In recent years, some common themes in the development of sex-specific traits in different animal lineages have started to emerge since the discovery of the Dmrt (doublesex-mab3-related transcription ...factor gene) genes. Bivalves are characterized by a diversity of sexual systems, including simultaneous hermaphroditism, sequential hermaphroditism, and strict gonochorism. However, to date, no research has focused on the genome-wide characterization and analysis of Dmrt genes in bivalves. In this study, the identification and analysis of Dmrt genes in 15 bivalves were performed using bioinformatics methods. A total of 55 Dmrt genes were retrieved in the studied bivalve genomes. The number of Dmrt genes in different species ranged from 3 to 5. The phylogenetic tree showed that Dmrt genes in bivalves can be subdivided into 5 classes: the Dmrt2-like class, Dmrt3-like class, Dmrt4/5-like class, Dsx-like class, and scallop-specific Dmrt class. The Ka/Ks ratios suggested that all Dmrt classes underwent purifying selection pressure. Furthermore, the spatiotemporal expression of Dmrt genes in four bivalve species suggested that different Dmrt genes may have different functions, and scallop-specific Dmrt genes may play a key role in sex determination/differentiation. In general, this study provides a molecular basis for in-depth examination of the functions of Dmrt genes and phylogenomic analyses in bivalves.
Color polymorphism, a high-valued trait, is frequently observed in molluscan shellfish. The QN Orange scallop, a new scallop strain successively selected from the interspecific hybrids of the bay ...scallop (Argopecten irradians irradians) and the Peruvian scallop (Argopecten purpuratus), is distinguished from other scallops by its orange adductor muscles. In this study, to reveal the mechanisms of the formation of adductor muscle coloration in the QN Orange scallops, we compared the proteome and transcriptome of orange adductor muscles of the QN Orange and those of white adductor muscles of the Bohai Red scallop, another strain selected from the interspecific hybrids of the bay scallop and the Peruvian scallop.
Transcriptomic analysis revealed 416 differentially expressed genes (DEGs) between white and orange adductor muscles, among which 216 were upregulated and 200 were downregulated. Seventy-four differentially expressed proteins (DEPs), including 36 upregulated and 38 downregulated proteins, were identified through label-free proteomics. Among the identified DEGs and DEPs, genes related to carotenoids biosynthesis including apolipophorin, and Cytochrome P450 and those related to melanin biosynthesis including tyrosinase and Ras-related protein Rab-11A were found to express at higher levels in orange adductor muscles. The high expression levels of VPS (vacuolar protein sorting) and TIF (translation initiation factor) in orange adductor muscle tissues indicated that carotenoid accumulation may be affected by proteins outside of the carotenoid pathway.
Our results implied that the coloration of orange adductor muscles in the QN Orange scallops may be controlled by genes modulating accumulation of carotenoids and melanins. This study may provide valuable information for understanding the mechanisms and pathways underlying adductor muscle coloration in molluscan shellfish.
Phosphatase and tensin homolog deleted on chromosome ten (PTEN) has been found to regulate longevity through the PI3K/Akt/FoxO pathway and maintenance of genome integrity in worms, flies, and ...mammals. However, limited information is available on the roles of PTEN in longevity of aquatic animals. Here we extended this paradigm using two closely related
Argopecten
scallops,
Argopecten purpuratus
, and Argopecten
irradians
, with significantly distinct life spans, which are commercially important bivalve species for fishery and aquaculture in China, United States, Peru, and Chile. The ORFs of the
ApPTEN
and
AiPTEN
were 1,476 and 1,473 bp, which encoded 491 and 490 amino acids, respectively. There were 48 synonymous and 16 non-synonymous SNPs and one InDel of three nucleotides between
ApPTEN
and
AiPTEN
, resulting in variations in 15 amino acids and lack of S453 in AiPTEN. Differences in conformation and posttranslational modification were predicted between ApPTEN and AiPTEN, which may indicate different activities of ApPTEN and AiPTEN. When the animals were subjected to nutrition restriction, the expression of both
ApPTEN
and
AiPTEN
was upregulated, with
AiPTEN
responded faster and more robust than
ApPTEN
. Ionizing radiation induced significantly elevated expression of
ApPTNE
but not
AiPTEN
in the adductor muscle, and the mortality rate of
A. purpuratus
was significantly lower than that of
A. irradians
, indicating that
ApPTNE
may play a protective role by maintaining the genome integrity. RNAi of
ApPTNE
significantly downregulated the expression of its downstream regulated genes known to favor longevity, such as
FoxO
,
Mn-SOD
, and
CAT
. These results indicated that PTEN may contribute to the longevity of
A. purpuratus
through regulation of nutrient availability and genomic stability, probably
via
PI3K/Akt/FoxO pathway. Our study may provide new evidence for understanding of the conservative functions of PTEN in regulation of lifespan in animals and human, and it may also benefit the selection of scallops strains with long lifespan and thus larger size.
