Mitogenome organization, diversity, and evolutionary relationships of proteocephalidean tapeworms (Cestoda, Onchoproteocephalidea) unveiled by a genome skimming approach
Creators: name: Vieira Alves, Philippe
name: da Silva, Reinaldo J.
name: Janies, Daniel
name: Taylor, Willian
name: Harris, April
name: New, Gari
name: Jacob Machado, Denis
Publisher: name: Zenodo
Year: 2024

description: This presentation was delivered at the ASP 99th Annual Meeting (Denver, Colorado, USA) by Dr. Philippe Vieira Alves (Dept. of Parasitology, São Paulo State University-UNESP).

AUTHORS

Philippe V. Alves(1,2), Reinaldo J. da Silva(1), Daniel Janies (2,3), Willian Taylor(3), April Harris(3), Gari New(3), Denis J. Machado (2,3).

INSTITUTIONS

(1) São Paulo State University (UNESP), Institute of Biosciences, Section of Parasitology, Botucatu, SP, Brazil; (2) University of North Carolina at Charlotte, Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Charlotte, NC, USA (3) University of North Carolina at Charlotte (UNC Charlotte), Department of Bioinformatics & Genomics (BiG)

TITLE

Mitogenome organization, diversity, and evolutionary relationships of proteocephalidean tapeworms (Cestoda, Onchoproteocephalidea) unveiled by a genome skimming approach

ABSTRACT

Proteocephalidean tapeworms (Onchoproteocephalidea I) are a diverse group of acetabulate cestodes that primarily infect bony fishes, snakes, and lizards worldwide. While molecular data, mainly from Sanger sequencing of the nuclear 28S rRNA and the mitochondrial MT-CO1, has been crucial to a better understanding of the taxonomy and systematics of proteocephalids, long-standing questions on the evolution of this taxon remain to be answered. Here, we subjected ethanol-preserved proteocephalid specimens to high-throughput DNA sequencing, using a genome skimming approach, to unravel the mitogenome organization and diversity of dozens of species. Posteriormost proglottids of vouchered specimens were provided by the Natural History Museum (Platyhelminthes collection), Geneva, Switzerland (MHNG-PLAT), and the Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic (IPCAS). Of 96 Illumina sequenced libraries, 90 yielded complete or partial mitogenomes. These 90 mitogenomes correspond to 83 species in 40 genera from all continents except Antarctica, including parasites of fishes (87%), snakes, monitor lizards (Varanidae), and the common opossum Didelphis marsupialis (the only mammal known to host proteocephalids). The resulting mitogenomes varied from 13,522 to 14,008 bp, encompassing 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 non-coding regions, with identical gene arrangements. The newly characterized mitogenomes will be used to assess the evolutionary relationships of proteocephalids under a total evidence framework, and the outcomes will be presented at this meeting.

UPLOADED FILES

This project contains the original slides and additional information in separated compressed directories.



2024_ASP_slides.pdf



Slide deck for this presentation






Scripts_Assembly&Annotation.zip



interleave-fastqgz-MITOBIM.py: Script for interleaving Illumina paired-end reads (Reads 1 and 2).

assemble.sh: Script for assembling the mitogenome using the baiting and iterative mapping strategy (MIRA + MITOBIM).

manifest.conf: Configuration file that provides the necessary parameters and inputs to run the assembly and baiting processes effectively.

awa_pipe.sh: Script for running AWA that assesses the circularity of the mitogenomes and gives basic stats of the data (see https://gitlab.com/MachadoDJ/awa)

cma.py: Script for running the Cestode Mitogenome Annotator—CMA (see https://gitlab.com/MachadoDJ/cma). It provides the DNA sequences of each CDS, rRNA, and tRNA, as well as some statistics regarding annotation quality.






Scripts_Phylogenetics.zip



concatFasta.py: Script for concatenating individual protein coding-genes alignments.

tsearch_ew_reps.RUN: TNT script used for Tree Search under Parsimy criterium.

consensus.RUN: TNT script for creating the strict consensus tree.

blen.RUN: TNT script for recovering the branch length (number of transformations per branch).

PhylogenomicSupport.run: TNT script for measuring the branch support based on the Goodman-Bremer and Jackknife values.

phrename.py: Script for replacing synonyms of terminal names.




FUNDING

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), proc. no. 2023/00714-5.