Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster（Crassostrea ariakensis） is an economically and ecologically important species in China. In the present study, RNA sequencing（RNA-seq） and assay for transposase-accessible chromatin using sequencing（ATAC-seq） were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents. Analysis identified9 ?483 differentially expressed genes（DEGs） and 7 ?215genes with significantly differential chromatin accessibility（DCAGs） were obtained, with an overlap of 2 ?600 genes between them. Notably, a significant proportion of these genes were enriched in pathways related to glycogen metabolism, including “Glycogen metabolic process” and“Starch and sucrose metabolism”. In addition, genomewide association study（GWAS） identified 526 single nucleotide polymorphism（SNP） loci associated with glycogen content. These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C. ariakensis.

Head and neck squamous cell carcinoma (HNSCC) is the most common malignant tumor of the head and neck, and the incidence rate is increasing year by year. Protein post-translational modification, recognized as a pivotal and extensive form of protein modification, has been established to possess a profound association with tumor occurrence and progression. This study employed bioinformatics analysis utilizing transcriptome sequencing data, patient survival data, and clinical data from HNSCC to establish predictive markers of genes associated with glycosylation as prognostic risk markers. The R procedure WGCNA was employed to construct a gene co-expression network using the gene expression profile and clinical characteristics of HNSCC samples. Multiple Cox Proportional Hazards Regression Model (Cox regression) and LASSO analysis were conducted to identify the key genes exhibiting the strongest association with prognosis. A risk score, known as the glycosylation-related genes risk score (GLRS), was subsequently formulated utilizing the aforementioned core genes. This scoring system facilitated the classification of samples into high-risk and low-risk categories, thereby enabling the prediction of patient prognosis. The association between GLRS and clinical variables was examined through both univariate and multivariate Cox regression analysis. The validation of six core genes was accomplished using quantitative real-time polymerase chain reaction (qRT-PCR). The findings demonstrated noteworthy variations in risk scores among subgroups, thereby affirming the efficacy of GLRS in prognosticating patient outcomes. Furthermore, a correlation has been observed between the risk-scoring model and immune infiltration. Moreover, significant disparities exist in the expression levels of diverse immune checkpoints, epithelial-mesenchymal transition genes, and angiogenic factors between the high and low-risk groups.

在物流系统中,堆码对运输包装件的危害一般来源于两个方面,一是包装件受到的压力,二是仓储过程中包装件的堆码受多种因素的影响会有倒塌的风险.为了有针对性地验证包装件在流通过程中的抗压性和堆垛稳定性,将静态堆码试验进行了分类,通过对国内外静态堆码试验标准的解析和对比,表明了不同标准对静态堆码方法的规定各有特点.着重解读了每个标准中所提出的要点,并且对每个标准进行了评价,为堆码试验标准的选用提供了指导意见,为产品包装设计提供参考的依据.

Characiformes is a diverse and evolutionarily significant order of freshwater fish encompassing over 2,300 species. Despite its diversity, our understanding of Characiformes' evolutionary relationships and adaptive mechanisms is limited due to insufficient genome sequences. In this study, we sequenced and assembled the genomes of four Characiformes species, three of which were chromosome-level assemblies. Our analyses revealed dynamic changes in gene family evolution, repeat sequences and variations in chromosomal collinearity within these genomes. With the assembled genomes, we were not only able to elucidate the evolutionary relationship of the four main orders in Otophysi but also indicated Characiformes as the paraphyletic group. Comparative genomic analysis with other available fish genomes shed light on the evolution of genes related to tooth development in Characiformes. Notably, variations in the copy number of secretory calcium-binding phosphoproteins (SCPP) genes were observed among different orders of Otophysi, indicating their potential contribution to the diversity of tooth types. Our study offers invaluable genome sequences and novel insights into Characiformes' evolution, paving the way for further genomic and evolutionary research in fish.

Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on regulatory interactions remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyse genomes, epigenomes and transcriptomes during early development in two Heliocidaris sea urchin species that exhibit highly divergent life histories and in an outgroup species. Positive selection and chromatin accessibility modifications within putative regulatory elements are enriched on the branch leading to the derived life history, particularly near dGRN genes. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near conserved cell fate specification genes. Experimentally perturbing key transcription factors reveals profound evolutionary changes to early embryonic patterning events, disrupting regulatory interactions previously conserved for ~225 million years. These results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change. More broadly, even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.

COPYRIGHT © 2022 Zhao, Guo, Jia, Dong and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Data Report PUBLISHED 25 August 2022 DOI 10.3389/fmars.2022.988397

In the present study, we successfully assembled a high-quality genome of Planiliza haematocheila (redlip mullet) based on Oxford Nanopore long read, single-tube long fragment read (stLFR), and Hi-C chromatin interaction sequencing. The size of the P. haematocheila genome was 652.91 Mb. More than 93.8% of BUSCO genes were detected, and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb, respectively, thus demonstrating outstanding genome completeness and sequence continuity. A total of 21 045 protein-coding genes were predicted in the assembled genome, and 99.77% of those genes were functionally annotated. Comparative genomic and phylogenetic analyses revealed the adaptability of P. haematocheila to complex living environments at the genomic level, highlighting its broad adaptability and resistance to multiple stresses as an important economic fish. The high-quality reference chromosome-level genome of P. haematocheila provides a powerful genomic resource for further systematic study of Mugilidae. Planiliza haematocheila (FishBase ID: 13000), which belongs to Mugiliformes, Mugilidae, is an economically value fish. This species can survive under different salinities and water quality, and it shows strong adaptability to hypoxia compared to other aquaculture fish (Qi et al., 2016). Thus, P. haematocheila is an excellent model for studying fish adaptation to complex environments. However, despite its economic value, research on P. haematocheila is slow, with a focus on geographical (Durand & Borsa, 2015) and seasonal resource distribution (Shen et al., 2011), population dynamics (Pankov et al., 2009), nutritional supplementation (Zhang et al., 2013), and disease prevention (Qi et al., 2016). At present, our understanding of the in-depth mechanisms underlying its biological processes remains poor, which may be due to a lack of good genetic resources. Liyanage et al. (2019) previously established a draft genome of P. haematocheila at the contig level, however better-quality genomes are needed to meet the higher requirements of analysis. In the current study, we successfully assembled a high-quality genome of P. haematocheila via a combination of Oxford Nanopore long read, stLFR, and Hi-C chromatin interaction sequencing. Comparative genomic and phylogenetic analyses revealed the adaptability of P. haematocheila to complex living environments at the genomic level, highlighting its broad adaptability and resistance to multiple stresses as an important economic fish. This high-quality reference chromosome-level genome of P. haematocheila provides a powerful genomic resource for further systematic studies of Mugilidae. Liver, blood, and muscle tissue samples from a P. haematocheila female were used for DNA extraction. Fresh samples were obtained from the Bohai Sea by the Tianjin Fisheries Research Institute, China. All sequencing libraries were established based on high-quality purified DNA. The chromosome-level genome was accomplished with a mixed assembly strategy. The stLFR data were first used to conduct genome k-mer analysis. Clean reads with duplications removed were filtered using SOAPnuke and then analyzed using Jellyfish v2.2.6 to obtain a histogram. GenomeScope v1.0.0 converted the histogram to the final visual result, as shown in Figure 1A. Oxford Nanopore sequencing data were employed to assemble a de novo contig-level genome using wtdbg2 (parameters: -p 0 -k 15 -AS 2 -s 0.05 -L 5 000, as suggested by the software when assembling a genome <1 G in size using nanopore/ont data). The output was polished with Pilon using stLFR data, as the quality values of single bases in these reads were far more precise than the Nanopore reads. Lastly, contigs were assembled into scaffolds by mapping HiC read pairs to the polished assembly with HiC-Pro, Juicer, and 3D-DNA. Additional details are provided in the Supplementary Materials and Methods. The P. haematocheila chromosome-level genome statistics are shown in Table 1. The length of the 24 chromosomes obtained by Hi-C ranged from 32.04 Mb to 20.79 Mb, covering 99.31% of the genome

