Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Wenyan Nong; Jianquan Cao; Yiqian Li; Zhe Qu; Jin Sun; Thomas Swale; Ho Yin Yip; Pei Yuan Qian; Jianwen Qiu; Hoi Shan Kwan; William Bendena; Stephen Tobe; Ting Fung Chan; Kevin Y. Yip; Ka Hou Chu; Sai Ming Ngai; Karl Yk Tsim; Peter W.H. Holland; Jerome H.L. Hui

doi:10.1038/s41467-020-16801-9

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Wenyan Nong, Jianquan Cao, Yiqian Li, Zhe Qu, Jin Sun, Thomas Swale, Ho Yin Yip, Pei Yuan Qian, Jianwen Qiu, Hoi Shan Kwan, William Bendena, Stephen Tobe, Ting Fung Chan, Kevin Y. Yip, Ka Hou Chu, Sai Ming Ngai, Karl Yk Tsim, Peter W.H. Holland^*, Jerome H.L. Hui^*

^*Corresponding author for this work

Department of Biology

Research output: Contribution to journal › Journal article › peer-review

47 Citations (Scopus)

Abstract

The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.

Original language	English
Article number	3051
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-16801-9
Publication status	Published - 1 Dec 2020

Scopus Subject Areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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Nong, W., Cao, J., Li, Y., Qu, Z., Sun, J., Swale, T., Yip, H. Y., Qian, P. Y., Qiu, J., Kwan, H. S., Bendena, W., Tobe, S., Chan, T. F., Yip, K. Y., Chu, K. H., Ngai, S. M., Tsim, K. Y., Holland, P. W. H., & Hui, J. H. L. (2020). Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing. Nature Communications, 11(1), Article 3051. https://doi.org/10.1038/s41467-020-16801-9

@article{e5e42e14395441cf9b080af6cd44222b,

title = "Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing",

abstract = "The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.",

author = "Wenyan Nong and Jianquan Cao and Yiqian Li and Zhe Qu and Jin Sun and Thomas Swale and Yip, {Ho Yin} and Qian, {Pei Yuan} and Jianwen Qiu and Kwan, {Hoi Shan} and William Bendena and Stephen Tobe and Chan, {Ting Fung} and Yip, {Kevin Y.} and Chu, {Ka Hou} and Ngai, {Sai Ming} and Tsim, {Karl Yk} and Holland, {Peter W.H.} and Hui, {Jerome H.L.}",

note = "Funding Information: This work was supported by the TUYF Charitable Trust (Grant number: 6903956), Hong Kong Research Grants Council (RGC) General Research Fund (GRF) (14103516, 14100919), and The Chinese University of Hong Kong (CUHK) Direct Grant (BL13937/ 4053043) to JHLH. We would like to thank Suzanne Gendron and the Aquarium Department of the Ocean Park Hong Kong and other local companies for specimens and photographs; and C.K. Cheung, W.C. Yiu, and A. Leung for help with the extraction of samples.",

year = "2020",

month = dec,

day = "1",

doi = "10.1038/s41467-020-16801-9",

language = "English",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

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Nong, W, Cao, J, Li, Y, Qu, Z, Sun, J, Swale, T, Yip, HY, Qian, PY, Qiu, J, Kwan, HS, Bendena, W, Tobe, S, Chan, TF, Yip, KY, Chu, KH, Ngai, SM, Tsim, KY, Holland, PWH & Hui, JHL 2020, 'Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing', Nature Communications, vol. 11, no. 1, 3051. https://doi.org/10.1038/s41467-020-16801-9

TY - JOUR

T1 - Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

AU - Nong, Wenyan

AU - Cao, Jianquan

AU - Li, Yiqian

AU - Qu, Zhe

AU - Sun, Jin

AU - Swale, Thomas

AU - Yip, Ho Yin

AU - Qian, Pei Yuan

AU - Qiu, Jianwen

AU - Kwan, Hoi Shan

AU - Bendena, William

AU - Tobe, Stephen

AU - Chan, Ting Fung

AU - Yip, Kevin Y.

AU - Chu, Ka Hou

AU - Ngai, Sai Ming

AU - Tsim, Karl Yk

AU - Holland, Peter W.H.

AU - Hui, Jerome H.L.

N1 - Funding Information: This work was supported by the TUYF Charitable Trust (Grant number: 6903956), Hong Kong Research Grants Council (RGC) General Research Fund (GRF) (14103516, 14100919), and The Chinese University of Hong Kong (CUHK) Direct Grant (BL13937/ 4053043) to JHLH. We would like to thank Suzanne Gendron and the Aquarium Department of the Ocean Park Hong Kong and other local companies for specimens and photographs; and C.K. Cheung, W.C. Yiu, and A. Leung for help with the extraction of samples.

PY - 2020/12/1

Y1 - 2020/12/1

N2 - The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.

AB - The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.

UR - http://www.scopus.com/inward/record.url?scp=85086671021&partnerID=8YFLogxK

U2 - 10.1038/s41467-020-16801-9

DO - 10.1038/s41467-020-16801-9

M3 - Journal article

C2 - 32561724

AN - SCOPUS:85086671021

SN - 2041-1723

VL - 11

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 3051

ER -

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

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