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
- Filter reads using Schizont transcriptional profile.
- Align to reference sequences (using HISAT2).
- Remove human reads from alignment (using Samtools).
- Map remaining reads to P. vivax genome (using Rsubread) and count gene frequencies.
- Perform deconvolution of the samples (using CIBERSORTx).
- 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.
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 |
Plasmodium vivax P01 (Version: 2018-02-28) from PlasmoDB: https://plasmodb.org/plasmo/app/downloads/Current_Release/PvivaxP01/gff/data/
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