RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus

Geng, Xiaofang; Zhang, Lu; Zang, Xiayan; Guo, Jiuxin; Xu, Chi

doi:10.1007/s00427-019-00641-9

Cited by 5 publications

(4 citation statements)

References 46 publications

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“…The distribution of the top BLAST hits indicates that putative proteins were similar to those of the Xenopus tropicalis and Chrysemys picta bellii which are amphibians (Fig. 1c), suggesting that the CGS transcriptome was well-assembled and approximate previous study [39].…”

Section: Functional Annotation Of Transcripts Of Cgs Meatsupporting

confidence: 53%

Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

Guan¹,

Tan²,

Li³

et al. 2024

Food Science and Human Wellness

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Andrias davidianus (Chinese giant salamander, CGS) is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in China. However, the progress of functional peptides mining was slow due to lack of reference genome and protein sequence data. In this study, we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10,703 coding DNA sequences. By functional annotation and amino acid composition analysis, we have discovered various genes related to signal transduction, and 16 genes related to longevity. We have also found vast variety of functional peptides through protein coding sequence (CDS) analysis by comparing the data obtained with the functional peptide database. Val-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis, suggesting that our approach is reliable. This study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat, thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.

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Section: Functional Annotation Of Transcripts Of Cgs Meatsupporting

confidence: 53%

Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

Guan¹,

Tan²,

Li³

et al. 2024

Food Science and Human Wellness

View full text Add to dashboard Cite

show abstract

“…RNA-seq analysis is an ideal high-throughput sequencing method, which provides high efficiency and rapidity for gene discovery and is useful for studying the large and complex genomes of amphibians 4 . In this study, RNA-seq technology was used to sequence the cDNA library of 45 samples from 9 tissues of five Heilongjiang brown frogs to construct a high-quality reference gene set and further analyze its tissue-specific expression.…”

Section: Discussionmentioning

confidence: 99%

“…Only one genome is available from Ranidae (true frogs), the North American bullfrog (Rana [Lithobates] catesbeiana), which is surprising as it is the largest frog family with species found on every continent except Antarctica 3 . Sequenced frog genomes may be limited by the high cost of large-genome sequencing, yet transcriptome analysis is economically viable for studying the large and complex genomes of amphibians 4 . Indeed, transcriptome sequencing technology has been used in many amphibian species [5][6][7] , and has provided novel insights into their gene expression profiles and the evolution of their immune systems.…”

mentioning

confidence: 99%

Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis)

Lan

Wang

et al. 2022

Sci Rep

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The Heilongjiang brown frog (Rana amurensis) is widely used in traditional Chinese medicine. In particular, the oviduct and skin have been developed into various health products. However, limited numbers of complete genomes of amphibian species have been reported, excluding the Heilongjiang brown frog. Here, the transcriptomes of 45 samples from the liver, spleen, heart, ovaries, thigh muscles, skin, oviduct, stomach and intestine of five Heilongjiang brown frog were reassembled and analyzed. A total of 1,085,532 unigenes with an average length of 676.6 bp and N50 of 722 bp were obtained. Comparative transcriptomics of different tissues detected tissue-specific expression. There were 3248 differentially expressed genes (DEGs) in the ovary, and the number of unique DEGs between the ovary and spleen was the largest. The results of DEGs enrichment showed there were many pathways and items related to protein synthesis and metabolism in the oviduct. The DEGs of the skin were enriched with many bacterial defense items, indicating that there were a large number of antimicrobial peptides in the skin. Thus, these were suitable as biological sources for the development and extraction of antimicrobial peptides. Through the assembly of transcriptome sequencing data and functional annotation of the Heilongjiang brown frog genome, this study provides reference materials for further exploring and utilizing functional gene resources of frogs and lays a foundation for medical research and the development of new products.

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“…A comparative transcriptomic analysis of the ovaries and testes revealed genes that facilitate adaptation to the environment as well as important sex-biased genes in A. davidianus [ 15 , 16 ]. An RNA-seq analysis from different parts of the skin has provided insight into the molecular adaptations of A. davidianus [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing

et al. 2021

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The Chinese giant salamander, Andrias davidianus, is the largest amphibian species in the world; it is thus an economically and ecologically important species. The skin of A. davidianus exhibits complex adaptive structural and functional adaptations to facilitate survival in aquatic and terrestrial ecosystems. Here, we report the first full-length amphibian transcriptome from the dorsal skin of A. davidianus, which was assembled using hybrid sequencing and the PacBio and Illumina platforms. A total of 153,038 transcripts were hybrid assembled (mean length of 2,039 bp and N50 of 2,172 bp), and 133,794 were annotated in at least one database (nr, Swiss-Prot, KEGG, KOGs, GO, and nt). A total of 58,732, 68,742, and 115,876 transcripts were classified into 24 KOG categories, 1,903 GO term categories, and 46 KEGG pathways (level 2), respectively. A total of 207,627 protein-coding regions, 785 transcription factors, 27,237 potential long non-coding RNAs, and 8,299 simple sequence repeats were also identified. The hybrid-assembled transcriptome recovered more full-length transcripts, had a higher N50 contig length, and a higher annotation rate of unique genes compared with that assembled in previous studies using next-generation sequencing. The high-quality full-length reference gene set generated in this study will help elucidate the genetic characteristics of A. davidianus skin and aid the identification of functional skin proteins.

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RNA-seq analysis provides insight into molecular adaptations of Andrias davidianus

Cited by 5 publications

References 46 publications

Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

Comparative transcriptomes of nine tissues for the Heilongjiang brown frog (Rana amurensis)

Full-length transcriptome assembly of andrias davidianus (amphibia: caudata) skin via hybrid sequencing

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