Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3’ end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.

单细胞原生动物寄生虫利什曼原虫（Leishmania）可引发被忽视的热带病利什曼病（leishmaniasis），目前全球98个国家已有1200万人受其感染。在维埃尼亚亚属（Viannia subgenus）占主导的南美洲，迄今仅巴西利什曼原虫（L. (Viannia) braziliensis）与巴拿马利什曼原虫（L. (V.) panamensis）完成了测序、组装并注释为参考基因组。填补这一分子信息缺口，可为物种分型、流行病学监测与临床治疗提供重要参考。本研究对纳伊夫利什曼原虫（L. (V.) naiffi）和圭亚那利什曼原虫（L. (V.) guyanensis）的基因组DNA进行测序，利用短序列读段（short sequence reads）组装得到这两个物种的草图参考基因组。我们以已发布参考基因组的巴西利什曼原虫M2904的短序列读段作为对照，对所用组装方法进行了验证。该组装与注释流程（assembly and annotation pipeline）在原始M2904参考基因组中额外鉴定出70个未被注释的基因。通过对圭亚那利什曼原虫、纳伊夫利什曼原虫与另外10个维埃尼亚亚属基因组开展系统发育与进化比较分析，发现所有维埃尼亚亚属物种共有的4项特征：非整倍性（aneuploidy）、其他利什曼原虫亚属均缺失的22个直系同源基因簇（orthologous groups of genes）、拷贝数升高的TATE转座子（TATE transposon），以及较高的NADH依赖型延胡索酸还原酶（NADH-dependent fumarate reductase）基因拷贝数。在维埃尼亚亚属内部，各物种特异性的基因组结构变异较为有限：仅莱氏利什曼原虫（L. lainsoni）缺失34号染色体（chromosome 34）上一段45kb的扩增区域；纳伊夫利什曼原虫的毒力因子利什曼蛋白酶（leishmanolysin）拷贝数更高；实验室分离株沙氏利什曼原虫（L. shawi）M8408存在一条源自34号染色体3'端的潜在微小染色体（minichromosome）。本研究结合基因组组装、系统发育分析与跨多样化维埃尼亚亚属物种的比较分析，为该亚属的起源与演化提供了新见解，同时有助于优化利什曼病监测的诊断手段。