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

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

doi:10.1038/s41467-020-16801-9

Cited by 60 publications

(82 citation statements)

References 108 publications

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“…BUSCOs found in genomes obtained from previous studies [10,14,19,23,24,64,65,[104][105][106][107][108][109] were used to generate multiple alignments. Genes were aligned with mafft version 7.427 using the E-INS-i model and a maximum 1000 refinement iterations [22].…”

Section: Divergence Estimatesmentioning

confidence: 99%

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Zimmermann

Robb

Genikhovich

et al. 2020

Preprint

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Cnidaria (sea anemones, jellyfish, corals and hydra) form a close sister group to Bilateria. Within this clade, the sea anemone Nematostella vectensis has emerged as a slow evolving model for investigating characteristics of the cnidarian-bilaterian common ancestor, which diverged near the Cambrian explosion. Here, using long read sequencing and high throughput chromosome conformation capture, we generate high quality chromosome-level genome assemblies for N. vectensis and the closely related edwardsiid sea anemone, Scolanthus callimorphus. In both cases we find a robust set of 15 chromosomes comprising a stable linkage group detectable within all major clades of sequenced cnidarian genomes. Further, both genomes show remarkable chromosomal conservation with chordates. In contrast with Bilateria, we report that extended Hox and NK gene clusters are chromosomally linked but do not retain a tight spatial conservation. Accordingly, there is a lack of evidence for topologically associated domains, which have been implicated in the evolutionary pressure to retain tight microsyntenic gene clusters. We also uncover ultra-conserved noncoding elements at levels previously undetected in non-chordate lineages. Both genomes are accessible through an actively updated genome browser and database at https://simrbase.stowers.org

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Section: Divergence Estimatesmentioning

confidence: 99%

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Zimmermann

Robb

Genikhovich

et al. 2020

Preprint

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“…There are very few published studies of jellyfishes in Hong Kong (Lam et al 2014;Nong et al 2020). This observation highlighting the new record of A. shawi can help further improve the knowledge on the range of this species and encourage new studies that may attempt to describe the biology and ecology of this rare species.…”

Section: Introductionmentioning

confidence: 85%

Sighting of the rare jellyfish Anomalorhiza shawi Light, 1921 in a marine protected area of Hong Kong

Ricca¹,

Cheung²

2021

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Anomalorhiza shawi Light, 1921 is a species of rhizostome jellyfish (Cnidaria, Rhizostomeae), which is the most diverse order of scyphozoan jellyfishes. This species has rarely been observed, such that little information exists on its distribution or biology. We report a new sighting of A. shawi in the Hoi Ha Wan Marine Park of Hong Kong, which extends this species’ geographic distribution by 1,116 km northwards from Manila Bay, Philippines. We also highlight the value of community science platforms for species identification and range extension.

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“…Raw sequencing reads from 4 transcriptome datasets were downloaded from the Sequence Read Archive (SRA) (SRR7899951, SRR7899952, SRR7899953 and SRR7899954) for gene model prediction using Trimmomatic [ 50 ], Funannotate [ 51 ], Trinity [ 52 ] and PASA [ 53 ] as previously described procedures and parameters [ 41 , 54 ].…”

Section: Methodsmentioning

confidence: 99%

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

Nong

et al. 2020

BMC Genomics

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Background Teleost fish play important roles in aquatic ecosystems and aquaculture. Threadfins (Perciformes: Polynemidae) show a range of interesting biology, and are of considerable importance for both wild fisheries and aquaculture. Additionally, the four-finger threadfin Eleutheronema tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is classified as endangered. However, no genomic resources are currently available for the threadfin family Polynemidae. Results We sequenced and assembled the first threadfin fish genome, the four-finger threadfin E. tetradactylum. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date. Just 9.07–10.91% of the genome sequence was found to consist of repetitive elements (standard RepeatMasker analysis vs custom analysis), making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, and we include analyses of developmental transcription factors, including the Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. Conclusions The four-finger threadfin E. tetradactylum genome presented here represents the first available genome sequence for the ecologically, biologically, and commercially important clade of threadfin fish. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this valuable group of food fish.

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

Cited by 60 publications

References 108 publications

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Sighting of the rare jellyfish Anomalorhiza shawi Light, 1921 in a marine protected area of Hong Kong

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

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