Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation
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DOI：
10.1038/s41598-019-42511-4
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发表时间：
2019-04-16
影响因子：
4.6
通讯作者：
Aguado, Begoiia
中科院分区：
文献类型：
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作者：
Camacho, Esther;Gonzalez-de La Fuent, Sandra;Aguado, Begoiia
杜氏利什曼原虫是一种单细胞寄生虫，导致内脏利什曼病，这是一种致命的疾病。在本研究中，一个完整的基因组组装的L。Donovani提供。除了是该菌株（HU 3）的第一个公布的基因组之外，这构成了L. Donovani的基因组。使用测序平台的组合使得能够在没有任何序列缺口的情况下组装该物种的36条染色体。此外，基于该组装并使用来自poly-A + RNA的RNA-seq读数，描绘了该物种的转录组，尚未获得。对于大多数基因，通常观察到替代SL添加位点和聚腺苷酸添加位点的异质性。在对转录组进行完整注释后，确定了2，410个新的转录本。此外，测定了前鞭毛体阶段中存在的所有转录物的相对表达。已记录顺式剪接事件发生在源自基因LDHU3_07.0430和LDHU3_29.3990的转录物成熟期间。完整的基因组组装和基因模型的可用性（包括非翻译区的注释）是了解这种病原体中差异基因表达如何发生的重要部分，并破译组织嗜性，临床疾病和药物敏感性等表型特性。
Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.