Genomic Novelty at the Vertebrate Ancestor

Shigehiro Kuraku, Genome Resource and Analysis Unit, Center for Developmental Biology (CDB), RIKEN, Kobe, Japan

Published online: December 2012

DOI: 10.1002/9780470015902.a0024137

The group of vertebrates includes diverse evolutionary lineages, and typical laboratory-model vertebrates are confined to only limited groups (tetrapods and teleost fishes) of its entire diversity. Accumulating information of the molecular sequence for the still-missing lineages including jawless fishes can now provide deeper insights into the definition of the taxon Vertebrata at the genomic level. Above all, the so-called two-round whole genome duplications are described to have occurred in the early vertebrate evolution. Recent molecular phylogenetic analyses for some gene families resulted in a scenario in which the genome expansion might have been completed before the split of the lineage of cyclostomes (extant jawless fishes including hagfishes and lampreys) from the future jawed vertebrate lineage. In addition to this genome expansion, key features of genomic contents of the vertebrate ancestor are inferable, provided secondary changes introduced later in individual lineages are taken into deep consideration in ancestral phylogenetic reconstruction.

Key Concepts:

  • Large-scale sequencing of genomes and transcriptomes of non-model vertebrates in crucial phylogenetic positions provided valuable information about the vertebrates' entire diversity.
  • The two-round genome duplications likely define the vertebrates genomically.
  • De novo genes should also have contributed to the vertebrate gene repertoire.
  • Lineage-specific molecular changes should be taken into deep consideration in reconstructing the ancestral state as in morphological comparison.
  • Large-scale sequence resources for early branching vertebrates are expected to provide clearer insights into the genomics' novelty which established the vertebrates.

Keywords: vertebrate; lamprey; hagfish; genome duplication; endothelin

Figure 1. Alternative scenarios about the timing of the two-round whole genome duplications. The arrows indicate the timing of the whole genome duplications.
Figure 2. Identification of the genes involved in the endothelin system. Black vertical or diagonal lines indicate orthology between species. Identification of the genes in the lamprey and the cartilaginous fishes, as well as their nomenclature, is based on the author's previous study (Kuraku et al., 2010). Only the putative amphioxus ortholog of the endothelin receptors has been identified in its genome assembly and remains to be functionally characterised. Although the EdnrB2 is shown here as present in tetrapods, its ortholog was likely lost in the lineage leading to eutherian mammals (Braasch et al., 2009). The genes which were not identified within the taxonomic clades including species with sequenced genomes are indicated as ‘not found’. The node corresponding to the common ancestor of all extant vertebrates is shown with an open circle in the tree on the left.
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Related Sub-Topics:

Diversification of Plants and Animals | Evolution of Novelty | Macroevolution | Evolutionary Genomics
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Article Title: Genomic Novelty at the Vertebrate Ancestor
 
How to Cite close
Kuraku, Shigehiro(Dec 2012) Genomic Novelty at the Vertebrate Ancestor. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024137]