ArticleProceedings of the National Academy of Sciences of the United States of America2009
Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 82 citations in OpenAlex.
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- Identification of Cartilaginous Fish Endogenous Foamy Virus Rooting to Vertebrate Counterparts.Journal of virology · 2023Article
- Evolutionary divergence of a Hoxa2b hindbrain enhancer in syngnathids mimics results of functional assays.Development genes and evolution · 2021Article
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- An atlas of anterior hox gene expression in the embryonic sea lamprey head: Hox-code evolution in vertebrates.Developmental biology · 2019Article
- Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution.Scientific reports · 2019Article
- Evolution of dental tissue mineralization: an analysis of the jawed vertebrate SPARC and SPARC-L families.BMC evolutionary biology · 2018Article
- The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.Nature genetics · 2018Article
- Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828.BMC genomics · 2017Article
- Rab32 and Rab38 genes in chordate pigmentation: an evolutionary perspective.BMC evolutionary biology · 2016Article
- Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome.BMC genomics · 2015Article
- Enigmatic orthology relationships between Hox clusters of the African butterfly fish and other teleosts following ancient whole-genome duplication.Molecular biology and evolution · 2014Article
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- SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes.F1000Research · 2014Article
- Evidence for at least six Hox clusters in the Japanese lamprey (Lethenteron japonicum).Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Evolution of Hox gene clusters in deuterostomes.BMC developmental biology · 2013Review
- An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.Genome research · 2012Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have sequenced and analyzed Hox gene clusters from elephant shark, a holocephalian cartilaginous fish. Elephant shark possesses 4 Hox clusters with 45 Hox genes that include orthologs for a higher number of ancient gnathostome Hox genes than the 4 clusters in tetrapods and the supernumerary clusters in teleost fishes. Phylogenetic analysis of elephant shark Hox genes from 7 paralogous groups that contain all of the 4 members indicated an ((AB)(CD)) topology for the order of Hox cluster duplication, providing support for the 2R hypothesis (i.e., 2 rounds of whole-genome duplication during the early evolution of vertebrates). Comparisons of noncoding sequences of the elephant shark and human Hox clusters have identified a large number of conserved noncoding elements (CNEs), which represent putative cis-regulatory elements that may be involved in the regulation of Hox genes. Interestingly, in fugu more than 50% of these ancient CNEs have diverged beyond recognition in the duplicated (HoxA, HoxB, and HoxD) as well as the singleton (HoxC) Hox clusters. Furthermore, the b-paralogs of the duplicated fugu Hox clusters are virtually devoid of unique ancient CNEs. In contrast to fugu Hox clusters, elephant shark and human Hox clusters have lost fewer ancient CNEs. If these ancient CNEs are indeed enhancers directing tissue-specific expression of Hox genes, divergence of their sequences in vertebrate lineages might have led to altered expression patterns and presumably the functions of their associated Hox genes.
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