Phyloinformatics Lab

Genome skimming enabled efficient molecular prospecting of old museum specimens

Denis Jacob Machado December 18, 2025
genomicsparasitologypublicationbioinformatics

Mining natural history collections for molecular treasures

Figure 2, from Alves (2025), illustrating the mitogenome of _Pseudoendorchis auchenipteri_ (de Chambrier & Vaucher, 1999) (PX326305; MHNG-PLAT-86963). All other proteocephalids exhibit the same gene architecture, with all genes encoded on the same strand and transcribed in the same direction. PCG, protein-coding genes; tRNA, transfer RNA genes; rRNA, ribosomal RNA genes; NCR, non-coding regions.
Figure 2, from Alves (2025), illustrating the mitogenome of Pseudoendorchis auchenipteri (de Chambrier & Vaucher, 1999) (PX326305; MHNG-PLAT-86963). All other proteocephalids exhibit the same gene architecture, with all genes encoded on the same strand and transcribed in the same direction. PCG, protein-coding genes; tRNA, transfer RNA genes; rRNA, ribosomal RNA genes; NCR, non-coding regions.

Dr. Alves received a Research Intership Abroad (BEPE) Award from the São Paulo Research Foundations (FAPESP; Proc. No. Process No.2023/00714-5). This award funded Dr. Alves’ reserach in collaboration with the Phyloinformatics Lab from July 1, 2023, to June 30, 2024.

In a new article by Dr. Philippe Vieira Alves, we show that genome skimming enabled efficient molecular prospecting of decades-old museum specimens. Mitogenomes and nuclear ribosomal transcription unit sequence data were generated from 88 archived proteocephalid samples. We generated the most character-rich phylogeny to date for proteocephalids (Onchoproteocephalidea I). We also conducted phylogenetic analysis and observed that the general tree topologies are consistent with the phylogenies of previous studies.

The data generated in this new publication by Dr. Alvez, thanks to the funding by FAPESP, provides a solid foundation for future multilocus phylogenetic and comparative studies of cestodes and highlights the value of genome skimming using decades-old archived samples. New avenues for exploring the evolutionary history of proteocephalid cestodes are discussed.

Click here to read the full article

Previous post
Stoic Dedication and Scientific Discovery Next post