The goal of genetic breeding is to select variants with mutations that are related to expected traits, such as fast growth. Artificial induction has been widely used to obtain strains with more ...mutations for further selection. Ethylmethylsulfone (EMS) is one of the most commonly used chemical mutagens in plant and microorganism breeding. However, the application of EMS mutagenesis in shellfish has not been reported. The aim of this study is to evaluate the potential use of EMS as a mutagen in scallop breeding, especially in characterization of mutations in growth-related genes.
Our results indicated that hatching of about 50% of fertilized eggs was blocked by treatment with 20 mM EMS for 3 h and the resulted larvae developed normally into adult stages. We then evaluated the mutagenic effects of EMS by sequencing the genomes of 4 adult scallops from the control group and 12 from the treatment group at 8 months after fertilization. On average, after removing shared types of mutations, there were 1,151,380 ± 258,188 SNPs (Single Nucleotide Polymorphisms) and 229,256 ± 51,714 InDels (insertion-deletion) in each animal in the EMS treatment group, while there were only134841 ± 10,115 SNPs and 42,605 ± 5,136 InDels in the control group. The average mutation rate in the genome of the EMS treatment group (0.0137 ± 0.0013%) was about 9 times that of the control group (0.0015 ± 0.0002%). GO (Gene Ontology) annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed that mutations induced by EMS occurred evenly in most biological processes, cellular components and functions, as well in most pathways. However, significant lower percentage of mutations were found in the exonic region, in non-synonymous or Stopgain/Stoploss SNPs and in coding domains, suggesting apparent DNA repair or selection during grow-out stage. Analyses of the growth-related genes with mutations indicated that mutations in MFS (Major Facilitator Superfamily) and Tubulin were only found in the large-sized group (Five largest scallops: Treated-1, Treated-2, Treated-3, Treated-4, and Treated-5) and Homeobox and Socs (Suppressor of cytokine signaling) only in the small group (Two smallest scallops: Treated-11 and Treated-12). These results suggested that these genes may be involved in the regulation of growth in these animals, although further verification is certainly warranted.
Treatment of fertilized eggs with 20 mM EMS for 3 h induced 9 times more mutations in scallop genomes. We found that mutations in MFS and Tubulin may be related to fast growth in the large-sized group and those mutations in Homeobox and SOCs may be involved in the slow growth in the small-sized scallops. EMS can be used to accelerate selection of economically important traits in molluscs.
The bay scallop southern subspecies,
Argopecten irradians concentricus
, which is widely cultured in southern China waters, is a eurythermal animal that is more adaptive to high-temperature waters ...but less tolerant to low-temperature waters. Despite that temperature is one of the most dominant environmental factors affecting dramatically its growth, survival, and hence production, the mechanism underlying the responses to thermal stress has not been explored in this animal. In this study, transcriptomic and metabolomic analyses were carried out in the adductor muscles of the bay scallop southern subspecies exposed to low and high thermal stresses. Transcriptomic analyses revealed that differentially expressed genes (DEGs) were enriched in the calcium ion, kinase activity, phosphatase activity, and lipid-related pathways in the group exposed to thermal stress, while most DEGs were enriched in the RNA processing pathways in the group exposed to low-temperature thermal stress. A large number of differentially expressed transcription factors involved in oxidation-reduction process, membrane-related pathways, transmembrane signaling receptor activity, and transduction-related pathways were induced by exposure to thermal stress. Results from metabolomic analyses showed that the retinol metabolism, inositol phosphate metabolism, and phosphatidylinositol pathways may be involved in the responses to high thermal stress, while more signaling pathways were enriched in the group exposed to low thermal stress. Integrated analyses of the transcriptomic and metabolomic data indicated that the degradation of valine, leucine, and isoleucine and the tricarboxylic acid cycle may be the major events induced by low and high thermal stress, and the retinol pathway may play critical roles in the responses of the scallops to high thermal stress. It seems that the bay scallop southern species have evolved distinct pathways in dealing with low and high thermal stress. Our results may provide useful information for marker-assisted selection of high-resistant strains in this scallop.
The two subspecies of Atlantic bay scallop (Argopecten irradians), A. i. irradians and A. i. concentricus, are economically important aquacultural species in northern and southern China. Here, we ...performed the whole-genome sequencing, assembly, and gene annotation and produced draft genomes for both subspecies. In total, 253.17 and 272.97 gigabases (Gb) of raw reads were generated from Illumina Hiseq and PacBio platforms for A. i. irradians and A. i. concentricus, respectively. Draft genomes of 835.7 Mb and 874.82 Mb were assembled for the two subspecies, accounting for 83.9% and 89.79% of the estimated sizes of their corresponding genomes, respectively. The contig N50 and scaffold N50 were 78.54 kb and 1.53 Mb for the A. i. irradians genome, and those for the A. i. concentricus genome were 63.73 kb and 1.25 Mb. Moreover, 26,777 and 25,979 protein-coding genes were predicted for A. i. irradians and A. i. concentricus, respectively. These valuable genome assemblies lay a solid foundation for future theoretical studies and provide guidance for practical scallop breeding.
