Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between fast- and slow-growing king ratsnakes (Elaphe carinata)

Khan, Shaukat Ali; He, Jun; Deng, Shuaitao; Zhang, Huijuan; Liu, Guangxuan; Li, Shikun; Tang, Dong; Zhang, Jihui; Shu, Yilin

doi:10.1016/j.cbpb.2020.110482

Cited by 2 publications

(2 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…When threatened, E.carinata can use its anal glands to secrete a foul-smelling fluid [ 3 ] . King ratsnakes are farmed in many countries as an important food source as they provide a large amount of proteins [ 4 ] . According to the China Red Data Book of Endangered Animals [ 5 ] , the king ratsnake is listed as a vulnerable species.…”

Section: Data Descriptionmentioning

confidence: 99%

Genome assembly and annotation of the king ratsnake, Elaphe carinata

Fan,

Huang,

Yang

et al. 2023

Gigabyte

View full text Add to dashboard Cite

The king ratsnake (Elaphe carinata) of the genus Elaphe is a common large, non-venomous snake widely distributed in Southeast and East Asia. It is an economically important farmed species. As a non-venomous snake, the king ratsnake predates venomous snakes, such as cobras and pit vipers. However, the immune and digestive mechanisms of the king ratsnake remain unclear. Despite their economic and research importance, we lack genomic resources that would benefit toxicology, phylogeography, and immunogenetics studies. Here, we used single-tube long fragment read sequencing to generate the first contiguous genome of a king ratsnake from Huangshan City, Anhui province, China. The genome size is 1.56 GB with a scaffold N50 of 6.53M. The total length of the genome is approximately 621 Mb, while the repeat content is 42.26%. Additionally, we predicted 22,339 protein-coding genes, including 22,065 with functional annotations. Our genome is a potentially useful addition to those available for snakes.

show abstract

Section: Data Descriptionmentioning

confidence: 99%

Genome assembly and annotation of the king ratsnake, Elaphe carinata

Fan,

Huang,

Yang

et al. 2023

Gigabyte

View full text Add to dashboard Cite

show abstract

“…Although the functions of miRNAs and lncRNAs in humans and other model organisms have been gradually recognized over the last two decades ( Beermann et al 2016 ), their roles in specialized species and organs, such as the snake venom gland, remain enigmatic. To date, several studies have covered the unidirectional modulating effects of miRNAs on toxin synthesis in venomous snakes and on muscle growth in nonvenomous snakes ( Durban et al 2013 ; Durban et al 2017 ; Durban et al 2018 ; Khan et al 2020 ), but only one study has involved the identification of venom-related lncRNAs, which were supposed to encode two functional myotoxins in the prairie rattlesnake ( Gopalan et al 2022 ). More importantly, as lncRNAs can provide decoy targets for miRNAs and act as competing endogenous RNAs (ceRNAs) ( Cesana et al 2011 ), the probable interactions among these ceRNAs, miRNAs, and mRNAs in the regulation of venom protein expression are currently poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Comparative Venom Multiomics Reveal the Molecular Mechanisms Driving Adaptation to Diverse Predator–Prey Ecosystems in Closely Related Sea Snakes

Zheng

Wang

Huang

et al. 2023

Molecular Biology and Evolution

View full text Add to dashboard Cite

Predator-prey arms races are ideal models for studying the natural selection and adaptive evolution that drive the formation of biological diversity. For venomous snakes, venom is a key bridge linking snakes with their prey, but whether and how venom evolves under the selection of diet remains unclear. Here, we focused on two closely related sea snakes, Hydrophis cyanocinctus and H. curtus, which show significant differences in prey preferences. Data-independent acquisition (DIA)-based proteomic analysis revealed different degrees of homogeneity in the venom composition of the two snakes, which was consistent with the differential phylogenetic diversity of their prey. By investigating the sequences and structures of three-finger toxins (3FTx), a predominant toxin family in elapid venom, we identified significant differences between the two sea snakes in the binding activity of 3FTx to receptors from different prey populations, which could explain the trophic specialization of H. cyanocinctus. Furthermore, we performed integrated multi-omics profiling of the transcriptomes, miRNAs, lncRNAs, and proteomes of the venom glands; constructed venom-related mRNA-miRNAs-lncRNA networks; and identified a series of ncRNAs involved in the regulation of toxin gene expression in the two species. These findings are highly informative for elucidating the molecular basis and regulatory mechanisms that account for discrepant venom evolution in response to divergent diets in closely related snakes, providing valuable evidence for the study of co-selection and co-evolution in predator-prey ecosystems.

show abstract

Integrated analysis of mRNA and miRNA expression profiles reveals muscle growth differences between fast- and slow-growing king ratsnakes (Elaphe carinata)

Cited by 2 publications

References 79 publications

Genome assembly and annotation of the king ratsnake, Elaphe carinata

Genome assembly and annotation of the king ratsnake, Elaphe carinata

Comparative Venom Multiomics Reveal the Molecular Mechanisms Driving Adaptation to Diverse Predator–Prey Ecosystems in Closely Related Sea Snakes

Contact Info

Product

Resources

About