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Background  Currently in China, the trend of  Plasmodium vivax  cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in  P. vivax  cases and stronger need for vaccine and drug development, several  P. vivax  isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now.    Results  The sequencing of the first  P. vivax  isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads. A percentage of 10.6 of the quality-evaluated reads were aligned onto 99.9% of the reference strain Sal I genome in 62-fold coverage with an average of 4.8 SNPs per kb. We present a 539-SNP marker data set for  P. vivax  that can identify different parasites from different geographic origins with high sensitivity. We also identified exceptionally high levels of genetic variability in members of multigene families such as RBP, SERA,  vir , MSP3 and AP2. The de-novo assembly yielded a database composed of 8,409 contigs with N50 lengths of 6.6 kb and revealed 661 novel predicted genes including 78  vir  genes, suggesting a greater functional variation in  P. vivax  from this area.    Conclusion  Our result contributes to a better understanding of  P. vivax  genetic variation, and provides a fundamental basis for the geographic differentiation of vivax malaria from China-Myanmar border area using a direct sequencing approach without leukocyte depletion. This novel sequencing method can be used as an essential tool for the genomic research of  P. vivax  in the near future.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3523-y) contains supplementary material, which is available to authorized users.

bmc genomics

Whole-genome sequencing of a Plasmodium vivax clinical isolate exhibits geographical characteristics and high genetic variation in China-Myanmar border area