A high-quality chromosome-level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation.

The cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here, we generated a high-quality, chromosome-scale genome assembly (521.26 Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93 Mb and a scaffold N50 of 24.06 Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900 genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosome-scale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.

Resolving the origins of invertebrate colonists in the Yangtze River Estuary with molecular markers: Implications for ecological connectivity.

Understanding connectivity over different spatial and temporal scales is fundamental for managing of ecological systems. However, controversy exists for wintertime ecological connectivity between the Yangtze River Estuary (YRE) and inner southwestern Yellow Sea. Here, we investigated ecological connectivity between the YRE and inner southwestern Yellow Sea in wintertime by precisely pinpointing the source of the newly colonized populations of a winter-spawning rocky intertidal invertebrate, Littorina brevicula (Philippi, 1844), on artificial structures along the coast of the Yangtze River Delta (YRD) using mitochondrial ND6 sequences and microsatellite data. Clear phylogeographic and genetic differentiation were detected between natural rocky populations south and north of the YRE, which resulted from the lack of hard substrate for rocky invertebrates in the large YRD coast. For the newly colonized populations on the coast of YRD, most individuals (98%) to the south of ~33.5°N were from natural rocky populations to the south of the YRE and most of those (94%) to the north of ~33.5°N were from the northern natural rocky populations, which demonstrated strong ecological connectivity between the inner southwestern Yellow Sea and the YRE in winter time. We presented the first genetic evidence that demonstrated a northward wintertime coastal current in the inner southwestern Yellow Sea, and precisely illustrated the boundary of the coastal current recently proposed by numerical experiment. These results indicated that the YRE serves as an important source of materials and energy for the inner southwestern Yellow Sea in winter, which can be crucial for the function of the Yellow Sea ecosystem.

Female-specific genomic regions and molecular sex identification of the clearhead icefish (Protosalanx hyalocranius).

BACKGROUND: The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. Since 1980s, P. hyalocranius was widely introduced into lakes and reservoirs of northern China for aquaculture. However, the lack of a rapid and cost-effective sex identification method based on sex specific genetic markers has hindered study on sex determination mechanisms and breeding applications. RESULTS: Female-specific genomic regions were discovered by comparing whole genome re-sequencing data of both males and females. Two female-specific genomic regions larger than 50 bp were identified, and one (598 bp) contained a putative FOXI gene, which was paralogous to another FOXI gene with sex-associated SNPs. The two FOXI sequences displayed significant length difference with nine deletions of total length of 230 bp. This deletion-type structural variation could be easily and efficiently detected by traditional PCR and agarose gel electrophoresis with one 569 bp band for males and two bands (569 and 339 bp) for females, which were validated in 50 females and 40 males with known phenotypic sexes. CONCLUSIONS: The results provided structural genomic evidence for the ZZ/ZW sex determination system in P. hyalocranius discovered in our previous study with association analysis of SNPs. Moreover, the female-specific markers and rapid and cost-effective PCR-based genetic sex identification method should have applications in further studies of sex determination mechanism for this species.

Genome-wide association analyses based on whole-genome sequencing of Protosalanx hyalocranius provide insights into sex determination of Salangid fishes.

Identification of sex determination system and sex-determining genes have important implications in conservation, ecology and evolution. However, much remains to be discovered about the evolution of different sexual determination systems in teleost fishes, of which the mechanisms of sex determination are remarkably variable. In the present study, the whole genomes of 20 males and 20 females of a Salangid fish, Protosalanx hyalocranius, were sequenced and genome wide association analyses were conducted to uncover its sex determination system and putative sex-determining genes. A total of 150 SNPs were significantly associated with sex, which showed high differentiation between sexes (FST ranged from 0.245 to 0.556). Of the 150 sex-associated SNPs, 76 SNPs displayed sex specificity with even coverage of depth and were female heterogametic, which suggested a ZZ/ZW sex determination system. Interestingly, one scaffold containing sex-specific SNPs displayed synteny to the sex chromosome of medaka. Annotations of sex-associated loci suggested that both transcriptional regulators (e.g., FOX genes) and secreted hormones and their receptors might be involved in the sex determination/differentiation of P. hyalocranius. More strikingly, we found a nonsense mutation in one copy of GALNT homology gene of all females, which suggested that "Z dosage" effect might play a vital role in the processes of sex determination/differentiation. These sex-specific loci could be a valuable resource for further research on sex determination of Salangid fishes and the results could contribute to the understanding of sex determination mechanisms and the evolution of sex chromosome in teleost fishes.

