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

Abstract

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.

The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes

“…Bilaterians tend to have a similar split of their ANTP-class gene families across approximately four distinct chromosomes, consisting of the Hox cluster genes with a handful of HoxL genes on one chromosome, the NK cluster genes and a few NKL genes on another, with the ParaHox cluster and the NK2 genes on two further distinct chromosomes [ 18 , 19 , 31 – 33 ]. In contrast, some cnidarians have been found to have mixtures of a small number of Hox, HoxL, NK and NKL genes dispersed around their respective genomes [ 34 , 35 ] ( figure 2 ). To our surprise, we found the first case of the existence of the previously hypothetical mega-homeobox array of Hox cluster, HoxL, NK cluster and NKL genes in an extant species, on Actinernus chr 1 ( figure 2 ; electronic supplementary material, S6 and figures S7–S10).…”

“…Recently, genes for this pathway were unexpectedly revealed in jellyfish genomes [ 32 ]. Sesquiterpenoid hormone systems are now also known in other cnidarian genomes, and farnesoic acid has also been detected in jellyfish [ 34 , 35 , 38 ]. In the Actinernus sp.…”

“…MicroRNAs are 21–23 nucleotides small RNAs that play important post-transcriptional gene regulation roles in animals. Previous studies have shown that cnidarians and bilaterians only share one conserved microRNA (miR-100) between them [ 32 , 34 , 35 , 39 , 40 ]. We produced small RNA transcriptomes for Actinernus sp.…”

“…Potential homeobox genes were identified by searching with homeodomain sequences from N. vectensis [66], Branchiostoma floridae, Drosophila melanogaster (retrieved from HomeoDB2 [67] in the Actinernus sp. genome and previous published high-quality cnidarian genomes [14,31,32,34,35,57,[68][69][70][71][72][73]) using tBLASTN (electronic supplementary material, S4). NCBI CD-Search [74] was then used to validate the presence of homeodomains in the retrieved sequences.…”

Genome of elegance coral Catalaphyllia jardinei (Euphylliidae)

“…Homeobox genes are important developmental genes in animals and have been used as markers to understand genomic changes in animal evolution (e.g. Nong et al, 2020, Nong et al, 2021Li et al, 2020;So et al, 2022;Qu et al, 2020;Shum et al, 2022). A total of 93 ANTP-class homeobox genes have been identified in the C. jardinei genome, including clusters of Hox-like and NK-like genes, and a ParaHox gene cluster (Figure 3; Supplementary Information S5).…”