DOI: 10.5061/dryad.j0zpc86p9
title: Genome assemblies and gene models of of the zoantharians Palythoa mizigama and Palythoa umbrosa

description: Anthozoan hexacorals are an important animal group in many marine
 environments and include at least ~3,500 extant species. Zoantharia is an
 order among the Hexacorallia (Anthozoa: Cnidaria) and is a sister group to
 a clade consisting of four orders: Actiniaria, Antipatharia,
 Corallimorpharia, and Scleractinia. Previously reported genomes from
 scleractinian corals and actiniarian sea anemones have illuminated part of
 the hexacorallian diversification. However, little is known about
 zoantharian genomes and the early evolution of hexacorals. We generated
 two Palythoa genomes from the order Zoantharia within Hexacorallia,
 providing novel insights into early hexacorallian evolution by comparing
 with genomes of diversified scleractinian corals and actiniarian sea
 anemones. Draft genomes generated from ultra-low input PacBio sequencing
 totaled 373 Mbp and 319 Mbp for Palythoa mizigama (Pmiz) and
 Palythoa umbrosa (Pumb), respectively. 30,394 and 24,800 protein-coding
 genes were predicted in genomes of Pmiz and Pumb, respectively.
 Comparative genomic analyses identified 3,035 conserved gene families,
 which were found in all analyzed hexacoral genomes. Some of the genes
 related to toxins, chitin degradation, and prostaglandin biosynthesis were
 expanded in these two Palythoa genomes and many of which aligned tandemly.
 Extensive gene family loss was not detected in the Palythoa lineage and
 five of ten putatively lost gene families (GRIN1, TAAR7E, FEZF2, NRXN3,
 and SPATA7) likely had neuronal function, suggesting biased gene loss in
 Palythoa. These first available gene-sets (gene models) from zoantharians
 demonstrate genome conservation with restricted neuronal gene loss.
 Overall, our analyses imply that lineage-specific tandem duplication of
 enzyme genes have occurred in the genome evolution of Zoantharia.
description: <em>Sample collection</em> The two
 target species of the genus <em>Palythoa</em> (<em>P.
 mizigama</em> and <em>P. umbrosa</em>) were collected
 from different sites in southern Japan. <em>P. mizigama</em>
 was sampled at Mizugama, Okinawa Island, Okinawa, Japan on October 9,
 2023. The sampling location of <em>P. umbrosa</em> was at
 Nakano, Iriomote Island, Okinawa, Japan on September 16, 2023. Each
 <em>Palythoa </em>polyp was added into 50 mL tubes and they
 were chopped into small pieces with scissors. Fragmented tissues were put
 into 3.3x PBS and were kept for 30 min. By 5 min vortexing during this
 period, we dissociated the tissue into individual cells. Dissociated cells
 were centrifuged at 1,000 g for 5 min. After discarding the supernatant,
 they were quickly frozen in liquid nitrogen and were kept in a -80 °C
 freezer until processing. <em>DNA isolation and
 sequencing</em> High molecular weight DNAs from
 dissociated cells were extracted using innuPREP Plant DNA Kit I (Analytik
 Jena AG, Germany) following the manufacturer’s protocol. Sequencing
 libraries from the genomic DNAs of each species were constructed according
 to HiFi Ultra-Low Input DNA protocol from Pacific Bioscience (Menlo Park,
 California, USA). The library construction included a whole-genome
 amplification step by PCR methods (Schneider et al. 2021) and some
 amplification bias may be caused. Sequencing was performed on the PacBio
 Sequel II systems (Pacific Bioscience, Menlo Park, CA, USA) using two SMRT
 (Single Molecule Real-Time) cells for each species.
