Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes

Kurosawa, Gene; Takamatsu, Naofumi; Takahashi, Masayoshi; Sumitomo, Mariko; Sanaka, Emi; Yamada, Kouji; Nishii, Kazuhiro; Matsuda, Masaru; Asakawa, Shuichi; Ishiguro, Hiroshi; Miura, Katsukiyo; Kurosawa, Yoshikazu; Shimizu, Nobuyoshi; Kohara, Yuji; Hori, Hiroshi

doi:10.1016/j.gene.2005.11.015

Cited by 50 publications

(44 citation statements)

References 25 publications

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“…As shown in Figure 2, the amphioxus Hox cluster is about four times larger than the respective human Hox clusters. This same trend holds for all of the vertebrates for which Hox cluster sequences have been obtained, including sharks (Kim et al, 2000;Venkatesh et al, 2007), various teleosts (Chiu et al, 2004;Kurosawa et al, 2006;Hoegg et al, 2007), and chicken (Richardson et al, 2007). Conversely, the amphioxus cluster is comparable in size with that of the sea urchin (558 kb; Cameron et al, 2006;vs. 448 kb in the sequenced region of amphioxus), whereas it is relatively compact in comparison with several protostome clusters (data compiled e.g.…”

Section: Isolation Sequencing and Characterizationmentioning

confidence: 52%

The amphioxus Hox cluster: characterization, comparative genomics, and evolution

Amemiya¹,

Prohaska²,

Hill-Force³

et al. 2008

J Exp Zool Pt B

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The amphioxus Hox cluster is often viewed as ''archetypal'' for the chordate lineage.Here, we present a descriptive account of the 448 kb region spanning the Hox cluster of the amphioxus Branchiostoma floridae from Hox14 to Hox1. We provide complete coding sequences of all 14 previously described amphioxus sequences and give a detailed analysis of the conserved noncoding regulatory sequence elements. We find that the posterior part of the Hox cluster is so highly derived that even the complete genomic sequence is insufficient to decide whether the posterior Hox genes arose by independent duplications or whether they are true orthologs of the corresponding gnathostome paralog groups. In contrast, the anterior region is much better conserved. The amphioxus Hox cluster strongly excludes repetitive elements with the exception of two repeat islands in the posterior region. Repeat exclusion is also observed in gnathostomes, but not protostome Hox clusters. We thus hypothesize that the much shorter vertebrate Hox clusters are the result of extensive resolution of the redundancy of regulatory DNA after the genome duplications rather than the consequence of a selection pressure to remove nonfunctional sequence from the Hox cluster.

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Section: Isolation Sequencing and Characterizationmentioning

confidence: 52%

The amphioxus Hox cluster: characterization, comparative genomics, and evolution

Amemiya¹,

Prohaska²,

Hill-Force³

et al. 2008

J Exp Zool Pt B

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“…Holland and Garcia-Fernandez, 1996), what could have been the adaptive value, for teleostei, to have twice as many Hox clusters as us? Here again, a closer look at the teleost Hox clusters reveals an unexpected picture, as illustrated by the zebrafish, Fugu and medaka genomes displaying similar global organizations (Kurosawa et al, 2006), although with some differences that are not relevant to this argument. In contrast to what is commonly believed, a comparison between zebrafish and murine Hox clusters at the same scale (Fig.…”

Section: The Teleost Alternativementioning

confidence: 94%

The rise and fall of Hox gene clusters

2007

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Although all bilaterian animals have a related set of Hox genes, the genomic organization of this gene complement comes in different flavors. In some unrelated species, Hox genes are clustered; in others, they are not. This indicates that the bilaterian ancestor had a clustered Hox gene family and that, subsequently, this genomic organization was either maintained or lost. Remarkably, the tightest organization is found in vertebrates, raising the embarrassingly finalistic possibility that vertebrates have maintained best this ancestral configuration. Alternatively, could they have co-evolved with an increased `organization' of the Hox clusters, possibly linked to their genomic amplification, which would be at odds with our current perception of evolutionary mechanisms? When discussing the why's and how's of Hox gene clustering, we need to account for three points: the mechanisms of cluster evolution; the underlying biological constraints; and the developmental modes of the animals under consideration. By integrating these parameters, general conclusions emerge that can help solve the aforementioned dilemma. “See my son, here time becomes space” Gurnemanz, in Parsifal (R. Wagner)

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“…In this regard, questions such as the characterization of evolutionary patterns after the FSGD including Hox gene retention/deletion, and evolution at the nucleotide level is of particular interest (Holland et al, '94;Malaga-Trillo and Meyer, 2001;Wagner et al, 2003;Prohaska and Stadler, 2004;Hoegg and Meyer, 2005;Crow et al, 2006;Kurosawa et al, 2006). Available DNA sequences from teleosts have shown a variety of gene retention and deletion patterns.…”

mentioning

confidence: 99%

PCR survey of hox genes in the goldfish Carassius auratus auratus

Luo

Stadler

et al. 2006

J Exp Zool Pt B

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A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.

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Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes

Cited by 50 publications

References 25 publications

The amphioxus Hox cluster: characterization, comparative genomics, and evolution

The amphioxus Hox cluster: characterization, comparative genomics, and evolution

The rise and fall of Hox gene clusters

PCR survey of hox genes in the goldfish Carassius auratus auratus

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