High quality genome is of great significance for the mining of biological information resources of species. Up to now, the genomic information of several important economic flatfishes has been well explained. All these fishes are eyes on left side-type, and no high-quality genome of eyes on right side-type species has been reported. In this study, we applied a combined strategy involving stLFR and Hi-C technologies to generate sequencing data for constructing the chromosomal genome of Verasper variegates, which belongs to Pleuronectidae with characteristic of eyes on right side. The size of genome of V. variegatus is 556 Mb. More than 97.2% of BUSCO genes were detected, and N50 lengths of the contigs and scaffolds reached 79.8 Kb and 23.8 Mb, respectively, demonstrating the outstanding completeness and sequence continuity of the genome. A total of 22,199 protein-coding genes were predicted in the assembled genome, and more than 95% of those genes could be functionally annotated. Meanwhile, the genomic collinearity, gene family and phylogenetic analyses of similar species in Pleuronectiformes were also investigated and portrayed for metamorphosis and benthic adaptation. Sex related genes mapping has also been achieved at the chromosome level. This study is the first chromosomal level genome of a Pleuronectidae fish (V. variegatus). The chromosomal genome assembly constructed in this work will not only be valuable for conservation and aquaculture studies of the V. variegatus but will also be of general interest in the phylogenetic and taxonomic studies of Pleuronectiformes.

Pecan (Carya illinoinensis) is a tree nut crop of worldwide economic importance that is rich in health-promoting factors. However, pecan production and nut quality are greatly challenged by environmental stresses such as the outbreak of severe fungal diseases. Here, we report a high-quality, chromosome-scale genome assembly of the controlled-cross pecan cultivar ‘Pawnee’ constructed by integrating Nanopore sequencing and Hi-C technologies. Phylogenetic and evolutionary analyses reveal two whole-genome duplication (WGD) events and two paleo-subgenomes in pecan and walnut. Time estimates suggest that the recent WGD event and considerable genome rearrangements in pecan and walnut account for expansions in genome size and chromosome number after the divergence from bayberry. The two paleo-subgenomes differ in size and protein-coding gene sets. They exhibit uneven ancient gene loss, asymmetrical distribution of transposable elements (especially LTR/Copia and LTR/Gypsy), and expansions in transcription factor families (such as the extreme pecan-specific expansion in the far-red impaired response 1 family), which are likely to reflect the long evolutionary history of species in the Juglandaceae. A whole-genome scan of resequencing data from 86 pecan scab-associated core accessions identified 47 chromosome regions containing 185 putative candidate genes. Significant changes were detected in the expression of candidate genes associated with the chitin response pathway under chitin treatment in the scab-resistant and scab-susceptible cultivars ‘Excell’ and ‘Pawnee’. These findings enable us to identify key genes that may be important susceptibility factors for fungal diseases in pecan. The high-quality sequences are valuable resources for pecan breeders and will provide a foundation for the production and quality improvement of tree nut crops.

