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Gene Polymorphisms Among Plasmodium vivax Geographical Isolates and the Potential as New Biomarkers for Gametocyte Detection

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Gene Polymorphisms Among Plasmodium vivax Geographical Isolates and the Potential as New Biomarkers for Gametocyte Detection

Anthony Ford, Daniel Kepple, Jonathan Williams, Gabrielle Kolesar, Colby T. Ford,
Abnet Abebe, Lemu Golassa, Daniel A. Janies, Delenasaw Yewhalaw, and Eugenia Lo

Companion Respository for Frontiers in Cellular and Infection Microbiology Paper: https://www.frontiersin.org/articles/10.3389/fcimb.2021.789417

Process

  1. Filter reads using Schizont transcriptional profile.
  2. Align to reference sequences (using HISAT2).
  3. Remove human reads from alignment (using Samtools).
  4. Map remaining reads to P. vivax genome (using Rsubread) and count gene frequencies.
  5. Perform deconvolution of the samples (using CIBERSORTx).
  6. Compare the 43 transcript expressions (using DESeq2 or edgeR)...
    • relative to Saimiri (Duffy-negative) and Aotus monkey P. vivax from Gunalan et al. (2019) paper.
    • relative to the 26 Cambodian P. vivax from Kim et al. (2019) paper.

Reference Sequences

Plasmodium vivax ASM241v2 - From: https://www.ncbi.nlm.nih.gov/genome/35

Type Name RefSeq Size (Mb) GC% Proteins Genes
Chr 1 NC_009906.1 0.83 47.1 167 176
Chr 2 NC_009907.1 0.76 44.9 154 162
Chr 3 NC_009908.2 1.01 44.9 209 220
Chr 4 NC_009909.1 0.88 45.1 207 208
Chr 5 NC_009910.1 1.37 44.3 310 315
Chr 6 NC_009911.1 1.03 45.9 244 248
Chr 7 NC_009912.1 1.5 45.6 351 353
Chr 8 NC_009913.1 1.68 45.4 373 379
Chr 9 NC_009914.1 1.92 46.1 432 434
Chr 10 NC_009915.1 1.42 45 317 327
Chr 11 NC_009916.1 2.07 45.1 459 468
Chr 12 NC_009917.1 3 44.6 690 695
Chr 13 NC_009918.1 2.03 45.7 445 449
Chr 14 NC_009919.1 3.12 43 691 699
MT NC_007243.1 0.01 30.5 3 3

Annotation

Plasmodium vivax P01 (Version: 2018-02-28) from PlasmoDB: https://plasmodb.org/plasmo/app/downloads/Current_Release/PvivaxP01/gff/data/

Docker

To build Docker image, navigate to the docker folder and run:

docker build -t vivax_pipeline .

Then run the following to access an RStudio Server:

docker run --name vivax_pipeline --rm -p 8787:8787 vivax_pipeline