DOI: 10.5061/dryad.x95x69pwh
title: Data from: A phased chromosome-level genome of the annelid tubeworm <em>Galeolaria caespitosa</em>

description: Haplotype-resolved (phased) genome assemblies are emerging as important
 assets for genomic studies of species with high heterozygosity, but remain
 lacking for key animal lineages. Here, we use PacBio HiFi and Omni-C
 technologies to assemble the first phased, annotated, chromosome-level
 genome for any annelid: the reef-building tubeworm Galeolaria caespitosa
 (Serpulidae). The assembly is 803.5 Mbp long (scaffold N50 = 76.5 Mbp) for
 haplotype 1 and 789.3 Mbp long (scaffold N50 = 75.4 Mbp) for haplotype 2,
 which are arranged into 11 pairs of chromosomes showing no sign of sex
 chromosomes. This compares with cytological analyses reporting 12–13 pairs
 in G. caespitosa’s closest relatives, including species that are
 protandrous hermaphrodites. We combined long-read and short-read
 transcriptome sequencing to annotate both haplotypes, resulting in 30,495
 predicted proteins for haplotype 1, 27,423 proteins for haplotype two, and
 79.5% of proteins with at least one functional annotation. We also
 assembled a mitochondrial genome 23 Kbp long, annotating all genes
 typically found in mitochondrial DNA apart from those coding the 16S
 ribosomal subunit (rrnL) and the protein atp8 — a short, fast-evolving
 mitochondrial gene missing in other metazoans. Comparing G. caespitosa’s
 genome to those of three other annelids reveals limited collinearity
 despite 36.0% of shared orthologous gene clusters (4,238 of 11,763
 clusters counted in G. caespitosa), suggesting extensive chromosomal
 rearrangements among lineages. New high-quality annelid genomes may help
 resolve the genetic and evolutionary basis of this diversity.
description: # Data from: A phased chromosome-level genome of the annelid tubeworm
 *Galeolaria caespitosa* Dataset DOI:
 [10.5061/dryad.x95x69pwh](10.5061/dryad.x95x69pwh) ## Description of the
 Data Haplotype-resolved (phased) genome assemblies are emerging as
 important assets for genomic studies of species with high heterozygosity;
 however, they remain lacking for key animal lineages. Here, we use PacBio
 HiFi long-read sequencing and Omni-C scaffolding to assemble the first
 phased, annotated, chromosome-level genome for any annelid: the
 reef-building tubeworm *Galeolaria caespitosa* (Serpulidae). Assembly
 statistics: * Haplotype 1: 803.5 Mbp, scaffold N50 = 76.5 Mbp * Haplotype
 2: 789.3 Mbp, scaffold N50 = 75.4 Mbp Both haplotypes are arranged into 11
 pairs of chromosomes, with no evidence of sex chromosomes. Gene models
 were annotated using funannotate, integrating ab initio predictors,
 transcriptome alignments, and homology-based evidence (PFAM, InterPro,
 EggNog, COG). ## Files and variables ### Genome Assemblies #### File:
 Galeolaria_caespitosa_ChromAssemblyHap1_Mito.fasta.gz
 **Description:** Haplotype 1 assembly, this fasta file contains 11
 chromosomes (labeled chromosome_1 to chromosome_11), the mitochondrial
 genome (labeled mitochondrion), and 570 unplaced scaffolds (labelled
 scaffold_13 to scaffold_583). #### File:
 Galeolaria_caespitosa_ChromAssemblyHap2.fasta.gz
 **Description:** Haplotype 1 assembly, this fasta file contains 11
 chromosomes (labeled chromosome_1 to chromosome_11) and 278 unplaced
 scaffolds (labelled scaffold_12 to scaffold_289). Repeat regions are
 soft-masked in both assemblies. These data provide a chromosome-level,
 haplotype-resolved genomic resource for *Galeolaria caespitosa*, enabling