Background This investigation examined the effects of the microRNA miR-34c-5p on the proliferation, migration, and invasion of oral squamous cell carcinoma (OSCC) and the mechanisms involved. Methods The Gene Expression Omnibus (GEO) database was used to filter the chips, and the GEO2R software (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to analyze the microarray data (GSE28100 and GSE45238). Gene set enrichment analysis (GSEA) was used to study the relationship between the expression of miR-34c-5p and the distant metastasis and pathological grade of OSCC. The correlation between TRIM29 (tripartite motif containing 29) expression and the malignant clinical phenotype of OSCC was also examined. The mRNA and protein expression levels of miR-34c-5p and TRIM29 were measured by real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot analysis. The proliferation, migration, invasion and apoptosis of the human oral squamous carcinoma cell lines CAL-27 and Tca8113 was assessed by performing cell-counting kit-8 (CCK-8) assays, colony formation assays, transwell tests, wound scratch tests and flow cytometry. Luciferase reporter assays were used to predict the relationship between miR-34c-5p and TRIM29. A xenograft nude model was established and used to evaluate the effect of miR-34c-5p on tumor growth in female BALB/c mice. Results The expression of miR-34c-5p was significantly correlated with the proliferation, migration, and metastasis of OSCC. Overexpression of miR-34c-5p promoted the proliferation, migration, and invasion of CAL-27 and Tca8113 cells, and suppressed their apoptosis. Inversely, low expression of miR-34c-5p suppressed the proliferation, migration, and invasion of CAL-27 and Tca8113 cells, and promoted their apoptosis. Overexpression of miR-34c-5p promoted tumor growth in the xenograft nude mice model. The expression of TRIM29 was related to malignant clinical phenotype of OSCC. Overexpression of TRIM29 inhibited the proliferation, migration and invasion of CAL-27 and Tca8113 cell, and induced their apoptosis. TRIM29 knockout had just the opposite effect. Importantly, miR-34c-5p binds to TRIM29 and inhibited TRIM29 expression. Conclusions MiR-34c-5p regulates the proliferation, migration, invasion, and apoptosis of OSCC through targeted binding of TRIM29. This may represent a novel therapeutic target for the treatment of patients with OSCC.

Lytechinus variegatus is a camarodont sea urchin found widely throughout the western Atlantic Ocean in a variety of shallow-water marine habitats. Its distribution, abundance, and amenability to developmental perturbation make it a popular model for ecologists and developmental biologists. Here, we present a chromosomal-level genome assembly of L. variegatus generated from a combination of PacBio long reads, 10x Genomics sequencing, and HiC chromatin interaction sequencing. We show L. variegatus has 19 chromosomes with an assembly size of 870.4Mb. The contiguity and completeness of this assembly are reflected by a scaffold length N50 of 45.5Mb and BUSCO completeness score of 95.5%. Ab initio and transcript-informed gene modeling and annotation identified 27,232 genes with an average gene length of 12.6 kb, comprising an estimated 39.5% of the genome. Repetitive regions, on the other hand, make up 45.4% of the genome. Physical mapping of well-studied developmental genes onto each chromosome reveals nonrandom spatial distribution of distinct genes and gene families, which provides insight into how certain gene families may have evolved and are transcriptionally regulated in this species. Lastly, aligning RNA-seq and ATAC-seq data onto this assembly demonstrates the value of highly contiguous, complete genome assemblies for functional genomics analyses that is unattainable with fragmented, incomplete assemblies. This genome will be of great value to the scientific community as a resource for genome evolution, developmental, and ecological studies of this species and the Echinodermata.

Aureococcus anophagefferens caused brown tides for three consecutive years from 2009 to 2011 in the coastal waters of Qinhuangdao, China, with numerous, widespread ecological and economic impact on ecosystems. To understand the population dynamics of nanoplankton during the brown tides, sequences of the V9 region of the 18 S rDNA gene, used as a marker, were analyzed by Illumina sequencing to assess nanoplankton biomass, and real-time fluorescence quantitative PCR was performed to analyze spatial variation in the 18 S rDNA copy concentrations of nanoplankton off the Qinhuangdao coast in July, 2011. The results showed that A. anophagefferens and Minutocellus polymorphus were the dominant species in the local phytoplankton community during the brown tide in July 2011. The highest 18 S rDNA copy concentrations of A. anophagefferens and M. polymorphus were detected at stations SHG and FN, respectively. The central area most strongly affected by the brown tide migrated southward from 2011 to 2013. Redundancy analysis（RDA） showed that the decreasing NOx concentration might provide suitable nutrient conditions for the A. anophagefferens outbreak. During the brown tide caused by A. anophagefferens, other phytoplankton, such as diatoms, cryptophytes, chlorophytes, dinoflagellates and other flagellates, could co-occur with it. For zooplankton, due to less selective feeding behavior, Amoebozoa was the most abundant zooplankton at station SHG, while Ciliophora was the most abundant zooplankton at other stations for its more selective feeding.

