Comparative transcriptome sequencing analysis of female and male Decapterus macrosoma.

Sexual growth dimorphism is a common phenomenon in teleost fish and has led to many reproductive strategies. Growth- and sex-related gene research in teleost fish would broaden our understanding of the process. In this study, transcriptome sequencing of shortfin scad Decapterus macrosoma was performed for the first time, and a high-quality reference transcriptome was constructed. After identification and assembly, a total of 58,475 nonredundant unigenes were obtained with an N50 length of 2,266 bp, and 28,174 unigenes were successfully annotated with multiple public databases. BUSCO analysis determined a level of 92.9% completeness for the assembled transcriptome. Gene expression analysis revealed 2,345 differentially expressed genes (DEGs) in the female and male D. macrosoma, 1,150 of which were female-biased DEGs, and 1,195 unigenes were male-biased DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were mainly involved in biological processes including protein synthesis, growth, rhythmic processes, immune defense, and vitellogenesis. Then, we identified many growth- and sex-related genes, including Igf, Fabps, EF-hand family genes, Zp3, Zp4 and Vg. In addition, a total of 19,573 simple sequence repeats (SSRs) were screened and identified from the transcriptome sequences. The results of this study can provide valuable information on growth- and sex-related genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.

New perspective on the genetic structure and habitat adaptation of Pampus minor off the coast of China based on RAD-seq.

Understanding the genetic diversity and habitat adaptation patterns of different geographic populations of marine organisms is essential for the rational maintenance, development, and utilization of their resources. Pampus minor Liu and Li 1998 is an economically valuable marine fish species. To determine the population genetic structure and elucidate the genetic mechanism underlying the habitat adaptation of this species, restriction site-associated DNA sequencing (RAD-seq) was used to scan the whole genomes of three P. minor putative populations along the coast of China for single-nucleotide polymorphism (SNPs) and outlier SNPs. Our population genetic structure analysis based on 2388 SNPs and 731 outlier SNPs throughout the genome revealed no significant genetic differentiation among the three populations. Results suggested that the life-cycle characteristics of P. minor, its relatively large population sizes, and ocean current transport might have shaped its current genetic pattern. The annotation information of both assembled sequences (which included outlier SNPs) and candidate loci associated with adaptations indicated that genes involved in many processes, including ion exchange, osmotic pressure regulation, metabolism, and the immune response, have been very important in the adaptations of P. minor to its heterogeneous habitats. Against the background of increased human activities, increased fishing intensity, and destruction of marine habitats, the results of this study provide basic genetic information for the accurate division of protection units of P. minor.

Reidentification of Decapterus macarellus and D. macrosoma (Carangidae) reveals inconsistencies with current morphological taxonomy in China.

Decapterus macarellus and D. macrosoma are economically important pelagic fish species that are widely distributed in tropical and subtropical seas. The two species are often mistakenly identified due to their morphological similarities as described in the Chinese literature on fish identification. In this study, D. macarellus and D. macrosoma samples were collected in the Eastern Indian Ocean and the South China Sea and reidentified using morphological and DNA barcoding techniques. The characteristics that distinguish the two species primarily include the scute coverage of the straight portion of the lateral line (the most indicative characteristic for classification), the shape of the predorsal scaled area and its location relative to the middle axis of the eye, and the shapes of the posterior margin of the maxilla and the posterior margin of the operculum. The results revealed a large number of misidentified sequences among the homologous cytochrome oxidase (COI) sequences of the two species in the NCBI database and that the genus Decapterus may include cryptic species. In terms of genetic structure, the Sundaland has not blocked genetic exchange between D. macarellus populations in the South China Sea and the Eastern Indian Ocean, giving rise to a high level of genetic diversity. In this study, we made corrections to the Chinese classification standards for D. macarellus and D. macrosoma and the erroneous reference sequences in the NCBI database, thereby providing accurate reference points for the future exploration of cryptic species in the genus Decapterus.

Complete mitochondrial genome sequence and phylogenetic analysis of Lycodes polaris (Sabine, 1824).

Lycodes polaris is one of the most widely distributed and abundant eelpout species on the Arctic continental shelves with full mitogenome information unavailable. In this paper, complete mitochondrial genome of L. Polaris was determined with 16,595 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (origin of light strand replication and control region). All the protein-coding genes choose ATG as start codon in addition to that COI using GTG. Most genes use TAA or TAG as the stop codon while three others ended with incomplete stop codons. Phylogenetic relationship of L. polaris was also reconstructed. Our result will provide important basis for further studies of L. polaris.

Microplastic contamination in benthic organisms from the Arctic and sub-Arctic regions.

The seafloor is recognized as one of the major sinks for microplastics (MPs). However, to date there have been no studies reported the MP contamination in benthic organisms from the Arctic and sub-Arctic regions. Therefore, this study provided the first data on the abundances and characteristics of MPs in a total of 413 dominant benthic organisms representing 11 different species inhabiting in the shelf of Bering and Chukchi Seas. The mean abundances of MP uptake by the benthos from all sites ranged from 0.02 to 0.46 items g-1 wet weight (ww) or 0.04-1.67 items individual-1, which were lower values than those found in other regions worldwide. The highest value appeared at the northernmost site, implying that the sea ice and the cold current represent possible transport mediums. Interestingly, the predator A. rubens ingested the maximum quantities of MPs, suggesting that the trophic transfer of MPs through benthic food webs may play a critical role. Fibers constituted the major type (87%) in each species, followed by film (13%). The colors of fibers were classified as red (46%) and transparent (41%), and the film was all gray. The predominant composition was polyamide (PA) (46%), followed by polyethylene (PE) (23%), polyester (PET) (18%) and cellophane (CP) (13%). The most common sizes of MPs concentrated in the interval from 0.10 to 1.50 mm, and the mean size was 1.45 ±â€¯0.13 mm. Further studies about the temporal trends and detrimental effects of MPs remain to be carried out in benthic organisms from the Arctic and sub-Arctic regions.

Contamination of sulfonamide antibiotics and sulfamethazine-resistant bacteria in the downstream and estuarine areas of Jiulong River in Southeast China.

Surface water samples from downstream and estuarine areas of Jiulong River were collected in August 2011 and May 2012 for detecting sulfonamide antibiotic residues and isolating sulfamethazine-resistant bacteria. Sulfamethazine was detected in all samples in May 2012 at an average concentration of 78.3 ng L(-1), which was the highest among the nine sulfonamide antibiotics determined. Sulfamethazine-resistant bacteria (SRB) were screened using antibiotic-containing agar plates. The SRB average abundance in the samples was 3.69 × 10(4) and 2.17 × 10(3) CFUs mL(-1) in August 2011 and May 2012, respectively, and was positively correlated to sulfamethazine concentration in May 2012. The 16S rRNA gene sequencing of all the 121 SRB isolates revealed high diversity. Furthermore, the SRB isolates exhibited multidrug resistance, with 48.7% showing resistance to at least three antibiotics. The abundance and persistence of highly diverse SRB and their multidrug resistance are likely to demonstrate the transferable pressure from coastal environments on public health.