Chinese Academy of Fishery Sciences

About: Chinese Academy of Fishery Sciences is a nonprofit organization based out in Beijing, China. It is known for research contribution in the topics: Population & Gene. The organization has 8107 authors who have published 7929 publications receiving 92095 citations. The organization is also known as: Zhōngguó shuǐchǎn Kēxuéyánjiūyuàn & Chinese Academy of Fishery Sciences.

Population Genetic Studies Revealed Local Adaptation in a High Gene-Flow Marine Fish, the Small Yellow Croaker (Larimichthys polyactis)

Abstract: The genetic differentiation of many marine fish species is low. Yet local adaptation may be common in marine fish species as the vast and changing marine environment provides more chances for natural selection. Here, we used anonymous as well as known protein gene linked microsatellites and mitochondrial DNA to detect the population structure of the small yellow croaker (Larimichthys polyactis) in the Northwest Pacific marginal seas. Among these loci, we detected at least two microsatellites, anonymous H16 and HSP27 to be clearly under diversifying selection in outlier tests. Sequence cloning and analysis revealed that H16 was located in the intron of BAHCC1 gene. Landscape genetic analysis showed that H16 mutations were significantly associated with temperature, which further supported the diversifying selection at this locus. These marker types presented different patterns of population structure: (i) mitochondrial DNA phylogeny showed no evidence of genetic divergence and demonstrated only one glacial linage; (ii) population differentiation using putatively neutral microsatellites presented a pattern of high gene flow in the L. polyactis. In addition, several genetic barriers were identified; (iii) the population differentiation pattern revealed by loci under diversifying selection was rather different from that revealed by putatively neutral loci. The results above suggest local adaptation in the small yellow croaker. In summary, population genetic studies based on different marker types disentangle the effects of demographic history, migration, genetic drift and local adaptation on population structure and also provide valuable new insights for the design of management strategies in L. polyactis.

Effect of combined use of Bacillus and molasses on microbial communities in shrimp cultural enclosure systems

Abstract: To assess the effect of addition of probiotics and carbon source on the microbial community structure within the shrimp culture, an enclosure system simulating a high density, intensive aquaculture of Litopenaeus vannamei was set up in Dianbai, Maoming, Guangdong province, China. The phylogenetic profiles of microbial communities in the enclosure system after addition of Bacillus and molasses were studied in the middle and final culture season (on the 45th, 75th and 95th day) using polymerase chain reaction-denaturing gradient gel electrophoresis. A total of four groups, each containing a triplicate were set up: Group A (control), Group B (64% of daily feed was provided as molasses with Bacillus sp.), Group C (50% of daily feed amount provided as molasses with Bacillus sp.) and Group D (64% of daily feed amount as molasses alone). The results showed that α-Proteobacteria, δ-Proteobacteria, Bacteroidetes and Actinobacteria were the dominant bacteria. Moreover, the relative proportion of α-Proteobacteria increased and that of Bacteroidetes decreased gradually with time. Pathogenic Flexibacter was the dominant genus in Group A on the 45th day, while the functional strains (Sphingomonas sp., Erythrobacter sp., Roseobacter sp., and Rhodobacter sp.) were detected multiple times in Groups B and C. Bacillus sp. was the cultivable, dominant bacterium in Groups B and C on the 95th day. Therefore, the combined use of Bacillus and molasses helped increase diversity of the microbial community, effectively inhibit pathogens, and promote the formation and development of a beneficial microbial community structure in the high density, intensive aquaculture of L. vannamei.

Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C.

Abstract: Background The blood clam, Scapharca (Anadara) broughtonii, is an economically and ecologically important marine bivalve of the family Arcidae. Efforts to study their population genetics, breeding, cultivation, and stock enrichment have been somewhat hindered by the lack of a reference genome. Herein, we report the complete genome sequence of S. broughtonii, a first reference genome of the family Arcidae. Findings A total of 75.79 Gb clean data were generated with the Pacific Biosciences and Oxford Nanopore platforms, which represented approximately 86× coverage of the S. broughtonii genome. De novo assembly of these long reads resulted in an 884.5-Mb genome, with a contig N50 of 1.80 Mb and scaffold N50 of 45.00 Mb. Genome Hi-C scaffolding resulted in 19 chromosomes containing 99.35% of bases in the assembled genome. Genome annotation revealed that nearly half of the genome (46.1%) is composed of repeated sequences, while 24,045 protein-coding genes were predicted and 84.7% of them were annotated. Conclusions We report here a chromosomal-level assembly of the S. broughtonii genome based on long-read sequencing and Hi-C scaffolding. The genomic data can serve as a reference for the family Arcidae and will provide a valuable resource for the scientific community and aquaculture sector.