Iso-seq analysis and functional annotation of the Santa Fe cave crayfish (Procambarus erythrops) transcriptome.

Mar Genomics

Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, United States of America; School of Natural Resources and Environment, University of Florida, Gainesville, FL 32611, United States of America. Electronic address:

Published: August 2021


Category Ranking

98%

Total Visits

921

Avg Visit Duration

2 minutes

Citations

20

Article Abstract

The genus Procambarus represents a diverse genus of freshwater crayfish that includes epigean species, stygobitic species, and at least one parthenogenic species. Despite its evolutionary, ecological, and economic importance, most genomic and transcriptomic resources for this genus are limited to a couple of model species. We sequenced the transcriptome of a non-model species, P. erythrops, a geographically restricted stygobitic species from Florida. RNA isolated from gill, muscle and eye tissue was pooled to create a de novo transcriptome assembly using Single Molecule Real-Time sequencing (PacBio), resulting in 19,442 full-length isoforms. The assembly has been deposited in the NCBI (BioProject PRJNA657230). These data will make an important contribution to the comparative study of transcriptome evolution in crayfish and crustaceans.

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.margen.2021.100842DOI Listing

Publication Analysis

Top Keywords

stygobitic species
8
species
6
iso-seq analysis
4
analysis functional
4
functional annotation
4
annotation santa
4
santa cave
4
cave crayfish
4
crayfish procambarus
4
procambarus erythrops
4

Similar Publications

Groundwater ecosystems play a pivotal role in global biodiversity and ecosystem functioning, yet they face increasing pressures from climate change. The amphipod genus Niphargus, a dominant taxon in European groundwater habitats, has shown evidence of broad thermal adaptability that challenges prevailing theories on narrow thermal niches in groundwater species. This study investigated the locomotory behaviour of Niphargus longicaudatus (Costa, 1851), a stygobitic amphipod, under habitat temperature (9 °C) and preferred temperature (15 °C) using 3D tracking techniques.

View Article and Find Full Text PDF

Trophic ecology in an anchialine cave: A stable isotope study.

PLoS One

January 2025

Colección Nacional de Crustáceos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico, Ciudad de México, Mexico.

Article Synopsis
  • Carbon and nitrogen stable isotopes (δ13C and δ15N) are valuable tools in ecology for tracing energy flows in food webs, particularly in underexplored ecosystems like anchialine caves.
  • Sampling at Cenote Vaca Ha in Mexico revealed insights into the nutrient sources for seven endemic stygobitic species, highlighting that isotopic patterns are consistent over time despite some variation.
  • The study identified shrimp Typhlatya pearsei as a crucial species linking chemosynthetic microbial production to the anchialine food web, indicating a stable ecosystem reliant on bacterial sources for energy.
View Article and Find Full Text PDF

Environmental risk of diclofenac in European groundwaters and implications for environmental quality standards.

Sci Rep

September 2024

Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Campo Grande, Lisbon, Portugal.

Article Synopsis
  • - Groundwater is home to unique species that thrive in darkness, and these organisms contribute significantly to global ecosystem services, but they face threats from contamination, particularly from drugs like diclofenac.
  • - The study assessed the environmental risks of diclofenac in European groundwaters, analyzing its concentrations and potential effects on groundwater species, particularly the crustacean Proasellus lusitanicus.
  • - Results indicate that while current diclofenac levels are generally safe for P. lusitanicus, different groundwater species show varying sensitivities. The study recommends setting a precautionary environmental quality standard for diclofenac at 5 ng/L to protect these vital ecosystems.
View Article and Find Full Text PDF

Aliphatic chlorinated hydrocarbons, notably tetrachloroethylene (also known as perchloroethylene [PCE]), are persistent, mobile, and toxic (PMT) and/or very persistent, mobile, and toxic (vPMT) groundwater pollutants, often exceeding safe drinking water thresholds. The present study delves into the groundwater risk assessment of PCE with a novel focus on the sensitivity of stygobitic species-organisms uniquely adapted to groundwater environments. Through a comparative analysis of the subchronic effects of PCE on the locomotion behavior of two copepod species, the stygobitic Moraria sp.

View Article and Find Full Text PDF