Dataset Information

A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia.

ABSTRACT: The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.

SUBMITTER: Arenas Gomez CM

PROVIDER: S-EPMC7038590 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia.

Arenas Gómez Claudia M CM Woodcock M Ryan MR Smith Jeramiah J JJ Voss S Randal SR Delgado Jean Paul JP

Data in brief 20200211

The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled tr ...[more]

PMID: 32123704

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Project description:BackgroundPandi's mushroom-tongue salamander (Bolitoglossa pandi) is one of the threatened amphibians in South America, as well as a flagship species for the Colombian conservation agenda. This species is endemic to the Andean cloud forests of the western slope of the Cordillera Oriental of Colombia, occurring only in the department of Cundinamarca within a narrow elevational range. At night, B. pandi can be seen perching on the upper side of leaves at heights ranging from ground level to 2.5 m. During the day, it can be found under leaf litter or cover objects. Few studies have provided relevant information that can help the Colombian government to formulate lines of action for the conservation of this species; consequently, its threat assessments so far have been based on very limited information.MethodsWe conducted surveys for salamanders in four municipalities of Cundinamarca, Colombia, using two approaches: visual encounter surveys (Guaduas and Villeta) and the basic sampling protocol for single-species occupancy modeling (Supatá and Venecia). Multivariate analyses were employed to explore the correlation between habitat structure and natural history traits, abundance, and detection/non-detection of B. pandi. We evaluated the B. pandi activity pattern through kernel density curves for each sampling occasion and explored the variability of salamander abundance during their activity period by performing a nested ANOVA.ResultsWe report the discovery of two new populations of B. pandi, which represent the most northwestern records known. A significant correlation between body length, body mass, and habitat structure was observed. Multivariate analyses indicated that leaf litter depth, mean temperature, percent vegetation cover, and altitude were the habitat variables that together explained 60.3% of the B. pandi abundance variability, as well as the main determinants of its optimal habitat. Bolitoglossa pandi exhibits an activity pattern characterized by two main activity peaks, in which niche time-partitioning was observed. Across the surveyed area, we found a healthy, stable, highly dense population of B. pandi (>1,300 individuals), with seasonal variability between development stages.DiscussionGiven the high habitat specificity of B. pandi, the species is highly vulnerable to local changes. Thus, we recommend that B. pandi be retained as Endangered (EN) on the IUCN Red List, based on the IUCN Criterion B, given its restricted extent of occurrence (ca. 2,500 km2) and the ongoing threats from agriculture, cattle ranching, logging, and urban development, which continue to reduce its suitable habitat.

Dataset Information

A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia.

Publications

A <i>de novo</i> reference transcriptome for <i>Bolitoglossa vallecula</i>, an Andean mountain salamander in Colombia.

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