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Peer-reviewedCC BYBMC bioinformatics

ShEnrich: a functional annotation database and enrichment platform for penaeid shrimp.

  • Harikrishnan Udayakumar Geetha1
  • Ashok Kumar Jangam2
  • Vinaya Kumar Katneni1
  • Syama Dayal Jagabattula1
  • Panjan Nathamuni Suganya1
  • Mudagandur Shashi Shekhar3
  • Ritwika Das4
  • Monendra Grover4
  • Girish Kumar Jha4
4 affiliations
  1. 1Nutrition Genetics and Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, 600028, India.
  2. 2Nutrition Genetics and Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, 600028, India. [email protected].
  3. 3Aquatic Animal Health and Environment Division, ICAR- Central Institute of Brackishwater Aquaculture, Chennai, 600028, India.
  4. 4Agriculture Bioinformatics Division, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
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Abstract

Background

Penaeid shrimp are among the most commercially important aquaculture species globally, yet no dedicated integrated functional annotation and enrichment analysis platform currently for penaeid shrimp. Researchers working with shrimp transcriptomic data currently rely on generic enrichment tools built around model organisms that provide limited or no coverage for most penaeid species. In this context, current study aims to develop annotation and enrichment analysis platform for commercially important shrimp species.Methods

ShEnrich was developed using a multi-tiered annotation pipeline combining BLASTP searches against the NCBI non-redundant database, InterProScan domain prediction, and eggNOG-mapper orthology assignments. Cross-species ortholog clustering was performed using OrthoMCL across five commercially farmed penaeid species. GMT libraries for each species were constructed for KEGG and GO enrichment analysis, implemented using the clusterProfiler R package. The platform was built on a MySQL 8.0 relational database with a PHP 8.1 backend and an integrated JBrowse2 genome browser.Results

The database integrates 61,287 annotated proteins representing 34,169 genes, with 178,595 gene-pathway associations across 442 KEGG pathways and 138,077 proteins mapped to 12,897 GO terms across five species: Penaeus vannamei, Penaeus monodon, Penaeus indicus, Penaeus chinensis, and Penaeus japonicus. Cross-species comparative genomics is supported through 18,031 ortholog groups identified using OrthoMCL. The web platform provides KEGG and GO enrichment analysis, protein annotation search, ortholog browsing, and genome visualization. ShEnrich is freely available at https://bioinfo.ciba.res.in/shenrich/ .Conclusions

ShEnrich provides the first dedicated functional annotation and enrichment analysis resource for penaeid shrimp, filling a gap that has limited biological interpretation of transcriptomic data in this economically important group. The platform supports functional analysis of gene expression studies across disease, stress, and environmental conditions in commercially farmed shrimp species.

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Cite

BibTeXRIS
BibTeX
@article{geetha2026shenrich,
  title = {{ShEnrich: a functional annotation database and enrichment platform for penaeid shrimp.}},
  author = {Harikrishnan Udayakumar Geetha and Ashok Kumar Jangam and Vinaya Kumar Katneni and Syama Dayal Jagabattula and Panjan Nathamuni Suganya and Mudagandur Shashi Shekhar and Ritwika Das and Monendra Grover and Girish Kumar Jha},
  journal = {BMC bioinformatics},
  year = {2026},
  month = aug,
  doi = {10.1186/s12859-026-06567-0},
  url = {https://europepmc.org/article/MED/42963765},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - ShEnrich: a functional annotation database and enrichment platform for penaeid shrimp.
AU  - Harikrishnan Udayakumar Geetha
AU  - Ashok Kumar Jangam
AU  - Vinaya Kumar Katneni
AU  - Syama Dayal Jagabattula
AU  - Panjan Nathamuni Suganya
AU  - Mudagandur Shashi Shekhar
AU  - Ritwika Das
AU  - Monendra Grover
AU  - Girish Kumar Jha
PY  - 2026
DA  - 2026/08/03
JO  - BMC bioinformatics
DO  - 10.1186/s12859-026-06567-0
UR  - https://europepmc.org/article/MED/42963765
AB  - Background  Penaeid shrimp are among the most commercially important aquaculture species globally, yet no dedicated integrated functional annotation and enrichment analysis platform currently for penaeid shrimp. Researchers working with shrimp transcriptomic data currently rely on generic enrichment tools built around model organisms that provide limited or no coverage for most penaeid species. In this context, current study aims to develop annotation and enrichment analysis platform for commercially important shrimp species.Methods  ShEnrich was developed using a multi-tiered annotation pipeline combining BLASTP searches against the NCBI non-redundant database, InterProScan domain prediction, and eggNOG-mapper orthology assignments. Cross-species ortholog clustering was performed using OrthoMCL across five commercially farmed penaeid species. GMT libraries for each species were constructed for KEGG and GO enrichment analysis, implemented using the clusterProfiler R package. The platform was built on a MySQL 8.0 relational database with a PHP 8.1 backend and an integrated JBrowse2 genome browser.Results  The database integrates 61,287 annotated proteins representing 34,169 genes, with 178,595 gene-pathway associations across 442 KEGG pathways and 138,077 proteins mapped to 12,897 GO terms across five species: Penaeus vannamei, Penaeus monodon, Penaeus indicus, Penaeus chinensis, and Penaeus japonicus. Cross-species comparative genomics is supported through 18,031 ortholog groups identified using OrthoMCL. The web platform provides KEGG and GO enrichment analysis, protein annotation search, ortholog browsing, and genome visualization. ShEnrich is freely available at https://bioinfo.ciba.res.in/shenrich/ .Conclusions  ShEnrich provides the first dedicated functional annotation and enrichment analysis resource for penaeid shrimp, filling a gap that has limited biological interpretation of transcriptomic data in this economically important group. The platform supports functional analysis of gene expression studies across disease, stress, and environmental conditions in commercially farmed shrimp species.
SN  - 1471-2105
ER  -