 <em>Genome assembly and gene
 prediction</em> The mitochondrial genomes were
 first assembled from the HiFi reads with MitoHiFi pipeline v3.2.1
 (Uliano-Silva et al. 2023). HiFi reads that mapped to the mitochondrial
 genomes were removed from further steps. HiFi reads possibly originating
 from archaea, bacteria, viral, plasmid, and UniVec Core were identified
 with KRAKEN2 v2.1.3 (Wood et al. 2019) and its standard database (January
 2024 update) and were also removed from further steps. Prior to nuclear
 genome assembly, the k-mer profile (k=41 and 61) was performed with Meryl
 v1.4.1 (Rhie et al. 2020) and was used for genome size estimation with
 GenomeScope v2.0 (Ranallo-Benavidez et al. 2020). Contaminants- and
 mitochondrial-free HiFi reads were then assembled with Hifiasm
 v0.19.8-r603 (Cheng et al. 2021). Primary contigs assembled with Hifiasm
 were used for further analyses. Error-correction of the assembly was
 performed using Inspector v1.0.1 (Chen et al. 2021) with cleaned HiFi
 reads. Possible haplotypes were merged with HaploMerger2 v20180603 (Huang
 et al. 2017). This haplotype merging step was repeated for several times
 together with error collection using Inspector. Repetitive elements in the
 assembly were identified <em>de novo</em> with RepeatModeler
 v2.0.4 (Flynn et al. 2020) with option (-LTRStruct). Repeats identified
 <em>de novo</em> and known repeats in RepeatMasker database
 were concatenated and were soft-masked using RepeatMasker v4.1.5 (Smit et
 al. 2015). Simple tandem repeat detection was further performed by tantan
 v49 (Frith 2011). BUSCO completeness of the genome assembly was assessed
 with compleasm v0.2.5 (Huang and Li 2023) and “metazoa_odb10” database
 (n=954). To evaluate sequencing depth, cleaned HiFi reads were mapped to
 contigs with Minimap2 v2.26-r1175 and mean depth for each contig was
 calculated with BamDeal v0.27
 (https://github.com/BGI-shenzhen/BamDeal?tab=readme-ov-file). GC content
 for each contig was calculated with SeqKit v2.8.0 (Shen et al. 2016).
 These were visualized using the “ggplot2” package (Ginestet 2011) in R
 v4.3.2 (R Foundation for Statistical Computing 2018).
 Gene prediction was performed with BRAKER pipeline v3.0.8 (Hoff
 et al. 2019; Gabriel et al. 2021; Bruna et al. 2023). Softmasked genome
 and proteomes retrieved from OrthoDB v11 (metazoa) and proteomes from
 selected cnidarians registered in RefSeq ranging five orders were used as
 input in the pipeline. Gene with length larger than 100 bp were retained.
 Each gene was named ‘g’ plus a number from one end of each contig, e.g.,
 c0001.g001 is the first gene of contig c0001. Gene models were assessed
 using BUSCO v5.7.0 (Manni et al. 2021) with “metazoa_odb10” database
 (2024-01-08, n=954). To ensure that no possible contamination was
 included, gene models were also assessed by OMArk v0.3.0 (Nevers et al.
 2024) with OMAmer “Metazoa v2.0.0” database (n=3,244). Functional
 annotation of gene models were performed with BLASTP (E-value cutoff:
 1e-3) (Camacho et al. 2009) against the Swiss-Prot database (7 June
 2023).
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description: # Genome assemblies and gene models of of the zoantharians Palythoa
 mizigama and Palythoa umbrosa
 [https://doi.org/10.5061/dryad.j0zpc86p9](https://doi.org/10.5061/dryad.j0zpc86p9) We have submitted the genome assemblies and gene models of two *palythoa* (*P. mizigama and P. umbrosa)* as the following 8 files. Genome assembly of the zoantharian *Palythoa mizigama* in FASTA format File name: **Pmiz_final.hm11.contigs.20240419.fa.gz** Gene models of the zoantharian *Palythoa mizigama* in General Transfer Format (GTF) File name: **Pmiz_final.hm11.20240419.gtf.gz** mRNA sequences of protein-coding genes of the zoantharian *Palythoa mizigama* in FASTA format File name: **Pmiz_final.hm11.transcript.20240419.fa.gz** Amino acid sequences of protein-coding genes of the zoantharian *Palythoa mizigama* in FASTA format File name: **Pmiz_final.protein.20240419.fa.gz** Genome assembly of the zoantharian *Palythoa umbrosa* in FASTA format File name: **Pumb_final.hm11.contigs.20240419.fa.gz** Gene models of the zoantharian *Palythoa umbrosa* in General Transfer Format (GTF) File name: **Pumb_final.hm11.20240419.gtf.gz** mRNA sequences of protein-coding genes of the zoantharian *Palythoa umbrosa* in FASTA format File name: **Pumb_final.hm11.transcript.20240419.fa.gz** Amino acid sequences of protein-coding genes of the zoantharian *Palythoa umbrosa* in FASTA format File name: **Pumb_final.protein.longest.20240419.fa.gz** **Sharing/Access information** Raw genomic DNA sequence data of *Palythoa mizigama* and *Palythoa umbrosa* have been submitted at DDBJ Sequence Read Archive (DRA) under the accession DRR546399-DRR546402 (BioProjectID: PRJDB18008), respectively. Mitochondrial and genomic assemblies have been deposited at DDBJ under the accession AP031564, AP031565, BAACCD010000001-BAACCD010004032, and BAACCE010000001-BAACCE010002838.