EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Research advances in the genomics and applications for molecular breeding of aquaculture animals

Effects of single or conjoint administration of lactic acid bacteria as potential probiotics on growth, immune response and disease resistance of snakehead fish (Channa argus).

// Mi Ou 1, 2 , Cheng Yang 1, 2 , Qing Luo 3 , Rong Huang 1 , Ai-Di Zhang 1 , Lan-Jie Liao 1 , Yong-Ming Li 1 , Li-Bo He 1 , Zuo-Yan Zhu 1 , Kun-Ci Chen 3 and Ya-Ping Wang 1 1 State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2 University of Chinese Academy of Sciences, Beijing 100049, China 3 Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China Correspondence to: Ya-Ping Wang, email: wangyp@ihb.ac.cn Kun-Ci Chen, email: chenkunci@aliyun.com Keywords: next generation sequencing; sex-specific molecular markers; snakehead Received: April 19, 2017     Accepted: August 07, 2017     Published: October 19, 2017 ABSTRACT We described a next generation sequencing (NGS)-based approach to identify sex-specific markers and subsequently determine whether a species has male or female heterogamety. To test the accuracy of this technique, we examined the snakehead ( Channa argus ), which is economically important freshwater fish in China. Males grow faster than females, and there is significant interest in developing methods to skew breeding towards all-males to increase biomass yields. NGS was conducted on DNAs of individual female and male, the male reads were spitted into 60 bp K-mers and aligned to the female reference genome assembled by female reads, unaligned male K-mers-60 were kept in next filter process. Meanwhile, DNA sample of 48 females was pooled and sequenced, this data was further used to filter out the previous unaligned male K-mers-60. Hence, numbers of candidate Y chromosome-specific sequences were screened out, their sex-specificity were validated in wild snakeheads through PCR amplification. Finally, three Y chromosome-specific fragments (Contig-275834, Contig-359642, and Contig-418354) were identified, and specific primers were obtained to distinguish the sex of snakehead. Additionally, a pair of primers of Contig-275834 (275834X/Y-F and 275834X/Y-R) was exploited to distinguish XX females, XY males, and YY super-males, whose amplification products of different lengths were produced for different sexes. Therefore, our work demonstrated the ability of NGS data in identification of sex-specific markers, and the pipeline adopted in our study could be applied in any species of sex differentiation. Furthermore, the sex-specific markers have tremendous potential for improving the efficiency of all-male breeding practices in snakehead.

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An NGS-based approach for the identification of sex-specific markers in snakehead (Channa argus).

Transcriptome analysis of immune-related gene expression in hybrid snakehead (Channa maculata ♀ × Channa argus ♂) after challenge with Nocardia seriolae.

Background: The Northern snakehead (Channa argus), a member of the Channidae family of the Perciformes, is an economically important freshwater fish native to East Asia. In North America, it has become notorious as an intentionally released invasive species. Its ability to breathe air with gills and migrate short distances over land makes it a good model for bimodal breath research. Therefore, recent research has focused on the identification of relevant candidate genes. Here, we performed whole genome sequencing of C. argus to construct its draft genome, aiming to offer useful information for further functional studies and identification of target genes related to its unusual facultative air breathing. Findings: We assembled the C. argus genome with a total of 140.3 Gb of raw reads, which were sequenced using the Illumina HiSeq2000 platform. The final draft genome assembly was approximately 615.3 Mb, with a contig N50 of 81.4 kb and scaffold N50 of 4.5 Mb. The identified repeat sequences account for 18.9% of the whole genome. The 19 877 protein-coding genes were predicted from the genome assembly, with an average of 10.5 exons per gene. Conclusion: We generated a high-quality draft genome of C. argus, which will provide a valuable genetic resource for further biomedical investigations of this economically important teleost fish.

/pdf/draft-genome-of-the-northern-snakehead-channa-argus-1cgxhpgxko.pdf

Draft genome of the Northern snakehead, Channa argus

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

https://www.mdpi.com/1660-3397/17/7/426/pdf

Qiong Shi

Papers

Draft genome of the Northern snakehead, Channa argus

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes.