Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: A typical Hox structure for non-mammalian tetrapod vertebrates?

Stephen Randal Voss; Srikrishna Putta; John A. Walker; Jeramiah J. Smith; Nobuyasu Maki; Panagiotis A. Tsonis

doi:10.1186/1479-7364-7-9

Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: A typical Hox structure for non-mammalian tetrapod vertebrates?

Stephen Randal Voss, Srikrishna Putta, John A. Walker, Jeramiah J. Smith, Nobuyasu Maki, Panagiotis A. Tsonis

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Abstract

Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13-hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates.

Original language	English
Article number	9
Journal	Human Genomics
Volume	7
Issue number	1
DOIs	https://doi.org/10.1186/1479-7364-7-9
State	Published - 2013

Bibliographical note

Funding Information:
The research was supported by grant R24-OD010435 (SRV) and EY-10540 (PAT) from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). The project also used resources developed under Multidisciplinary University Research Initiative grant (W911NF-09-1-0305) from the Army Research Office (SRV) and resources from the Ambystoma Genetic Stock Center, which is funded by grant DBI-0951484 from the National Science Foundation (SRV). The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of NCRR, NIH, ARO, or NSF.

Keywords

Evolution
Genome
Hox
Salamander

ASJC Scopus subject areas

Molecular Medicine
Molecular Biology
Genetics
Drug Discovery

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10.1186/1479-7364-7-9

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title = "Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: A typical Hox structure for non-mammalian tetrapod vertebrates?",

abstract = "Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13-hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates.",

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note = "Funding Information: The research was supported by grant R24-OD010435 (SRV) and EY-10540 (PAT) from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). The project also used resources developed under Multidisciplinary University Research Initiative grant (W911NF-09-1-0305) from the Army Research Office (SRV) and resources from the Ambystoma Genetic Stock Center, which is funded by grant DBI-0951484 from the National Science Foundation (SRV). The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of NCRR, NIH, ARO, or NSF.",

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AU - Maki, Nobuyasu

AU - Tsonis, Panagiotis A.

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N2 - Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13-hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates.

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Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: A typical Hox structure for non-mammalian tetrapod vertebrates?

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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