Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles.
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| Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Artículo científico |
| Lenguaje: | en |
| Publicado: |
Molecular biology and evolution
2024
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| author | Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun |
| author_facet | Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun |
| collection | PubMed - marine biology |
| contents | Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles. Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun Animals Extremities Amphibians Reptiles Regulatory Sequences, Nucleic Acid Biological Evolution Evolution, Molecular Phylogeny Limbs are a defining characteristic of tetrapods, yet numerous taxa, primarily among amphibians and reptiles, have independently lost limbs as an adaptation to new ecological niches. To elucidate the genetic factors contributing to this convergent limb loss, we present a 12 Gb chromosome-level assembly of the Banna caecilian (Ichthyophis bannanicus), a limbless amphibian. Our comparative analysis, which includes the reconstruction of amphibian karyotype evolution, reveals constrained gene length evolution in a subset of developmental genes across 3 large genomes. Investigation of limb development genes uncovered the loss of Grem1 in caecilians and Tulp3 in snakes. Interestingly, caecilians and snakes share a significantly larger number of convergent degenerated conserved noncoding elements than limbless lizards, which have a shorter evolutionary history of limb loss. These convergent degenerated conserved noncoding elements overlap significantly with active genomic regions during mouse limb development and are conserved in limbed species, suggesting their essential role in limb patterning in the tetrapod common ancestor. While most convergent degenerated conserved noncoding elements emerged in the jawed vertebrate ancestor, coinciding with the origin of paired appendage, more recent degenerated conserved noncoding elements also contribute to limb development, as demonstrated through functional experiments. Our study provides novel insights into the regulatory elements associated with limb development and loss, offering an evolutionary perspective on the genetic basis of morphological specialization. |
| format | Artículo científico |
| id | pubmed_39530343 |
| institution | PubMed |
| language | en |
| publishDate | 2024 |
| publisher | Molecular biology and evolution |
| record_format | pubmed |
| spellingShingle | Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles. Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun Animals Extremities Amphibians Reptiles Regulatory Sequences, Nucleic Acid Biological Evolution Evolution, Molecular Phylogeny Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles. Zhu, Chenglong Li, Shengyou Zhang, Daizhen Zhang, Jinjin Wang, Gang Zhou, Botong Zheng, Jiangmin Xu, Wenjie Wang, Zhengfei Gao, Xueli Liu, Qiuning Xue, Tingfeng Zhang, Huabin Li, Chunhui Ge, Baoming Liu, Yuxuan Qiu, Qiang Zhang, Huixian Huang, Jinghui Tang, Boping Wang, Kun Animals Extremities Amphibians Reptiles Regulatory Sequences, Nucleic Acid Biological Evolution Evolution, Molecular Phylogeny Limbs are a defining characteristic of tetrapods, yet numerous taxa, primarily among amphibians and reptiles, have independently lost limbs as an adaptation to new ecological niches. To elucidate the genetic factors contributing to this convergent limb loss, we present a 12 Gb chromosome-level assembly of the Banna caecilian (Ichthyophis bannanicus), a limbless amphibian. Our comparative analysis, which includes the reconstruction of amphibian karyotype evolution, reveals constrained gene length evolution in a subset of developmental genes across 3 large genomes. Investigation of limb development genes uncovered the loss of Grem1 in caecilians and Tulp3 in snakes. Interestingly, caecilians and snakes share a significantly larger number of convergent degenerated conserved noncoding elements than limbless lizards, which have a shorter evolutionary history of limb loss. These convergent degenerated conserved noncoding elements overlap significantly with active genomic regions during mouse limb development and are conserved in limbed species, suggesting their essential role in limb patterning in the tetrapod common ancestor. While most convergent degenerated conserved noncoding elements emerged in the jawed vertebrate ancestor, coinciding with the origin of paired appendage, more recent degenerated conserved noncoding elements also contribute to limb development, as demonstrated through functional experiments. Our study provides novel insights into the regulatory elements associated with limb development and loss, offering an evolutionary perspective on the genetic basis of morphological specialization. |
| title | Convergent Degenerated Regulatory Elements Associated with Limb Loss in Limbless Amphibians and Reptiles. |
| topic | Animals Extremities Amphibians Reptiles Regulatory Sequences, Nucleic Acid Biological Evolution Evolution, Molecular Phylogeny |
| url | https://pubmed.ncbi.nlm.nih.gov/39530343/ |