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Rhizaria are a diverse group of unicellular protists characterized by their threadlike cytoplasmic extensions known as pseudopodia. These structures aid in both locomotion and feeding, giving Rhizaria an amoeboid appearance. Their amoeboid morphology once led to taxonomic confusion, but molecular phylogenetics has clarified their evolutionary placement and emphasized their shared use of pseudopodia despite divergent lineages.This clade comprises diverse lineages such as Chlorarachniophyta,...
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Amoebozoa represent a diverse group of terrestrial and aquatic protists that utilize lobe-shaped pseudopodia for locomotion and feeding. This characteristic differentiates them from the Rhizaria, which possess threadlike pseudopodia. The primary classifications within Amoebozoa include gymnamoebas, entamoebas, and the plasmodial and cellular slime molds. Phylogenetic evidence indicates that Amoebozoa diverged from a lineage that ultimately gave rise to fungi and animals.Gymnamoebas and...
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Updated: Jul 22, 2025

Assessing Intertidal Populations of the Invasive European Green Crab
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Where are the Penaeids crustins?

Marcel Martinez-Porchas1, Jorge Hernández-López2, Francisco Vargas-Albores1

  • 1Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.

Peerj
|July 25, 2023
PubMed
Summary

High-throughput sequencing can misidentify antimicrobial crustin proteins. This study highlights the need to integrate previous data for accurate crustin identification and phylogenetic analysis in crustaceans.

Keywords:
4-DSC domainAntimicrobial peptideCrustin signatureCys-rich regionShrimp

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Area of Science:

  • Marine Biology
  • Genomics
  • Immunology

Background:

  • Crustins are antimicrobial peptides belonging to the four-disulfide core (4-DSC) domain superfamily, exclusively found in crustaceans.
  • They possess a characteristic structure with a single 4-DSC domain and a cysteine-rich region.
  • High-throughput sequencing technologies generate vast genomic data, potentially leading to the misannotation or loss of information on previously identified molecules.

Purpose of the Study:

  • To assess information loss in crustin identification due to automated annotation in high-throughput sequencing.
  • To identify and list potential crustin sequences in Penaeids based on structural similarities.
  • To enable phylogenetic relationship establishment for crustin genes in shrimp.

Main Methods:

  • Retrieved all registered crustin sequences from Penaeids in databases.
  • Filtered sequences based on structural characteristics (4-DSC domain, cysteine-rich region).
  • Employed local alignments to identify sequences with high structural similarity, even if annotated differently.

Main Results:

  • Crustin sequences from Sanger and transcriptomics data, meeting structural criteria, were correctly identified.
  • Crustin sequences from whole-genome sequencing projects were often misclassified or uncharacterized.
  • Geographical clustering of crustin sequences was observed, with distinct groups for American and Asian shrimp species.

Conclusions:

  • Automated annotation in whole-genome sequencing projects can obscure or misidentify crustin sequences.
  • Revisiting and integrating previously validated data is crucial for accurate crustin annotation.
  • Structural analysis aids in understanding the evolutionary trajectory and phylogenetic relationships of crustins in shrimp.