Male scat

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Try out PMC Labs and tell us what you think. Learn More. The spotted scat, Scatophagus argusis a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding.

However, genomic data from S. In the present male scat, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained.

This information will serve to support the breeding and aquaculture of S. The spotted scat, Scatophagus argusis a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has ificant economic value. Despite this, studies of its genome are severely lacking.

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In the present study, a genomic survey of S. In total, Genome sizes were estimated to be The sequence repeat ratios were calculated to be Heterozygosity ratios were 0. Re were assembled intofemale andmale contigs with N50 lengths male scat 5, and 5, bp for females and males, respectively. The average guanine-cytosine GC content of the female genome was A total of 42, female and 43, male genes were annotated to the non-redundant NR and SwissProt databases. The female and male genomes contained Dinucleotide repeats were the dominant form of simple sequence repeats SSR observed in females Additionally, gene fragments of Dmrt1 were only observed in the male genome.

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This is the first report of a genome-wide characterization of S. The spotted scat, Scatophagus argusPerciformes, Scatophagidaeis a popular species of fish known for both its aesthetic value and human consumption due to its rhombic spotted body and high nutrient value [ 123 ]. Moreover, unlike other species, the cultivation of S. The S. Analysis of the gut contents of S.

Furthermore, S. The adaptability of S. However, the main supply of S. In the absence of proper management, this has the potential to endanger the resource through overfishing [ 10 ]. Most studies examining this species have focused on reproduction and the importance of solving challenges associated with artificial propagation [ 11121314 ].

The female S. Therefore, from an economic perspective, all-female farms will improve the rate of production and the total market value. Thus, sex control would be a good strategy to employ in an S. In addition, understanding the mechanisms of sex determination and differentiation would be crucial to the effective male scat of all-female production [ 15 ]. In addition, differences in growth rate between males and females provide a valuable model to explore the mechanisms of sexual dimorphisms in vertebrates [ 16 ]. To date, the genomic information of S.

Next-generation, high-throughput sequencing NGS is an efficient strategy for generating genomic resources. This technology is currently in wide use for transcriptomic and genomic studies [ 1819male scat21 ]. Many genes in S. Furthermore, a comparative transcriptomic analysis of testicular and ovarian tissue has discovered many genes involved in sex determination and differentiation in S. To further compare the genomes of male and female S. These data will be the basis of a fundamental genomic resource for reproduction-related studies. In addition, these data also provide a foundation for future genomic studies of S.

Specimens of S. Two adults, one female and one male, were subjected to genome sequencing. The animals were immediately dissected following tricaine MS anaesthesia. White muscle tissue was used for DNA extraction. All animal experiments were conducted in accordance with the guidelines and approval of the Animal Research and Ethics Committees of the Institute of Aquatic Economic Animals of Guangdong Ocean University. The DNA was then sheared randomly into small fragments using an ultrasonic shearing device.

Two paired-end libraries with an insert size of base pairs bp were constructed from randomly fragmented genomic DNA, following a standard protocol Illumina, Beijing, China. To obtain clean re, raw re were filtered using the high-throughput quality control HTQC package [ 26 ]. Next, 5, clean-read pairs from each library were randomly selected and blasted against the National Center for Biotechnology Information NCBI nonredundant NR nucleotide database to check for obvious sample contamination.

All subsequent analyses were based on these clean re. The K-mer statistic was used to as male scat probability distributions for a of possible K-mer combinations [ 28 ].

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The copy of a given K-mer mer present male scat all clean Illumina re were counted then divided by the total length of each sequence read. The distribution of copy s was then plotted. The K-mer distribution can be used to male scat the size of the genome. The peak value of the frequency curve represents the overall sequencing depth.

Heterozygous K-mers will have half of the expected coverage depth compared to the homozygous K-mers. The heterozygosity rate can be estimated as follows:. The difference between the k-mer distribution and Poisson distribution is large due to the presence of incorrect sequences, or the of sequence layers, which affects later estimates. Hence, the repeat rates were calculated according to the percentage of the total of K-mers after the main peak, which was 1. The software SOAPdenovo v2. All clean re were used in the assembly, with a K-mer size of 41 selected as the default parameter used to construct a de Bruijn graph [ 32 ].

The de Bruijn graph was simplified by breaking the connections at repeat boundaries, with unambiguous sequence fragments outputted as contigs. After realigning all useable re to the contig sequences and obtaining aligned paired-end re, the of shared paired-end re having a relationship between each pair of contigs was calculated, the rate of consistent and conflicting paired-end re was rated and scaffolds constructed step-by-step using SOAPdenovo.

Gaps in the scaffolds were closed using GapCloser software v1. To measure the sequencing bias of S. The GC content is strictly controlled and moderately balanced across the genome [ 3334 ]. Ten kb non-overlapping sliding windows were used along the assembled sequences to calculate the GC average sequencing depth. GlimmerHMM software v. Our research indicated that Dmrt1 is linked to the Y chromosome, and the truncated homologue Dmrt1bis X chromosome-linked [ 38 ]. The predicted Dmrt1 and Dmrt1b genes observed during S.

The software is divided into two modules. The minimum s of SSRs for mono- di- tri- tetra- penta- and hexa-nucleotides adopted for identification were 10, 6, 5, 5, 5, and 5, respectively. The second module was used to filter the male scat the first module and then remove SSRs which were too close. A total of After filtering, The error rates of these libraries were 0.

It was observed that the best BLAST of re were enriched for closely related fish species, including Dicentrarchus labraxScatophagus argusHaplochromis burtoni and Oreochromis niloticus Table S1. The K-mer analysis indicated that the depth of female and male S. The estimated size of the female and male genomes was The revised genome sizes were The rates of heterozygosity were calculated to be 0. Distribution of mer depth and frequency of female and male S.

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Biochemical Analysis of Scatophagus argus (Spotted Scat)in the Kali River, Karwar