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The genome of common long-arm octopus Octopus minor

BACKGROUND: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic...

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Autores principales: Kim, Bo-Mi, Kang, Seunghyun, Ahn, Do-Hwan, Jung, Seung-Hyun, Rhee, Hwanseok, Yoo, Jong Su, Lee, Jong-Eun, Lee, SeungJae, Han, Yong-Hee, Ryu, Kyoung-Bin, Cho, Sung-Jin, Park, Hyun, An, Hye Suck
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279123/
https://www.ncbi.nlm.nih.gov/pubmed/30256935
http://dx.doi.org/10.1093/gigascience/giy119
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author Kim, Bo-Mi
Kang, Seunghyun
Ahn, Do-Hwan
Jung, Seung-Hyun
Rhee, Hwanseok
Yoo, Jong Su
Lee, Jong-Eun
Lee, SeungJae
Han, Yong-Hee
Ryu, Kyoung-Bin
Cho, Sung-Jin
Park, Hyun
An, Hye Suck
author_facet Kim, Bo-Mi
Kang, Seunghyun
Ahn, Do-Hwan
Jung, Seung-Hyun
Rhee, Hwanseok
Yoo, Jong Su
Lee, Jong-Eun
Lee, SeungJae
Han, Yong-Hee
Ryu, Kyoung-Bin
Cho, Sung-Jin
Park, Hyun
An, Hye Suck
author_sort Kim, Bo-Mi
collection PubMed
description BACKGROUND: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. FINDINGS: The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. CONCLUSIONS: We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.
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spelling pubmed-62791232018-12-06 The genome of common long-arm octopus Octopus minor Kim, Bo-Mi Kang, Seunghyun Ahn, Do-Hwan Jung, Seung-Hyun Rhee, Hwanseok Yoo, Jong Su Lee, Jong-Eun Lee, SeungJae Han, Yong-Hee Ryu, Kyoung-Bin Cho, Sung-Jin Park, Hyun An, Hye Suck Gigascience Data Note BACKGROUND: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. FINDINGS: The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. CONCLUSIONS: We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats. Oxford University Press 2018-09-25 /pmc/articles/PMC6279123/ /pubmed/30256935 http://dx.doi.org/10.1093/gigascience/giy119 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Data Note
Kim, Bo-Mi
Kang, Seunghyun
Ahn, Do-Hwan
Jung, Seung-Hyun
Rhee, Hwanseok
Yoo, Jong Su
Lee, Jong-Eun
Lee, SeungJae
Han, Yong-Hee
Ryu, Kyoung-Bin
Cho, Sung-Jin
Park, Hyun
An, Hye Suck
The genome of common long-arm octopus Octopus minor
title The genome of common long-arm octopus Octopus minor
title_full The genome of common long-arm octopus Octopus minor
title_fullStr The genome of common long-arm octopus Octopus minor
title_full_unstemmed The genome of common long-arm octopus Octopus minor
title_short The genome of common long-arm octopus Octopus minor
title_sort genome of common long-arm octopus octopus minor
topic Data Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279123/
https://www.ncbi.nlm.nih.gov/pubmed/30256935
http://dx.doi.org/10.1093/gigascience/giy119
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