Identification of microRNAs is important in studies of regulation of gene expression in many biologyical processes. In this study, we developed an improved method for identification of microRNAs in ...Drosophila. We used the iLearn, PyFeat, and Pse-in-One methods to extract the features and then used Max-Relevance-Max-Distance (MRMD2.0) and t-Distributed Stochastic Neighbour Embedding (t-SNE) to reduce dimension of the features and the random forest classifier in Weka to identify miRNAs. With this method, we found that the discriminative features for identification of pre-miRNAs were, in Drosophila melanogaster, the occurrences of G_GUG and C_AGU when the value of the feature vector was greater than 2, and in Drosophila pseudoobscura, the 4-tuple nucleotide composition and the occurrence of 4-length neighbouring nucleic acids when the value of the feature vector was less than 0.02. These vectors covered all compositional information or the frequency of bases. Classification results showed the classification accuracy was 95.7% and 93.6%, the precision rate was 95.8% and 93.6%, and the recall rate was 95.7% and 93.6% in Drosophila melanogaster and Drosophila pseudoobscura, respectively, which are higher than those reported in previous studies.
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•Generation of a new chromosome-level reference genome for the king scallop.•Disapproval of previous claim of ‘gene-rich’ feature by improved genome annotation.•Neurotoxin tolerance ...potentially contributed by the expansion of GluF genes.
The king scallop, Pecten maximus is a well-known, commercially important scallop species and is featured with remarkable tolerance to potent phytotoxins such as domoic acid. A high-quality genome can shed light on its biology and innovative evolution of toxin resistance. A reference genome has recently been published for P. maximus, however, it is suspicious that over 67,700 genes are annotated in this genome, which is unexpectedly larger than its close relatives of pectinids. Herein, we provide an improved high-quality chromosome-level reference genome assembly and annotation for the king scallop P. maximus. A final set of 26,995 genes is annotated after carefully checking and curation of the predicted gene models, which significantly improves the accuracy of gene structure information. The large number of gene duplicates in the previous genome is mainly distorted by the fragmented annotation. Through integrated genomic, evolutionary and transcriptomic analyses, we reveal that the Phi subfamily of ionotropic glutamate receptors (iGluRs) are well preserved in molluscs, and P. maximus experienced the rapid expansion of the Phi class of iGluR (GluF) gene family. The GluF genes exhibit ubiquitously high expression and altered sequence characteristics for ligand selectivity, which may contribute to the remarkable tolerance to neurotoxins in P. maximus. Taken together, our study disapproves the previous claim of the 'gene-rich' genome of this species and provides a high-quality genome assembly for further understanding of its biology and evolution of toxin resistance.
Bay scallop culture has become a major sector in marine culture industry in China since its first introduction in early 1980s. However, despite various efforts including several re-introductions, ...decreases in major production traits such as survival and growth rates are still a major concern to the industry. This study aimed to evaluate the performance of offspring derived from mass spawning type crossbreeding between different populations in bay scallops. The results showed that significant differences in growth and survival existed among the four intra-population crosses at larval stages, but not at the adult stage. Increases in growth and survival rates were observed in most inter-population crosses at larval stages and in all inter-population crosses at the adult stage. The survival rate of the best inter-population crosses was 156.7% higher than the average survival rate of all the intra-population crosses. Through mass spawning type crossbreeding between different populations, we were able to produce offspring with improved production traits and the results may have immediate application in bay scallop culture.
Bay scallops are commercially important bivalve species for aquaculture worldwide, but the serious inbreeding depression is decreasing their production. Some interspecific hybrids of bay scallops ...(Argopecten irradians irradians) and Peruvian scallops (A. purpuratus) exhibit longer lifespan and significantly larger size for high yield, which may result from the longevity genes of Peruvian scallops. Insulin-like growth factor (IGF) system, as the conspicuous entry point of insulin/insulin-like growth factor signal (IIS) pathway, regulates various cellular processes including growth, autophagy, aging and longevity, but its roles remain unexplored in marine animals. In this study, we separately cloned a unique IGF2 (ApIGF2 and AiIGF2) and IGF1R (ApIGF1R and AiIGF1R) for the first time from two closely related Argopecten scallops with distinct lifespans and characterized for their ability to regulate longevity. Sequence analysis demonstrated that there were six-span transmembrane domains located at the additional extension of C-terminus special to AiIGF2, which appeared to relate to the differences in posttranslational processing. The amino acid variation (Y247) in TyrKc domain may be a key site affecting ApIGF1R kinase activity for longevity. Spatiotemporal expression of IGF2 and IGF1R during development and aging showed that the mantle and gonad are representative tissues for aging in scallops. The dietary restriction assay revealed the beneficial effects of attenuated IGF2 and IGF1R levels on longevity in scallops. The invigorated IGF1R conferred DNA repair and prosurvival properties to Peruvian scallops for radio-resistance after acute radioresistance. Inhibition of AiIGF1R upregulated the expression of senescence-associated genes (PENT, FoxO, CAT, Mn-SOD) and antioxidant enzyme activities, and suppressed the senescence marker β-GAL activity, indicating that IGF1R was a crucial regulator for longevity in scallops. Collectively, our work would bring us closer to understanding the longevity mechanism mediated by IGF system and breeding larger and long-lived hybrids for the sustainable development of aquaculture.
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