Brown tides caused by Aureococcus anophagefferens have occurred frequently in the coastal waters of Qinhuangdao since 2009. The Changli coast is the area most strongly affected by the brown tides, which result in significant economic losses and serious ecological harm. To understand the effects of brown tides on nanoplankton diversity and biomass, samples were collected from May to July in 2012 at station XKK, which is approximately 0.2 nautical miles off the Changli coast. The V9 region of the 18S rDNA gene was used as a marker and was analyzed by Illumina sequencing to assess the nanoplankton diversity and biomass, and real-time fluorescence quantitative PCR was performed to analyze the temporal variations in the copy concentrations of the 18S rDNA of nanoplankton. The results showed that nanoplankton diversity, as determined by the Shannon index, decreased from May to June and increased in July. Illumina sequencing analysis revealed that the plankton community differed among the samples from May to July, and over this period, the dominant phytoplankton groups changed from pelagophytes to chlorophytes. Sufficient nutrients and low grazing pressure by zooplankton and scallops accelerated the growth of small-celled phytoplankton. A. anophagefferens was the most dominant phytoplankton species, with an 18S rDNA maximum copy concentration detected on 26 June, followed by Micromonas sp. and Bathycoccus prasinos, with maximum copy concentrations observed on 3 July. Ciliophora, Arthropoda and Cercozoa were the dominant taxa of the local zooplankton community. The Ciliophora and Arthropoda biomasses decreased, and the Cercozoa biomass increased when the copy concentration of A. anophagefferens peaked on 26 June. We suspect that A. anophagefferens had a significantly negative effect on the growth of Ciliophora and Arthropoda and could be ingested by Cercozoa to promote its proliferation. The small and low-abundance plankton that are likely missed in microscopic and clone library analyses could be detected using Illumina sequencing and qPCR, which provide an effective method for a comprehensive analysis of the plankton community.

Cardiac activity has been widely used in marine molluscs as an indicator for their physiological status in response to environmental changes, which is, however, largely less studied in scallops. Here, we monitored cardiac performance of Zhikong scallop Chlamys farreri using an infrared-based method, and evaluated the effects of several biotic (shell height, total weight, and age) and environmental factors (circadian rhythm and temperature) on scallop heart rate (HR), amplitude (HA), and rate-amplitude product (RAP). Results revealed that size has a significant effect on both HR (negative) and HA (positive), but RAP values are similar in different sized scallops. Age also affects scallop cardiac performance, significantly for HR, but not for HA or RAP. Circadian rhythm affects cardiac activity, with significant elevation of HR, HA and RAP during 1:00-8:00 and 17:00-19:00. With seawater temperature elevation, HR peaks at 30.03 ± 0.23°C, HA at 15.08 ± 0.02°C, and RAP at 15.10 ± 0.19 and 30.12 ± 0.28°C. This suggests HR is a good indicator for thermal limit, whereas HA may indicate optimal growth temperature, and RAP could be an index of myocardial oxygen consumption to indicate myocardium stress. Our study provides basic information on the factors that may affect scallop cardiac performance. It also elucidates the feasibility of HA and RAP as cardiac indices in marine molluscs.