First mitochondrial genome of a periwinkle from the genus Littoraria: Littoraria sinensis.

The nearly complete sequence of the mitochondrial genome of the periwinkle Littoraria sinensis is presented. This is the first mitochondrial genome of the genus Littoraria and the fifth sequenced Littorinidae. The mitogenome of L. sinensis is 16,320 bp in size, with 37 genes and one partial control region. The genes order is identical to those observed in other Littorinidae mitogenomes. The overall base composition shows that AT content (64.76%) is higher than GC content (35.24%). This study should provide new information for the further phylogenetic studies of this species.

The function of carbon nanoparticles to improve lymph node dissection and identification of parathyroid glands during thyroid reoperation for carcinoma.

To evaluate the function of carbon nanoparticles during the thyroid reoperation for carcinoma, we conducted this study by retrospectively analyzing the data of patients who underwent at least completion thyroidectomy with bilateral central lymph nodes dissection for thyroid carcinoma from January 2009 to June 2016. The clinicopathologic characteristics and surgical details were compared between the patient who accepted intraoperative carbon nanoparticles injection and those who accepted nothing injection during the surgery. The main monitoring indicators were the number of dissected lymph nodes and metastatic lymph nodes in central zone, the number of identified parathyroid glands and autoplastic parathyroid glands and unintentionally resected parathyroid glands. A total of 69 patients were enrolled into the carbon nanoparticles group and 128 patients were enrolled into the control group.The average number of lymph nodes harvested in the central zone was higher in the carbon nanoparticles group than that in the control group (11.2 ±â€Š5.7 vs 7.7 ±â€Š4.0, P < .001), so was the average number of metastatic lymph nodes (4.5 ±â€Š4.5 vs 2.7 ±â€Š2.9, P = .004). The average number of identified parathyroid gland was greater in the carbon nanoparticles group than that in the control group (2.4 ±â€Š1.2 vs 1.6 ±â€Š1.1, P < .001). The average number of autoplastic parathyroid gland was comparable between the 2 groups (0.6 ±â€Š0.6 vs 0.4 ±â€Š0.7, P = .052). But the average number of unintentionally resected parathyroid gland was less in the carbon nanoparticles group than that in the control group (0.1 ±â€Š0.2 vs 0.2 ±â€Š0.4, P = .007). Carbon nanoparticles can improve lymph nodes dissection and identification of parathyroid gland during thyroid reoperation for carcinoma.

Surgical Outcomes Comparison Between Endoscopic and Conventional Open Thyroidectomy for Benign Thyroid Nodules.

BACKGROUND: The aim of this study was to compare the surgical outcomes of endoscopic thyroidectomy (ET) and conventional open thyroidectomy (COT) for benign thyroid nodules. METHODS: Between March 2001 and November 2014, 224 patients underwent ET via the breast approach and 218 patients underwent COT. Clinicopathological characteristics and surgical outcomes were retrospectively compared. RESULTS: The operation time was significantly longer in the ET group than in the COT group (P = 0.000). However, the ET group had less intraoperative blood loss (P = 0.000), less amount of drainage (P = 0.000), and shorter duration of drainage (P = 0.000). The cosmetic satisfaction was more excellent in the ET group than in the COT group (P = 0.000). CONCLUSIONS: ET via the breast approach is a safe and effective procedure with excellent cosmetic results for patients with benign thyroid nodules.