Transcriptomic annotation of the Chungtien schizothoracin (Ptychobarbus chungtienensis) using Iso-seq and RNA-seq data.

The Chungtien schizothoracin (Ptychobarbus chungtienensis), an endangered fish species endemic to the Zhongdian Plateau, remains underexplored in terms of transcriptomic sequencing. This investigation used tissues from five distinct organs (heart, liver, spleen, kidney, and brain) of the Chungtien schizothoracin for PacBio Iso-seq and RNA-seq analyses, yielding a repertoire of 16,598 full-length transcripts spanning lengths from 363 bp to 7,157 bp. Gene family clustering and phylogenetic analysis encompassed a comprehensive set of 13 fish species, all of which were cyprinids, including the zebrafish and the examined species Ptychobarbus chungtienensis. Moreover, the identification of long non-coding RNAs (lncRNAs) and coding sequences was accomplished across all five tissues. Comprehensive analyses of gene expression profiles and differentially expressed genes among the above five tissues were performed. In summary, the obtained full-length transcripts and detailed gene expression profiles of the Chungtien schizothoracin tissues furnish crucial expression data and genetic sequences, laying the groundwork for future investigations and fostering a holistic comprehension of the adaptive mechanisms inherent in the Chungtien schizothoracin under various conditions.

[Preliminary study on single nucleotide polymorphisms and linkage disequilibrium in promoter region of fibrinogen B beta gene].

OBJECTIVE: To investigate the distribution characters and linkage disequilibrium of single nucleotide polymorphisms (SNPs) -148C/T, -455G/A and -854G/A in the promoter region of fibrinogen B(FGB) beta gene. METHODS: Genotype and allele frequencies of FGB beta gene were examined by polymerase chain reaction-restriction fragment length polymorphism and nucleotide sequencing methods in 377 Chinese southern Han individuals. Three FGB beta SNPs Hardy-Weinberg equilibrium and linkage disequilibrium were analyzed with population genetics methods. RESULTS: The allele frequencies of 3 SNPs are in good agreement with Hardy-Weinberg equilibrium. A total of 9 genotypes among the 377 individuals were identified in 3 SNPs. The genotype frequencies of -148CC, CT and TT were 0.597, 0.358 and 0.045, respectively; the -455G/A genotype frequencies were the same as that of -148C/T SNP; the genotype frequencies of -854GG,GA, AA were 0.820,0.178,0.002, respectively. The frequencies of rare allele -148T, -455A and -854A were 0.224,0.224 and 0.092, respectively, while the common allele frequencies were 0.776 for -148C, 0.776 for -455G, and 0.908 for -854G. There were no statistically significant differences in genotype and allele frequencies between the male and female groups (P>0.05). The relationship between -455G and -148C was completely concordant, but there was a random distribution between -854 and -148 (-445) SNPs. CONCLUSION: The results show there is a complete linkage disequilibrium between -148C/T and -455G/A and a negative linkage disequilibrium between -854G/A and -148C/T, as well as between -854G/A and -455G/A. This study has provided population genetics data on FGB beta gene promoter in Chinese southern Han population.