sapiens'' revealed extensive macro-

with little or no micro-synteny. That is, across the Chordate clade the same genes are found clustered near each other although the order of the genes within the clusters has been shuffled. There are 135 identifiable segments in the human genome which retain synteny with the ancestral chordate

karyotype A karyotype is the general appearance of the complete set of metaphase chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is disce ...

. Synteny analysis indicates that there were 17 chromosomes in the last common ancestor to the Chordates.

Genome Duplication

Multiple lines of experimental evidence strongly suggest that twice in the lineage leading to the

teleost Teleostei (; Greek ''teleios'' "complete" + ''osteon'' "bone"), members of which are known as teleosts ), is, by far, the largest infraclass in the class Actinopterygii, the ray-finned fishes, containing 96% of all extant species of fish. Tel ...

the ancestral Chordate genome was duplicated. A comparison of the genomes of the Lancelet ''Branchiostoma floridae'', the Tunicates ''Ciona intestinalis'' and ''Oikopleura dioica'', the

lamprey Lampreys (sometimes inaccurately called lamprey eels) are an ancient extant lineage of jawless fish of the order Petromyzontiformes , placed in the superclass Cyclostomata. The adult lamprey may be characterized by a toothed, funnel-like s ...

''Petromyzon marinus'', the

''Fugu rubripes'' and ''Gasterosteus aculeatus'', the

''Gallus gallus'', and

human Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

''Homo sapiens'' confirmed that two whole-genome duplications occurred in the early history of the

Vertebrata Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, ...

clade."The amphioxus genome and the evolution of the chordate karyotype." Nicholas H. Putnam, ''et al.'' ''Nature'' 453 1064-1071, (2008)

References

Genomics {{genetics-stub