The genome sequence of an erect bryozoan, Bugulina stolonifera (Ryland, 1960)

We present a genome assembly from a Bugulina stolonifera colony (an erect bryozoan; Bryozoa; Gymnolaemata; Cheilostomatida; Bugulidae). The genome sequence is 235 megabases in span. Most of the assembly (99.85%) is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 14.4 kilobases long.


Background
Bugulina stolonifera (formerly known as Bugula stolonifera -see (Fehlauer-Ale et al., 2015) is characteristically found in artificial habitats such as harbours and marinas. Although described in 1960 from South Wales (UK), the species is considered native to the NW Atlantic (McCann et al., 2019). It is widely introduced as a fouling species in the Pacific and SW Atlantic, in Europe (including the Mediterranean), and in Australia and New Zealand (Fofonoff et al., 2018).
This lightly calcified bryozoan grows upwards into a flexible bush-like colony up to 40 mm tall, with narrow branches of just two rows of zooids side-by-side. Rhizoids (stolons) growing out across the substrate from the colony base can bud to give rise to satellite upright colonies. Sexual reproduction involves the brooding of embryos that are released as non-feeding (lecithotrophic) ciliated larvae.
As with many bryozoans, the zooids (the clonal modular individuals of the colony) occur in a variety of morphologies with different particular functions in the life of the colony. In Bugulina, these polymorphs include feeding zooids (autozooids), putatively defensive, non-feeding zooids (avicularia) and zooids attaching the colony to the substrate (rhizoids, a type of kenozooid). B. stolonifera can be cultured in the lab, which has allowed comparison of the transcriptomes of these different types of zooid to identify genes that are differentially expressed during the budding and maintenance of the various polymorphs (Treibergs & Giribet, 2020). Over 1000 genes were identified that were expressed differentially between the autozooids and the avicularia.

Genome sequence report
The genome was sequenced from a specimen of B. stolonifera ( Figure 1) collected from Queen Anne's Battery Marina visitors' pontoon in Plymouth (latitude 50.36, longitude -4.13). A total of 52-fold coverage in Pacific Biosciences singlemolecule HiFi long reads and 99-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 17 missing/misjoins and removed four haplotypic duplications, reducing the assembly length by 2.34% and the scaffold number by 16.67%, and increasing the scaffold N50 by 3.71%.
The final assembly has a total length of 235 Mb in 30 sequence scaffolds with a scaffold N50 of 20 Mb (Table 1). Most (99.85%) of the assembly sequence was assigned to 11 chromosomal-level scaffolds (Figure 2- Figure 5; Table 2). Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size. A heterozygous inversion was observed on chromosome 5 (7.9-9.1 Mb). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.
The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 84.1% (single 83.1% and duplicated 0.9%) using the OrthoDB-v10 metazoa reference set. Although BUSCO coverage falls below the benchmark of 95%, the assembly is validated by high k mer coverage and consensus quality QV scores (Table 1).

Sample acquisition and nucleic acid extraction
A colony of B. stolonifera (tzBugStol2) was collected from Queen Anne's Battery Marina visitors' pontoon, Plymouth, Devon, UK (latitude 50.36, longitude -4.13). The specimen was collected by hand from submerged rope on the marina pontoon and then preserved in liquid nitrogen. The collectors      Table 3 contains a list of all software tool versions used, where appropriate.

Ethics/compliance issues
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format? Yes