The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences

Manuel Maldonado; Lucia Pita; Ute Hentschel; Dirk Erpenbeck; Graeme Oatley; Elizabeth Sinclair; Eerik Aunin; Noah Gettle; Camilla Santos; Michael Paulini; Haoyu Niu; Victoria McKenna; Rebecca O'Brien; Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Wellcome Sanger Institute Tree of Life Core Informatics Team; EBI Aquatic Symbiosis Genomics Data Portal Team; Aquatic Symbiosis Genomics Project Leadership

doi:10.12688/wellcomeopenres.24154.1

The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences

Wellcome Open Res. 2025 May 23:10:275. doi: 10.12688/wellcomeopenres.24154.1. eCollection 2025.

Authors

Manuel Maldonado¹, Lucia Pita^{2

3}, Ute Hentschel⁴, Dirk Erpenbeck⁵, Graeme Oatley⁶, Elizabeth Sinclair⁶, Eerik Aunin⁶, Noah Gettle⁶, Camilla Santos⁶, Michael Paulini⁶, Haoyu Niu⁶, Victoria McKenna⁶, Rebecca O'Brien⁶; Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team; Wellcome Sanger Institute Scientific Operations: Sequencing Operations; Wellcome Sanger Institute Tree of Life Core Informatics Team; EBI Aquatic Symbiosis Genomics Data Portal Team; Aquatic Symbiosis Genomics Project Leadership

Affiliations

¹ Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain.
² Institute of Marine Sciences - CSIC, Barcelona, Spain.
³ Integrated Marine Ecology group, Institute of Marine Research IIM-CSIC, Vigo, Spain.
⁴ GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
⁵ Ludwig-Maximilians University of Munich, Munich, Germany.
⁶ Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK.

Abstract

We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.

Keywords: Crambe crambe; Poecilosclerida; chromosomal; genome sequence; marine sponge.