Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment
Abstract Background In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome an...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-05-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-025-11622-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849312184578867200 |
|---|---|
| author | Julia D. Sigwart Nur Leena W.S. Wong Vanessa Liz González Fabrizio Marcondes Machado Carola Greve Tilman Schell Zeyuan Chen |
| author_facet | Julia D. Sigwart Nur Leena W.S. Wong Vanessa Liz González Fabrizio Marcondes Machado Carola Greve Tilman Schell Zeyuan Chen |
| author_sort | Julia D. Sigwart |
| collection | DOAJ |
| description | Abstract Background In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called “the weirdest bivalves” for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway. Results The genome assembly of V. penis was about 507 Mb, with contig N50 of 5.33 Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1 N = 19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor. Conclusions While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design. |
| format | Article |
| id | doaj-art-8895bb085cbf49afab9512b980e8b39f |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-8895bb085cbf49afab9512b980e8b39f2025-08-20T03:53:08ZengBMCBMC Genomics1471-21642025-05-0126111010.1186/s12864-025-11622-wGenome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sedimentJulia D. Sigwart0Nur Leena W.S. Wong1Vanessa Liz González2Fabrizio Marcondes Machado3Carola Greve4Tilman Schell5Zeyuan Chen6Senckenberg Research Institute and Natural History Museum FrankfurtInternational Institute of Aquaculture and Aquatic Sciences, Universiti Putra MalaysiaInformatics and Data Science Center, Smithsonian Institution National Museum of Natural HistoryDepartamento de Biologia Animal, Universidade Estadual de Campinas (UNICAMP)Senckenberg Research Institute and Natural History Museum FrankfurtSenckenberg Research Institute and Natural History Museum FrankfurtSenckenberg Research Institute and Natural History Museum FrankfurtAbstract Background In this study, we present the first chromosome-scale genome of Verpa penis (Linnaeus, 1758), and the first for the bivalve clade Anomalodesmata. The present study has two separate foci. Primarily, we provide the genetic resource to bridge further studies from genome to phenome and propose hypotheses to guide future empirical investigations. Secondarily, based on morphology, we outline a conceptual exploration to address their adaptation. Watering-pot shells have been called “the weirdest bivalves” for their fused tubular shell resembling the spout of a watering can. This adventitious tube arose twice convergently in clavagelloidean bivalves. However, previous literature has never provided a convincing adaptive pathway. Results The genome assembly of V. penis was about 507 Mb, with contig N50 of 5.33 Mb, and has 96.5% of sequences anchored onto 19 pseudochromosomes. Phylogenomic analyses of this new genome in context of other bivalves confirms the placement for Anomalodesmata as sister to the clade Imparidentia. Contrary to expectations from its highly modified body plan, there is no evidence of chromosome reduction compared to the ancestral karyotype of heterodont bivalves (1 N = 19). Drawing on established principles from engineering as well as morphology, the thought experiment about the adventitious tube seeks to extend current understanding by exploring parallels with other built structures. A new hypothesis explains one possible interpretation of the adaptive significance of this body form: it is potentially structurally optimised for vertical stability in relatively soft sediments, with parallels to the engineering principles of a suction anchor. Conclusions While the conclusions presented here on morphological interpretations are theoretical, this serves as a foundation for further empirical validation and refinement. Our study offers new insights to a long-standing mystery in molluscan body forms and provides genomic resources that are relevant to understanding molluscan evolution, biomineralisation, and biomimetic design.https://doi.org/10.1186/s12864-025-11622-wBivalviaSuction CaissonClavagelloideaPhylogenomics |
| spellingShingle | Julia D. Sigwart Nur Leena W.S. Wong Vanessa Liz González Fabrizio Marcondes Machado Carola Greve Tilman Schell Zeyuan Chen Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment BMC Genomics Bivalvia Suction Caisson Clavagelloidea Phylogenomics |
| title | Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment |
| title_full | Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment |
| title_fullStr | Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment |
| title_full_unstemmed | Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment |
| title_short | Genome of the enigmatic watering-pot shell and morphological adaptations for anchoring in sediment |
| title_sort | genome of the enigmatic watering pot shell and morphological adaptations for anchoring in sediment |
| topic | Bivalvia Suction Caisson Clavagelloidea Phylogenomics |
| url | https://doi.org/10.1186/s12864-025-11622-w |
| work_keys_str_mv | AT juliadsigwart genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT nurleenawswong genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT vanessalizgonzalez genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT fabriziomarcondesmachado genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT carolagreve genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT tilmanschell genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment AT zeyuanchen genomeoftheenigmaticwateringpotshellandmorphologicaladaptationsforanchoringinsediment |