In selective breeding, a central parameter in summarizing the proportion of variance due to genetics for the purpose of predicting gains from selection is realized heritability (h(2)). We applied the genome-wide complex trait analysis (GCTA) method to genome-wide SNP data obtained by 2b-RAD reduced-representation genotyping and phenotypic data for four traits (shell length, shell height, shell width and whole wet weight) with the aim of establishing the heritability for growth in Zhikong scallop (Chlamys farreri) in a selective breeding program. The GCTA-based heritabilities of 0.42 (S.E. 0.09) for shell length, 0.47 (S.E. 0.07) for shell height, 0.54 (S.E. 0.11) for shell width and 0.28 (S.E. 0.03) for whole wet weight, which were estimated with uncommon SNPs (26,471 SNPs with MAF > 2%), were close to and strongly correlated (r = 0.957) with traditional estimates of realized heritability and in the moderate-to-high range, in line with values previously obtained for growth rates in bivalves. h(GCTA)2 with 20,000 and 10,000 SNPs were very close to estimates with uncommon SNPs and appeared relatively robust to SNP number. Removing causal SNPs had little effect on obtaining reliable estimates of h(GCTA)2, suggesting that causal SNPs is not necessary for accurate estimates of h(2). Chromosome-wise heritability estimates suggested that the genetic contribution to growth complex traits is scattered across the genome and driven by many loci with small effect rather than a few causal loci with a large effect. These results indicate that the genome-wide complex trait analysis method may be useful for estimating realized heritability for growth in Zhikong scallop with SNPs obtained by reduced-representation genotyping approaches, which is less expensive and faster than full-genome sequencing for non-model species growing in natural environments.

Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.

Cathepsin F is a unique papain cysteine proteinase with highly conserved structures: catalytic triad and a cystatin domain contained in the elongated N-terminal pro-region. It has been reported that cathepsin F is associated with the establishment of innate immune in several vertebrate including fish in aquaculture, but not known in bivalves. In this study, we firstly identified and characterized cathepsin F in the Yesso scallop (Patinopecten yessoensis). The protein structural and phylogenetic analyses were then conducted to determine its identity and evolutionary position. We've also investigated the expression levels of cathepsin F gene at different embryonic developmental stages, in healthy adult tissues and especially in the hemocytes and hepatopancreas after Gram-positive (Micrococcus luteus) and negative (Vibrio anguillarum) challenges using quantitative real-time PCR (qPCR). Cathepsin F was significantly up-regulated 3 h after infection of V. anguillarum in hemocytes, suggesting its participation in immune response. Our findings have provided strong evidence that cathepsin F may be a good target for enhancing the immune activity in Yesso scallop.

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

Thermal tolerance has become an active research area in marine poikilotherms due to the influence of increased sea temperature caused by global warming. Previous indicators of thermal tolerance in bivalves are generally laborious and time-consuming and even require killing the specimens. In this study, we demonstrated that heart rate (HR) was a stable and reliable indicator for scallop physiological status by applying an infrared-based cardiac performance monitoring system. The feasibility of HR-based Arrhenius break temperatures (ABTs) as a scallop thermal tolerance indicator was evaluated by investigating ABTs of four species with different thermal limits, including the Yesso scallop (Patinopecten yessoensis), the Zhikong scallop (Chlamys farreri), the bay scallop (Argopecten irradians), and the Catarina scallop (Argopecten ventricosus). In accordance with the thermal limits, ABTs of the Yesso scallop, Zhikong scallop, bay scallop, and Catarina scallop were 22.03 ± 0.19, 29.10 ± 0.25, 32.20 ± 0.25, and 34.09 ± 0.19 °C, respectively, suggesting that the ABT could indicate thermal limits in interspecific scallops. Variations in the ABTs were observed among intraspecific scallops with different sizes, weights, and ages, suggesting that smaller and younger scallops tend to have higher thermal limits. Significant differences in ABT were also observed between pre- and post-spawning individuals, implying that spawning behavior could decrease scallop thermal limits. The above results suggest that HR-based ABT can detect not only interspecific but also intraspecific thermal tolerance in scallops. This study reports the feasibility of infrared-based cardiac performance as a rapid, efficient, and noninvasive indicator for bivalve thermal tolerance.