The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba

Domínguez-Pérez, Dany; Durbán, Jordi; Agüero-Chapin, Guillermin; López, Javier Torres; Ruiz, Reinaldo Molina; Almeida, Daniela; Calvete, Juan J.; Vasconcelos, Vı́tor; Antunes, Agostinho

doi:10.1016/j.ygeno.2018.11.026

Cited by 10 publications

(11 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Lipocalin (LCN) family is involved in immune response and pheromone transport (Dominguez-Pérez et al 2019). It contains evolutionary conserved genes and almost all of them are present in all animal kingdoms (Charkoftaki et al 2019).…”

Section: Discussionmentioning

confidence: 99%

A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits

Villamayor¹,

Robledo

Fernandez³

et al. 2020

Preprint

View full text Add to dashboard Cite

The vomeronasal organ (VNO) is a chemosensory organ specialized in the detection of pheromones and consequently the regulation of behavioural responses mostly related to reproduction. VNO shows a broad variation on its organization, functionality and gene expression in vertebrates, and although the species analyzed to date have shown very specific features, its expression patterns have only been well-characterized in mice. Despite rabbits represent a model of chemocommunication, unfortunately no genomic studies have been performed on VNO of this species to date. The capacity of VNO to detect a great variety of different stimuli suggests a large number of genes with complex organization to support this function. Here we provide the first comprehensive gene expression analysis of the rabbit VNO through RNA-seq across different sexual maturation stages. We characterized the VNO transcriptome, updating the number of the two main vomeronasal receptor (VR) families, 129 V1R and 70 V2R. Among others, the expression of transient receptor potential channel 2 (TRPC2), a crucial cation channel generating electrical responses to sensory stimulation in vomeronasal neurons, along with the specific expression of some fomyl-peptide receptors and H2-Mv genes, both known to have specific roles in the VNO, revealed a the particular gene expression repertoire of this organ, but also its singularity in rabbits. Moreover, juvenile and adult VNO transcriptome showed consistent differences, which may indicate that these receptors are tuned to fulfill specific functions depending on maturation age. We also identified VNO-specific genes, including most VR and TRPC2, thus confirming their functional association with the VNO. Overall, these results represent the genomic baseline for future investigations which seek to understand the genetic basis of behavioural responses canalized through the VNO.HIGHLIGHTSFirst description of the rabbit vomeronasal organ (VNO) transcriptomeVNO contains a unique gene repertoire depending on the speciesHigh fluctuation of the VNO gene expression reveals changes dependent on age and specific functionsMost vomeronasal-receptors (VR) and transient receptor potential channel 2 (TRPC2) genes are VNO-specificReproduction-related genes shows a wide expression pattern

show abstract

Section: Discussionmentioning

confidence: 99%

A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits

Villamayor¹,

Robledo

Fernandez³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Although they can determine the biological activity of bioactive compounds relatively at high accuracy, are time-consuming and the yield of bioactive compounds is low as well as the coverage of the chemical space [ 140 ]. On the contrary, the HT analyses can be performed with around 1 cm 3 or 0.5–1 g of fresh or preserved tissues, for genomic/transcriptomic or proteomic purposes, respectively [ 53 , 141 , 142 ]. Generally, the HT methods allow covering the whole picture for potential bioactive compounds much faster.…”

Section: Considerations In the Workflow For The High-throughput Disco...mentioning

confidence: 99%

“…Among the NGS analyses, the RNA-seq has gained relevance because it can explore the coding regions of the genome by assembling, annotating and comparing expression profiles of the resulting transcripts [ 141 , 156 ]. Since elucidating the transcriptome demands lower computational cost than whole genome, and also provide useful information, its number has increasingly growth in databases.…”

Section: Considerations In the Workflow For The High-throughput Disco...mentioning

confidence: 99%

See 1 more Smart Citation

Emerging Computational Approaches for Antimicrobial Peptide Discovery

et al. 2022

Self Cite

View full text Add to dashboard Cite

In the last two decades many reports have addressed the application of artificial intelligence (AI) in the search and design of antimicrobial peptides (AMPs). AI has been represented by machine learning (ML) algorithms that use sequence-based features for the discovery of new peptidic scaffolds with promising biological activity. From AI perspective, evolutionary algorithms have been also applied to the rational generation of peptide libraries aimed at the optimization/design of AMPs. However, the literature has scarcely dedicated to other emerging non-conventional in silico approaches for the search/design of such bioactive peptides. Thus, the first motivation here is to bring up some non-standard peptide features that have been used to build classical ML predictive models. Secondly, it is valuable to highlight emerging ML algorithms and alternative computational tools to predict/design AMPs as well as to explore their chemical space. Another point worthy of mention is the recent application of evolutionary algorithms that actually simulate sequence evolution to both the generation of diversity-oriented peptide libraries and the optimization of hit peptides. Last but not least, included here some new considerations in proteogenomic analyses currently incorporated into the computational workflow for unravelling AMPs in natural sources.

show abstract

“…Transcription termination sites were predicted using sequence similarity [14] and manual inspection of raw reads showing transition to polyA at the respective termination position. SRR5440420 contains raw reads from the Harderian gland transcriptome of a wild-caught adult Caribbean watersnake (Tretanorhinus variabilis (Duméril, Bibron & Duméril, 1854); family Colubridae) from Santa Fe, La Habana, Cuba [15]. SRR9693197 contains raw reads from the venom gland transcriptome of a wild-caught juvenile Mexican black-tailed rattlesnake (Crotalus molossus nigrescens (Gloyd, 1936); family Viperidae) from Nuevo León, Mexico.…”

mentioning

confidence: 99%

Two novel bornaviruses identified in colubrid and viperid snakes

Pfaff

Rubbenstroth

2021

Arch Virol

View full text Add to dashboard Cite

We present the complete genome sequences of Caribbean watersnake bornavirus (CWBV) and Mexican black-tailed rattlesnake bornavirus (MRBV), which we identified in archived raw transcriptomic read data of a Caribbean watersnake (Tretanorhinus variabilis) and a Mexican black-tailed rattlesnake (Crotalus molossus nigrescens), respectively. The genomes of CWBV and MRBV have a length of about 8,900 nucleotides and comprise the complete coding regions and the untranslated regions. The overall genomic makeup and predicted gene content is typical for members of the genus Orthobornavirus within the family Bornaviridae. Alternative splicing was detected for the L and M genes. Based on a phylogenetic analysis of all viral proteins, we consider both viruses to be members of a single novel species within the genus Orthobornavirus. Both viruses form a distinct outgroup to all currently known orthobornaviruses. Based on the novel virus genomes, we furthermore identified closely related endogenous bornavirus-like nucleoprotein sequences in transcriptomic data of veiled chameleons (Chamaeleo calyptratus) and a common lancehead (Bothrops atrox).

show abstract

The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba

Abstract: The Harderian gland transcriptomes of Caraiba andreae, Cubophis cantherigerus and Tretanorhinus variabilis, three colubroid snakes from Cuba

Cited by 10 publications

References 76 publications

A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits

A comprehensive analysis of vomeronasal organ transcriptome reveals variable gene expression depending on age and function in rabbits

Emerging Computational Approaches for Antimicrobial Peptide Discovery

Two novel bornaviruses identified in colubrid and viperid snakes

Contact Info

Product

Resources

About