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Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration

Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assemble...

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Autores principales: Shum, Cheryl W.Y., Nong, Wenyan, So, Wai Lok, Li, Yiqian, Qu, Zhe, Yip, Ho Yin, Swale, Thomas, Ang, Put O., Chan, King Ming, Chan, Ting Fung, Chu, Ka Hou, Chui, Apple P.Y., Lau, Kwok Fai, Ngai, Sai Ming, Xu, Fei, Hui, Jerome H.L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9444052/
https://www.ncbi.nlm.nih.gov/pubmed/36072338
http://dx.doi.org/10.3389/fcell.2022.900321
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author Shum, Cheryl W.Y.
Nong, Wenyan
So, Wai Lok
Li, Yiqian
Qu, Zhe
Yip, Ho Yin
Swale, Thomas
Ang, Put O.
Chan, King Ming
Chan, Ting Fung
Chu, Ka Hou
Chui, Apple P.Y.
Lau, Kwok Fai
Ngai, Sai Ming
Xu, Fei
Hui, Jerome H.L.
author_facet Shum, Cheryl W.Y.
Nong, Wenyan
So, Wai Lok
Li, Yiqian
Qu, Zhe
Yip, Ho Yin
Swale, Thomas
Ang, Put O.
Chan, King Ming
Chan, Ting Fung
Chu, Ka Hou
Chui, Apple P.Y.
Lau, Kwok Fai
Ngai, Sai Ming
Xu, Fei
Hui, Jerome H.L.
author_sort Shum, Cheryl W.Y.
collection PubMed
description Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.
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spelling pubmed-94440522022-09-06 Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration Shum, Cheryl W.Y. Nong, Wenyan So, Wai Lok Li, Yiqian Qu, Zhe Yip, Ho Yin Swale, Thomas Ang, Put O. Chan, King Ming Chan, Ting Fung Chu, Ka Hou Chui, Apple P.Y. Lau, Kwok Fai Ngai, Sai Ming Xu, Fei Hui, Jerome H.L. Front Cell Dev Biol Cell and Developmental Biology Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals. Frontiers Media S.A. 2022-08-17 /pmc/articles/PMC9444052/ /pubmed/36072338 http://dx.doi.org/10.3389/fcell.2022.900321 Text en Copyright © 2022 Shum, Nong, So, Li, Qu, Yip, Swale, Ang, Chan, Chan, Chu, Chui, Lau, Ngai, Xu and Hui. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cell and Developmental Biology
Shum, Cheryl W.Y.
Nong, Wenyan
So, Wai Lok
Li, Yiqian
Qu, Zhe
Yip, Ho Yin
Swale, Thomas
Ang, Put O.
Chan, King Ming
Chan, Ting Fung
Chu, Ka Hou
Chui, Apple P.Y.
Lau, Kwok Fai
Ngai, Sai Ming
Xu, Fei
Hui, Jerome H.L.
Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title_full Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title_fullStr Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title_full_unstemmed Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title_short Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration
title_sort genome of the sea anemone exaiptasia pallida and transcriptome profiles during tentacle regeneration
topic Cell and Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9444052/
https://www.ncbi.nlm.nih.gov/pubmed/36072338
http://dx.doi.org/10.3389/fcell.2022.900321
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