About Archivesica marissinica

The Deep-Sea Chemosymbiotic Clam Archivesica marissinica is a species of deep-sea clam in the family Vesicomyidae, commonly found at the Haima cold seep on the northwest continental slope of the South China Sea. This species is well-adapted to extreme environments and relies on symbiotic sulfur-oxidizing bacteria housed in its gills for nutrition. Archivesica marissinica plays a significant role in cold seep ecosystems by contributing to nutrient cycling and supporting diverse microbial and faunal communities.

Classification

Animalia (Kingdom); Mollusca (Phylum); Bivalvia (Class); Autobranchia (Subclass); Venerida (Order); Vesicomyidae (Family); Archivesica (Genus); Archivesica marissinica (Species)

Original Name

Archivesica marissinica (Chen, Okutani, Liang & Qiu, 2018)

Key Reference Paper

1. Chen C, Okutani T, Liang Q, et al. A noteworthy new species of the family Vesicomyidae from the South China Sea (Bivalvia: Glossoidea)[J]. Venus (Journal of the Malacological Society of Japan), 2018, 76(1-4): 29-37. (Chen et al., 2018)

Description

Shell thin, rather lightly-built, chalky, elongate-oval in profile, slightly attenuated in front and somewhat flared posteriorly. Shell height about a quarter of shell length. Umbo situated at about 20% anteriorly, with weakly prosogyrous beaks. External surface covered by straw-colored, varnished periostracum, which is occasionally commarginally lamellate, particularly in front of umbonal region and marginal region. Periostracum corroded behind umbonal region suggesting presence of boundary between buried portion and exposed portion. Round antero- dorsal and anterior margins gently continuous to sub-straight ventral margin. No lunule present. Posterior margin also round. A low, obscure radial ridge running from umbo to postero-ventral corner. Escutcheon not demarcated, dorso-posterior margin weakly convex, representing greatest position in shell height, and generating nearly flat area between dorsal margin and dorsal rim of radial ridge. Ligament amphidetic, strong, extending about half length from umbo to posterior tip. Calcareous fibrous layer rather weak

Etymology

meaning “Chinese Sea”

Distribution

Hitherto known only from the type locality: Haima methane seep, south off Hainan Island. 1,372–1,398 meters depth


Basic Information
SpeciesPhylumCommon NameEcosystemDepthHabitatNCBI Taxonomy ID
Archivesica marissinicaMolluscaDeep-Sea ClamHydrothermal vent1,361Haima cold seep in the South China Sea2291877

Genome Assembly Information
Genome AssemblyGenome SizeAssembly levelReleased yearWGS accessionSubmitterBioProjectBUSCO completeness (%)Scaffold/Contig N50 (kb)GC content (%)Repeat Rate (%)Gene Number
ASM1484369v11.5GbChromosome2020JABXNX01Hong Kong Baptist UniversityPRJNA62989893.50 74,300/79.13952.8128,949

References
TitleJournalPubmed ID
Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic ClamMolecular Biology and Evolution32956455

Gene Information

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Gene IDDescription
Ama05907ALDEHYDE DEHYDROGENASE-RELATED
Ama05910-
Ama05911RAS-ASSOCIATING DOMAIN-CONTAINING PROTEIN
Ama05912BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN FAMILY MEMBER
Ama05914CYTOKINE RECEPTOR
Ama05917-
Ama05919DUAL SPECIFICITY PROTEIN PHOSPHATASE
Ama05921SURFACE ANTIGEN BSPA-LIKE-RELATED
Ama05922KELCH PROTEIN
Ama05923THAP DOMAIN PROTEIN
Ama05925TRANSMEMBRANE PROTEIN
Ama05926-
Ama05927-
Ama05930CALCIUM-ACTIVATED POTASSIUM CHANNEL ALPHA CHAIN
Ama05931-
Ama05932DENTIN MATRIX PROTEIN 4 PROTEIN FAM20
Ama059336-PHOSPHOGLUCONOLACTONASE
Ama05934-
Ama05935TETRATRICOPEPTIDE REPEAT PROTEIN 38
Ama05936PEPTIDYL-TRNA HYDROLASE 2

Results of comparison between Archivesica marissinica and its nearshore relatives from the paper (Chi-Ho Ip et al., 2021)

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Annotation IDDescriptionTypeSubtypeGeneRatioEvolution TypeP-valueQ-value
GO:0035652cargo loading into clathrin-coated vesicleGOBiological Process47expanded-6.98E-08
GO:0060260regulation of transcription initiation from RNA polymerase II promoterGOBiological Process92expanded-1.96E-05
GO:0035459cargo loading into vesicleGOBiological Process61expanded-2.24E-05
GO:0043939negative regulation of sporulationGOBiological Process22expanded-0.000380302
GO:0007062sister chromatid cohesionGOBiological Process83expanded-0.00058477
GO:0033363secretory granule organizationGOBiological Process85expanded-0.001045836
GO:0043937regulation of sporulationGOBiological Process22expanded-0.001181872
GO:0034307regulation of ascospore formationGOBiological Process22expanded-0.001242481
GO:0071444cellular response to pheromoneGOBiological Process22expanded-0.003797717
GO:0006384transcription initiation from RNA polymerase III promoterGOBiological Process30expanded-0.005224062
GO:0019236response to pheromoneGOBiological Process24expanded-0.009234132
GO:0048918posterior lateral line nerve developmentGOBiological Process19expanded-0.019616942
GO:0006302double-strand break repairGOBiological Process227expanded-0.019943185
GO:0090083regulation of inclusion body assemblyGOBiological Process48expanded-0.023871281
GO:0060876semicircular canal formationGOBiological Process18expanded-0.027381017
GO:0032290peripheral nervous system myelin formationGOBiological Process18expanded-0.027710909
GO:0070230positive regulation of lymphocyte apoptotic processGOBiological Process55expanded-0.037668635
GO:0009617response to bacteriumGOBiological Process374contracted-0.009719681
GO:0034622cellular macromolecular complex assemblyGOBiological Process674contracted-0.01744258
GO:0051248negative regulation of protein metabolic processGOBiological Process672contracted-0.028576899
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