A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes.
A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes.
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DOI：
10.12688/wellcomeopenres.9876.1
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发表时间：
2016-11-15
影响因子：
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通讯作者：
Otto, Thomas D
中科院分区：
文献类型：
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作者：
Auburn, Sarah;Bohme, Ulrike;Otto, Thomas D
间日疟原虫现在是亚太、南美洲和非洲之角疟疾的主要病因。该物种的实验室研究受到无法保持寄生虫连续离体培养的限制，但基因组方法提供了一种替代和补充的途径来调查寄生虫的生物学和流行病学。迄今为止，间日疟原虫的分子研究依赖于萨尔瓦多-I参考基因组序列，该序列来自南美洲的猴适应菌株。然而，萨尔瓦多-I参考仍然高度分散，有超过2500个未组装的支架。使用高深度Illumina序列数据，我们组装并注释了一个新的参考序列PvP 01，该序列直接来源于来自巴布亚印度尼西亚的患者。还制备了来自中国（PvC 01）和泰国（PvT 01）的分离株的组装草案，以进行比较。与Salvador-I相比，PvP 01组装的质量大大提高，碎片减少到226个支架。详细的人工管理确保了高度全面的注释，PvP 01中58%的核心基因具有功能，而Salvador-I中为38%。PvP 01、PvC 01和PvT 01的组装比Salvador-I的组装大（28-30对27 Mb），这是由于亚端粒组装的改进。在PvP 01中鉴定了超过1200个疟原虫散布重复序列（Pir）基因的广泛库，而在Salvador-I中鉴定了346个，这表明在寄生虫生存或发育中起着至关重要的作用。人工策划的PvP 01参考和PvC 01和PvT 01草案汇编是研究间日疟的重要新资源。PvP 01由GeneDB维护，持续的策展将确保组装和注释质量的持续改进。
Plasmodium vivax is now the predominant cause of malaria in the Asia-Pacific, South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology. To date, molecular studies of P. vivax have relied on the Salvador-I reference genome sequence, derived from a monkey-adapted strain from South America. However, the Salvador-I reference remains highly fragmented with over 2500 unassembled scaffolds. Using high-depth Illumina sequence data, we assembled and annotated a new reference sequence, PvP01, sourced directly from a patient from Papua Indonesia. Draft assemblies of isolates from China (PvC01) and Thailand (PvT01) were also prepared for comparative purposes. The quality of the PvP01 assembly is improved greatly over Salvador-I, with fragmentation reduced to 226 scaffolds. Detailed manual curation has ensured highly comprehensive annotation, with functions attributed to 58% core genes in PvP01 versus 38% in Salvador-I. The assemblies of PvP01, PvC01 and PvT01 are larger than that of Salvador-I (28-30 versus 27 Mb), owing to improved assembly of the subtelomeres. An extensive repertoire of over 1200 Plasmodium interspersed repeat (pir) genes were identified in PvP01 compared to 346 in Salvador-I, suggesting a vital role in parasite survival or development. The manually curated PvP01 reference and PvC01 and PvT01 draft assemblies are important new resources to study vivax malaria. PvP01 is maintained at GeneDB and ongoing curation will ensure continual improvements in assembly and annotation quality.