Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens.
Whole-genome assembly of Babesia ovata and comparative genomics between closely related pathogens.
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DOI：
10.1186/s12864-017-4230-4
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发表时间：
2017-10-27
期刊：
影响因子：
4.4
通讯作者：
Kawazu SI
中科院分区：
文献类型：
--
作者：
Yamagishi J;Asada M;Hakimi H;Tanaka TQ;Sugimoto C;Kawazu SI
卵形巴贝虫属于顶复门，是牛科动物的一种传染性寄生虫。与由B引起的其他类型的牛巴贝虫病相比，它与严重症状的表现无关。bovis和B.二联虫;然而，在与东方泰勒虫共同感染时，它偶尔会引起加重的症状。牛的无症状慢性感染通常仅见于B。卵形的比较基因组学分析可能揭示参与这些区别特征的因素;然而，这些表型的基因组和分子基础仍然难以捉摸，特别是在B中。卵形的从技术的角度来看，目前开发的一个非常长的读取测序仪，MinION，将有助于获得高度整合的基因组序列。因此，我们应用下一代测序技术获得了高质量的寄生虫基因组，这为了解顶复门提供了基础信息。基因组组装成14，453，397 bp大小，具有5031个蛋白质编码序列（91个重叠群和N50 = 2，090，503 bp）。基因家族分析表明，ves 1 α和β在B中属于多基因家族。牛，缺席B。卵圆形，与B相同。二联。相反，ves 1 a和ves 1 B，它们最初在B中指定。bigemina，在场。B。ovata和B. bigemina ves 1a一起配置一个集群，即使它们根据spp被划分为两个子集群。相比之下，ves 1 B簇更加分散，B之间重叠。ovata和B.二联胎是有限的。观察到的冗余和快速进化的顺序可能反映了这些寄生虫的适应历史。此外，通过功能分析确定了可能参与不同表型的相同候选基因。anamorsin同系物就是其中之一。人无性繁殖素与造血有关，其同系物存在于B中。卵圆形但B无。二联胎会导致严重贫血综合这些发现，比较基因组学所显示的差异可能解释了这些寄生虫的进化历史及其表型的差异。此外，基因组草图为进一步鉴定和了解这些寄生虫提供了基础信息。本文的在线版本（10.1186/s12864-017-4230-4）包含补充材料，可供授权用户使用。
Babesia ovata, belonging to the phylum Apicomplexa, is an infectious parasite of bovids. It is not associated with the manifestation of severe symptoms, in contrast to other types of bovine babesiosis caused by B. bovis and B. bigemina; however, upon co-infection with Theileria orientalis, it occasionally induces exacerbated symptoms. Asymptomatic chronic infection in bovines is usually observed only for B. ovata. Comparative genomic analysis could potentially reveal factors involved in these distinguishing characteristics; however, the genomic and molecular basis of these phenotypes remains elusive, especially in B. ovata. From a technical perspective, the current development of a very long read sequencer, MinION, will facilitate the obtainment of highly integrated genome sequences. Therefore, we applied next-generation sequencing to acquire a high-quality genome of the parasite, which provides fundamental information for understanding apicomplexans. The genome was assembled into 14,453,397 bp in size with 5031 protein-coding sequences (91 contigs and N50 = 2,090,503 bp). Gene family analysis revealed that ves1 alpha and beta, which belong to multigene families in B. bovis, were absent from B. ovata, the same as in B. bigemina. Instead, ves1a and ves1b, which were originally specified in B. bigemina, were present. The B. ovata and B. bigemina ves1a configure one cluster together even though they divided into two sub-clusters according to the spp. In contrast, the ves1b cluster was more dispersed and the overlap among B. ovata and B. bigemina was limited. The observed redundancy and rapid evolution in sequence might reflect the adaptive history of these parasites. Moreover, same candidate genes which potentially involved in the distinct phenotypes were specified by functional analysis. An anamorsin homolog is one of them. The human anamorsin is involved in hematopoiesis and the homolog was present in B. ovata but absent in B. bigemina which causes severe anemia. Taking these findings together, the differences demonstrated by comparative genomics potentially explain the evolutionary history of these parasites and the differences in their phenotypes. Besides, the draft genome provides fundamental information for further characterization and understanding of these parasites. The online version of this article (10.1186/s12864-017-4230-4) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Jackson AP;Otto TD;Darby A;Ramaprasad A;Xia D;Echaide IE;Farber M;Gahlot S;Gamble J;Gupta D;Gupta Y;Jackson L;Malandrin L;Malas TB;Moussa E;Nair M;Reid AJ;Sanders M;Sharma J;Tracey A;Quail MA;Weir W;Wastling JM;Hall N;Willadsen P;Lingelbach K;Shiels B;Tait A;Berriman M;Allred DR;Pain A
通讯作者：
Pain A
影响因子：
--
作者：
Cho, Shin-Hyeong;Kim, Tong-Soo;Lee, Chung-Gil
通讯作者：
Lee, Chung-Gil
影响因子：
14.9
作者：
Balaji S;Babu MM;Iyer LM;Aravind L
通讯作者：
Aravind L
影响因子：
14.9
作者：
Lagesen K;Hallin P;Rødland EA;Staerfeldt HH;Rognes T;Ussery DW
通讯作者：
Ussery DW