Gang Lin

Background: Barnacles are important marine fouling organisms, and their complex life cycle involves key metamorphic nodes from nauplius to cyprid larvae and then to sessile adults. However, the molecular mechanisms underlying their larval development remain poorly understood. Metabolomics and transcriptomics are powerful tools for exploring biological development pathways and regulatory networks. Methods: We employed non-targeted metabolomics and transcriptomics to analyze three key developmental stages of embryonic stage, nauplius stage, and cyprid stage. Differential metabolites were screened using fold change (FC), p-value, and variable importance in projection (VIP) values, while DEGs were identified with adjusted p-value and |log₂(fold change)| criteria. WGCNA was used to construct gene co-expression networks, and qRT-PCR validated RNA-seq results. Results: A total of 3683 metabolites were identified, with the bile secretion pathway serving as a core regulatory pathway throughout early development. Transcriptomic analysis identified 7234 DEGs, which were clustered into four modules corresponding to different developmental stages. Key pathways such as chitin metabolism, and linoleic acid metabolism were significantly enriched, and qRT-PCR confirmed the reliability of RNA-seq data. Conclusions: This study reveals the metabolic and molecular regulatory mechanisms underlying the early development of M. volcano, highlighting stage-specific metabolic characteristics and core gene modules. The findings provide a theoretical basis for understanding barnacle developmental adaptation strategies and offer potential targets for the development of novel antifouling agents.

Noctiluca scintillans, known as a global red tide species, is a common red tide species found in Pingtan Island. To examine the bacterial community structure in different environments during the red tide period of N. scintillans on Pingtan Island, samples were collected from the Algal Bloom Area (ABA), Transition Area (TA), and Non-Algal Bloom Area (NBA) on 6 April 2022, and the environmental physicochemical factors and bacterial community were determined. The outbreak of N. scintillans red tide significantly impacted the water quality and bacterial community structure in the affected sea area. The water quality in the ABA has deteriorated markedly, with the contents of COD, NH₄⁺-N, and PO₄³⁻ in the ABA being significantly higher than those in the TA and NBA, while the pH is significantly lower than that in the TA and NBA. The richness, diversity, and evenness of the bacterial community in the ABA are all lower than those of the TA and NBA. For instance, the Shannon index values of the three sampling points are 4.41, 5.41, and 6.37, respectively. At the phylum level, the dominant bacterial phyla in the ABA are Proteobacteria, Firmicutes, and Cyanobacteria; in the TA, they are Proteobacteria, Bacteroidetes, and Firmicutes; and in the NBA, they are Proteobacteria, Bacteroidetes, and Cyanobacteria. At the genus level, the dominant bacterial genera in the ABA are Vibrio, Carnobacterium, Candidatus_Megaira, Planktomarina, and Pseudoalteromonas; in the TA, they are Vibrio, Planktomarina, Lentibacter, Glaciecola, and Jannaschia; and in the NBA, they are Planktomarina, Amylibacter, NS5_marine_group, Aurantivirga, and marine_metagenome. In the ABA, the combined proportion of Vibrio and Carnobacterium exceeds 50%, with Vibrio_splendidus accounting for 93% of the total Vibrio population. These research results can provide a scientific basis for clarifying the environmental characteristics and bacterial composition during the large-scale N. scintillans red tide in Pingtan Island.

Oysters, particularly Portuguese oyster (Crassostrea angulata), are highly valued for their nutritional and flavor qualities, making them important in global aquaculture. Triploid oysters have gained attention for maintaining higher meat quality year-round compared to diploids, but there is limited research on how ploidy affects their biochemical and flavor profiles. This study uses a non-targeted metabolomics approach, including gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS), to investigate flavor substance differences between triploid and diploid C. angulata. A total of 13 volatile compounds were identified in diploid oysters, while 28 were found in triploids. Significant upregulation of inosine, guanosine, L-aspartic acid, and taurine in triploids contributes to their enhanced flavor profile. Additionally, triploids showed higher nicotinamide concentrations, while diploids had increased 25-hydroxycholesterol. These findings highlight the advantages of triploid oysters in aquaculture for improved flavor and nutrition, supporting their potential for year-round production.

Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis.

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding of the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole-genome duplications, which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its three-dimensional chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulatory networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome assembly of I. galbana LG007, which has a genome size of 92.73 Mb, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenetic analysis confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ∼ 133 million years ago. Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1, and IgDEGS1. Metabolome analysis showed that the content of carotenoids in I. galbana cultured under green light for 7 days was higher than that under white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive multi-omics analysis revealed that the content of β-carotene, antheraxanthin, zeaxanthin, and Fx was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to the understanding of Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Rotation is an important method to improve land utilization and the economic benefits of aquaculture. Shrimp vegetable rotation is a new farming and planting rotation model. The purpose of this study is to reveal the community of microorganisms in pond sediments under shrimp-vegetable rotation and provide theoretical basis for maintaining soil fertility. In this study, three groups were set: cultivated areas (CC, shrimp-vegetable rotation mode), uncultivated area (CG, shrimp farming and fallow mode), and flooded area (CS, continuous shrimp farming mode). Diversity and community composition of microorganism communities were displayed using real-time PCR and high-throughput sequencing platforms. The results showed that the shrimp-vegetable rotation significantly reduced the content of total nitrogen (TN, compared with CG and CS, CS has dropped by about 50% and 80%, respectively),total carbon (TC, compared with CS, CS has dropped by about 50% and 70%, respectively) and total phosphorus (TP, compared with CG and CS, CS has dropped by about 60%) in the sediment and removing excess nutrients in the aquaculture environment. The relative abundance of Proteobacteria and Gemmatimonadetes phylum was significantly higher in the CC and CG groups than in CS. And the majority of denitrifying bacteria are concentrated in the Proteobacteria that increased abundance of denitrifying bacteria confirms results of increased copy number of nosZ and phoD genes. Herein, a conclusion was drawn that shrimp-vegetable rotation had stronger restoration ability of soil bacterial diversity and soil fertility than the other two farming mode. Also, the rotation mode promoted a good ammonia nitrogen cycle. This study will provide a scientific basis and data support for the application of shrimp vegetable rotation.

The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into the vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation, and forms two topologically associated domains at the Hox gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes, and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.

Chromosome Genome Assembly and Annotation of the Capitulum mitella With PacBio and Hi-C Sequencing Data