Background: Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. Results: A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on. Conclusions: Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

With the continuous rise of the sea cucumber aquaculture industry in China, the tropical sea cucumber aquaculture industry is also improving. However, research on the gut microorganisms of tropical sea cucumbers in captivity is scarce. In this study, high-throughput sequencing methods were used to analyze the gut microbial composition of Stichopus monotuberculatus and Holothuria scabra in the dry season and wet season of artificial environments. The results showed that 66 phyla were obtained in all samples, of which 59 phyla were obtained in the dry season, and 45 phyla were obtained in the wet season. The Tax4Fun analysis showed that certain gut bacterial communities affect the daily metabolism of two sea cucumber species and are involved in maintaining gut microecological balance in the gut of two sea cucumber species. In addition, compared with differences between species, PCoA and UPGMA clustering analysis showed the gut prokaryotes of the same sea cucumber species varied more in different seasons, indicating that the influence of environment was higher than the feeding choices of sea cucumbers under relatively closed conditions. These results revealed the gut bacterial community composition of S. monotuberculatus and H. scabra and the differences in gut bacterial structure between two sea cucumber species in different seasons were compared, which would provide the foundation for tropical sea cucumber aquaculture in the future.

MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.

Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus are three important sipunculan species in tropical intertidal zones. In this study, the particle size, organic matter content, and bacterial community composition in the gut contents of three different sipunculans and their surrounding sediments were analyzed. The grain size fractions of sipunculans’ guts were significantly different from those of their surrounding sediments; particle size fractions < 500 μm were favored by the sipunculans. As for the total organic matter (TOM), higher contents of organic matter were observed in the guts than in the surrounding sediments in all three sipunculan species. The bacterial community composition of all the samples was investigated by 16S rRNA gene sequencing, in which a total of 8974 OTUs were obtained from 24 samples based on a 97% threshold. The predominant phylum identified from the gut contents of three sipunculans was Planctomycetota, while the predominant phylum in their surrounding sediments was Proteobacteria. At the genus level, the most abundant genus was Sulfurovum (average 4.36%) in the surrounding sediments, while the most abundant genus was Gplla (average 12.76%) in the gut contents. The UPGMA tree showed that the samples from the guts of three different sipunculans and their surrounding sediments were clustered separately into two groups, which showed that these three sipunculans had a different bacterial community composition with their surrounding sediments. The grain size and total organic matter (TOM) had the greatest impacts on the bacterial community composition at both the phylum and genus levels. In conclusion, the differences in particle size fractions, organic matter content, and bacterial community composition between the gut contents and surrounding sediments in these three sipunculan species might be caused by their selective ingestion.