Cui Zhang1, Cihan Oguz2,3, Sue Huse2,3, Lu Xia1,4, Jian Wu1, Yu-Chih Peng1, Margaret Smith1, Jack Chen5, Carole A Long1, Justin Lack2,3, Xin-Zhuan Su6. 1. Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA. 2. NIAID Collaborative Bioinformatics Resource (NCBR), Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA. 3. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA. 4. State Key Laboratory of Medical Genetics, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, People's Republic of China. 5. The NCI sequencing facility, 8560 Progress Drive, Room 3007, Frederick, MD, 21701, USA. 6. Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA. xsu@niaid.nih.gov.
Abstract
BACKGROUND: Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii 17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. RESULTS: We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. CONCLUSIONS: The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.
BACKGROUND: Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. The genomes and transcriptomes of several P. yoelii strains have been analyzed and annotated, including the lethal strains of P. y. yoelii YM (or 17XL) and non-lethal strains of P. y. yoelii17XNL/17X. Genomic DNA sequences and cDNA reads from another subspecies P. y. nigeriensis N67 have been reported for studies of genetic polymorphisms and parasite response to drugs, but its genome has not been assembled and annotated. RESULTS: We performed genome sequencing of the N67 parasite using the PacBio long-read sequencing technology, de novo assembled its genome and transcriptome, and predicted 5383 genes with high overall annotation quality. Comparison of the annotated genome of the N67 parasite with those of YM and 17X parasites revealed a set of genes with N67-specific orthology, expansion of gene families, particularly the homologs of the Plasmodium chabaudi erythrocyte membrane antigen, large numbers of SNPs and indels, and proteins predicted to interact with host immune responses based on their functional domains. CONCLUSIONS: The genomes of N67 and 17X parasites are highly diverse, having approximately one polymorphic site per 50 base pairs of DNA. The annotated N67 genome and transcriptome provide searchable databases for fast retrieval of genes and proteins, which will greatly facilitate our efforts in studying the parasite biology and gene function and in developing effective control measures against malaria.
Entities:
Keywords:
DNA sequence; Mouse; Plasmodium; Polymorphism; Proteome; Transcript
Authors: Sethu C Nair; Sittiporn Pattaradilokrat; Martine M Zilversmit; Jennifer Dommer; Vijayaraj Nagarajan; Melissa T Stephens; Wenming Xiao; John C Tan; Xin-Zhuan Su Journal: Mol Biochem Parasitol Date: 2014-03-29 Impact factor: 1.759
Authors: Hanaa Y Bakir; Fatma G Sayed; Salma A Rahman; Amany I Hamza; Abeer E Mahmoud; Lamia A Galal; Rasha A Attia Journal: J Egypt Soc Parasitol Date: 2009-08
Authors: Jean Langhorne; Pierre Buffet; Mary Galinski; Michael Good; John Harty; Didier Leroy; Maria M Mota; Erica Pasini; Laurent Renia; Eleanor Riley; Monique Stins; Patrick Duffy Journal: Malar J Date: 2011-02-02 Impact factor: 2.979
Authors: Alister G Craig; Georges E Grau; Chris Janse; James W Kazura; Dan Milner; John W Barnwell; Gareth Turner; Jean Langhorne Journal: PLoS Pathog Date: 2012-02-02 Impact factor: 6.823
Authors: S Pattaradilokrat; J Li; J Wu; Y Qi; R T Eastman; M Zilversmit; S C Nair; M C Huaman; M Quinones; H Jiang; N Li; J Zhu; K Zhao; O Kaneko; C A Long; X-z Su Journal: Genes Immun Date: 2014-01-23 Impact factor: 2.676