 studies in molecular ecology, adaptation, and genome evolution in
 annelids. ### Gene Annotations #### File:
 Galeolaria_caespitosa_H1_genome_annotation.gff3.gz
 **Description:** Annotation file for haplotype 1. #### File:
 Galeolaria_caespitosa_H2_genome_annotation.gff3.gz
 **Description:** Annotation file for haplotype 2. Annotation files
 include: * gene features (coordinates, identifiers, locus tags). * mRNA
 transcripts (with predicted products, GO terms, and database
 cross-references). * CDS coding sequence regions linked to predicted
 proteins. * protein_id, product, note, and Dbxref fields for functional
 interpretation. * Genes annotated as **“hypothetical protein”** lack
 strong functional assignments but were predicted based on gene structure
 evidence. Both files are in **GFF3 (General Feature Format version 3)**,
 which is a standardized format for describing genomic features. These
 files have 9 columns: Example Entry (from Hap1 annotation) ```
 chromosome_1 funannotate gene 310900 311955 . + . ID=galc_g2;
 locus_tag=ABL822_00002; gene=NACHRB1; ``` ``` chromosome_1 funannotate
 mRNA 310900 311955 . + . ID=galc_g2.t1; Parent=galc_g2;
 product=Neurotransmitter-gated ion-channel transmembrane region;
 Ontology_term=GO:0007268,GO:0042391;
 Dbxref=PFAM:PF02932,InterPro:IPR006029; ``` ``` chromosome_1 funannotate
 CDS 310900 311556 . + 0 ID=galc_g2.t1.cds1; Parent=galc_g2.t1;
 protein_id=t1.ABL822_00002; ``` ## Methods Summary We assembled the
 *Galeolaria caespitosa* genome from a wild male collected in Victoria,
 Australia. High-molecular-weight DNA was extracted from sperm and
 sequenced with **PacBio HiFi** (Sequel II) for contig generation, and an
 **Omni-C library** from muscle tissue was sequenced on the Illumina HiSeq
 X for scaffolding. ### Assembly * **Assembler:** HiFiasm v0.15.4 (Hi-C
 mode, phased assembly) * **Scaffolding:** YaHS v1.1 with Omni-C reads *
 **Quality control:** QUAST v5.0.2, BUSCO v5.1.3 (eukaryota_odb10), Merqury
 v1.3 * **Chromosome assignment:** chromatin contact maps (Juicebox
 v1.9.8), k-means clustering of scaffold lengths, and minimap2 alignments
 between haplotypes * **Final assembly:** 11 chromosome pairs, haplotype 1
 = 803.5 Mb (N50 = 76.5 Mb), haplotype 2 = 789.3 Mb (N50 = 75.4 Mb) ###
 Mitochondrial Genome Extracted from haplotype 1 with **MitoHiFi v3.2.1**,
 annotated with MITOS v2.1.0 and MitoFinder v1.4.0, and validated by
 comparison with other serpulid mitogenomes. ### Transcriptome Data *
 **Long-read Iso-Seq:** pooled adult and developmental samples, sequenced
 on PacBio Sequel IIe * **Short-read RNA-Seq:** 91 embryonic and larval
 samples sequenced on Illumina NovaSeq X Plus * **Pre-processing:** Iso-Seq
 reads processed with lima v2.9.0 and isoseq3 v4.0.0; RNA-Seq reads trimmed
 with fastp v0.20.0 ### Annotation * **Repeat modeling/masking:**
 RepeatModeler2 v2.0.5, RepeatMasker v4.1.1, ProtExcluder v1.2 * **Gene
 prediction:** BRAKER3 pipeline integrating RNA-Seq, Iso-Seq, and UniProtKB
 annelid proteins, plus GeneMarkS-T and TSEBRA for evidence integration *
 **Post-processing:** Conversion and cleaning with AGAT v1.0.0 and GFFtk
 v24.2.4; low-expression models filtered with edgeR * **Functional
 annotation:** InterProScan v5.61, EggNog-mapper v2.1.10, funannotate
 v1.8.14, Diamond-BLASTp v1.19, merged with gffutils v0.13 ## Code/software
 Code is available on GitHub:
 [https://github.com/moniquevdor/GaleolariaReferenceGenome](https://github.com/moniquevdor/GaleolariaReferenceGenome)