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Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolve...

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Autores principales: Sun, Shao’e, Xiao, Ning, Sha, Zhongli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339218/
https://www.ncbi.nlm.nih.gov/pubmed/35919401
http://dx.doi.org/10.7717/peerj.13730
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author Sun, Shao’e
Xiao, Ning
Sha, Zhongli
author_facet Sun, Shao’e
Xiao, Ning
Sha, Zhongli
author_sort Sun, Shao’e
collection PubMed
description Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser(AGY) with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser(AGY). No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
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spelling pubmed-93392182022-08-01 Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea Sun, Shao’e Xiao, Ning Sha, Zhongli PeerJ Evolutionary Studies Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser(AGY) with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser(AGY). No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea. PeerJ Inc. 2022-07-28 /pmc/articles/PMC9339218/ /pubmed/35919401 http://dx.doi.org/10.7717/peerj.13730 Text en ©2022 Sun et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
Sun, Shao’e
Xiao, Ning
Sha, Zhongli
Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title_full Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title_fullStr Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title_full_unstemmed Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title_short Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
title_sort complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of echinoidea
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339218/
https://www.ncbi.nlm.nih.gov/pubmed/35919401
http://dx.doi.org/10.7717/peerj.13730
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