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2021;16 (4): e0249801.

De novo assembly of the freshwater prawn Macrobrachium carcinus brain transcriptome for identification of potential targets for antibody development.

Jonathan L Crooke-Rosado, Sara C Diaz-Mendez, Yamil E Claudio-Roman, Nilsa M Rivera, Maria A Sosa
Author Information
  1. Jonathan L Crooke-Rosado: Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.
  2. Sara C Diaz-Mendez: Department of Biology, Cayey Campus, University of Puerto Rico, Cayey, Puerto Rico. ORCID
  3. Yamil E Claudio-Roman: Department of Biology, Cayey Campus, University of Puerto Rico, Cayey, Puerto Rico.
  4. Nilsa M Rivera: Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico.
  5. Maria A Sosa: Department of Anatomy & Neurobiology, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, Puerto Rico. ORCID
PMID: 33836025 DOI: 10.1371/journal.pone.0249801

Abstract

Crustaceans are major constituents of aquatic ecosystems and, as such, changes in their behavior and the structure and function of their bodies can serve as indicators of alterations in their immediate environment, such as those associated with climate change and anthropogenic contamination. We have used bioinformatics and a de novo transcriptome assembly approach to identify potential targets for developing specific antibodies to serve as nervous system function markers for freshwater prawns of the Macrobrachium spp. Total RNA was extracted from brain ganglia of Macrobrachium carcinus freshwater prawns and Illumina Next Generation Sequencing was performed using an Eel Pond mRNA Seq Protocol to construct a de novo transcriptome. Sequencing yielded 97,202,662 sequences: 47,630,546 paired and 1,941,570 singletons. Assembly with Trinity resulted in 197,898 assembled contigs from which 30,576 were annotated: 9,600 by orthology, 17,197 by homology, and 3,779 by transcript families. We looked for glutamate receptors contigs, due to their main role in crustacean excitatory neurotransmission, and found 138 contigs related to ionotropic receptors, 32 related to metabotropic receptors, and 18 to unidentified receptors. After performing multiple sequence alignments within different biological organisms and antigenicity analysis, we were able to develop antibodies for prawn AMPA ionotropic glutamate receptor 1, metabotropic glutamate receptor 1 and 4, and ionotropic NMDA glutamate receptor subunit 2B, with the expectation that the availability of these antibodies will help broaden knowledge regarding the underlying structural and functional mechanisms involved in prawn behavioral responses to environmental impacts. The Macrobrachium carcinus brain transcriptome can be an important tool for examining changes in many other nervous system molecules as a function of developmental stages, or in response to particular conditions or treatments.

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Grants

  1. G12 MD007600/NIMHD NIH HHS
  2. R25 GM061838/NIGMS NIH HHS
  3. U54 MD007600/NIMHD NIH HHS

MeSH Term

Animals
Antibodies
Brain
Ecosystem
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Molecular Sequence Annotation
Palaemonidae
Receptors, Glutamate
Transcriptome

Chemicals

Antibodies
Receptors, Glutamate
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 1

Word Cloud

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