Molluscs are extremely diverse invertebrate animals with a rich fossil record, highly divergent life cycles, and considerable economical and ecological importance. Key representatives include worm-like aplacophorans, armoured groups (e.g. polyplacophorans, gastropods, bivalves) and the highly complex cephalopods. Molluscan origins and evolution of their different phenotypes have largely remained unresolved, but significant progress has been made over recent years. Phylogenomic studies revealed a dichotomy of the phylum, resulting in Aculifera (shell-less aplacophorans and multi-shelled polyplacophorans) and Conchifera (all other, primarily uni-shelled groups). This challenged traditional hypotheses that proposed that molluscs gradually evolved complex phenotypes from simple, worm-like animals, a view that is corroborated by developmental studies that showed that aplacophorans are secondarily simplified. Gene expression data indicate that key regulators involved in anterior-posterior patterning (the homeobox-containing Hox genes) lost this function and were co-opted into the evolution of taxon-specific novelties in conchiferans. While the bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signalling pathway, that mediates dorso-ventral axis formation, and molecular components that establish chirality appear to be more conserved between molluscs and other metazoans, variations from the common scheme occur within molluscan sublineages. The deviation of various molluscs from developmental pathways that otherwise appear widely conserved among metazoans provides novel hypotheses on molluscan evolution that can be tested with genome editing tools such as the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein9) system.

The evolution of molluscs

The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.

/pdf/massive-gene-presence-absence-variation-shapes-an-open-pan-51jomqm00y.pdf

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel.

Research advances in the genomics and applications for molecular breeding of aquaculture animals

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long-reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi-C, we generated a high-continuity chromosome-scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome-size scaffolds covering 98.8% of the complete assembly (N50 = 37.4 Mb, L50 = 11). We also provide a first characterization of the yellow perch sex determination locus that contains a male-specific duplicate of the anti-Mullerian hormone type II receptor gene (amhr2by) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex-specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (amhr2by+ ) from XX genetic females (amhr2by- ). Our high-quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the amhr2by gene as a candidate sex-determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.

/pdf/molluscdb-an-integrated-functional-and-evolutionary-genomics-4sb48tuhpv.pdf

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

Selection of a new scallop strain, the Bohai Red, from the hybrid between the bay scallop and the Peruvian scallop

Effects of light on growth, feeding rate, digestion, and antioxidation in juvenile razor clams Sinonovacula constricta

The invention relates to a method for establishing a three-line support breeding system of Argopecten purpuratus and Argopecten irradians concentricus hybrid scallops and application. Three lines comprise the male sterile line, the maintainer line and the restoring line of the Argopecten purpuratus and Argopecten irradians concentricus hybrid scallops, wherein the Argopecten purpuratus and Argopecten irradians concentricus hybrid scallops are filial generations of Argopecten purpuratus eggs and Argopecten irradians concentricus sperms. The method includes the steps firstly, a large number of Argopecten purpuratus and Argopecten irradians concentricus hybrid first filial generation families are established, and male sterile individuals are found from the families; then, the Argopecten irradians concentricus sperms are adopted for continuous backcross, and male sterile line-maintainer line combinations in which all later generations are the male sterile individuals and male sterile line-restoring line combinations in which all later generations are hermaphrodite individuals are bred respectively; finally, male sterile line parent scallops are hybridized through the male sterile line and the maintainer line, and Argopecten purpuratus and Argopecten irradians concentricus hybrid scallop commercial fry are hybridized through the male sterile line and the restoring line. The three-line support breeding system of the Argopecten purpuratus and Argopecten irradians concentricus hybrid scallops is established in animals for the first time, obstacles of self-fertilization in hermaphrodite scallop hybridization are effectively overcome, and the yield in the same year is increased by more than 42% compared with that of Argopecten irradians concentricus.

Method for establishing three-line support breeding system of Argopecten purpuratus and Argopecten irradians concentricus hybrid scallops and application

Enhancing the Thermotolerance of Isochrysis zhangjiangensis Through Co-culturing With Algoriphagus marincola

The current invent relates to the construction and application of a three-line breeding system in the Peruvian scallop×bay scallop southern subspecies hybrids. The said three-line consists of a male sterile line, a maintainer line and a restorer line. A combination of male sterile line and maintainer line is obtained by continuously backcrossing the male sterile individuals selected from F1 inter-specific hybrid families with sperm of the selfing family of the sperm-providing bay scallops until the progenies are all male sterile. The restorer line is obtained by continuously backcrossing selected individuals from the male sterile line with sperm of the selfing family of a bay scallop until the progenies are all hermaphroditic and exhibit excellent production traits. Commercial male sterile brood stocks are produced by backcrossing the male sterile line with the maintainer line and commercial hybrid spats are produced by backcrossing the male sterile line and the restorer line.

Peruvian scallop×bay scallop southern subspecies hybrid three-line breeding system and method

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