Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.
Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.
复制标题
DOI：
10.1101/gr.262816.120
复制
发表时间：
2021-05
期刊：
影响因子：
7
通讯作者：
Boyle JP
中科院分区：
文献类型：
--
作者：
Xia J;Venkat A;Bainbridge RE;Reese ML;Le Roch KG;Ay F;Boyle JP
刚地弓形虫是一种有用的细胞内寄生模型，因为它易于在实验室培养和基因组资源。然而，与许多其他真核生物一样，弓形虫基因组包含数百个序列缺口，这是由于重复和/或不可克隆的序列破坏了组装过程。在这里，我们使用Oxford Nanopore Minion平台为多个弓形虫菌株及其近亲犬新弓形虫菌株生成近乎完整的从头基因组组装。我们显著提高了弓形虫基因组的连续度（平均N50为~ 6.6 Mb），并增加了~ 2 Mb的新组装序列。对于我们测序的所有弓形虫菌株（RH, ME49， CTG， II×III后代克隆CL13， S27, S21， S26和D3X1），最大的染色体长度范围在11.9到12.1 Mb之间，比以往报道的任何弓形虫染色体都要大，并且发现这是由于染色体VIIb和VIII的一致融合。这些数据通过将现有的弓形虫ME49 Hi-C数据映射到我们的组装中得到验证，提供了平行的证据，证明弓形虫核型由13条染色体组成，而不是14条染色体。通过使用该技术，我们还解析了数百个不同长度的串联重复序列，包括众所周知的宿主靶向效应位点，如蜂状体蛋白5 （ROP5）和ROP38。最后，当我们将弓形虫与犬奈瑟虫进行比较时，我们发现，虽然13染色体核型是保守的，但自从它们最近的共同祖先以来，弓形虫和犬奈瑟虫已经发生了广泛的、以前未被发现的染色体尺度重排。
Toxoplasma gondii is a useful model for intracellular parasitism given its ease of culture in the laboratory and genomic resources. However, as for many other eukaryotes, the T. gondii genome contains hundreds of sequence gaps owing to repetitive and/or unclonable sequences that disrupt the assembly process. Here, we use the Oxford Nanopore Minion platform to generate near-complete de novo genome assemblies for multiple strains of T. gondii and its near relative, N. caninum. We significantly improved T. gondii genome contiguity (average N50 of ∼6.6 Mb) and added ∼2 Mb of newly assembled sequence. For all of the T. gondii strains that we sequenced (RH, ME49, CTG, II×III progeny clones CL13, S27, S21, S26, and D3X1), the largest contig ranged in size between 11.9 and 12.1 Mb in size, which is larger than any previously reported T. gondii chromosome, and found to be due to a consistent fusion of Chromosomes VIIb and VIII. These data were validated by mapping existing T. gondii ME49 Hi-C data to our assembly, providing parallel lines of evidence that the T. gondii karyotype consists of 13, rather than 14, chromosomes. By using this technology, we also resolved hundreds of tandem repeats of varying lengths, including in well-known host-targeting effector loci like rhoptry protein 5 (ROP5) and ROP38. Finally, when we compared T. gondii with N. caninum, we found that although the 13-chromosome karyotype was conserved, extensive, previously unappreciated chromosome-scale rearrangements had occurred in T. gondii and N. caninum since their most recent common ancestry.
登录
查看更多内容
影响因子：
2.7
作者：
Cabanettes F;Klopp C
通讯作者：
Klopp C
影响因子：
3.6
作者：
Blank, Matthew L.;Parker, Michelle L.;Boyle, Jon P.
通讯作者：
Boyle, Jon P.
影响因子：
14.9
作者：
Khan A;Taylor S;Su C;Mackey AJ;Boyle J;Cole R;Glover D;Tang K;Paulsen IT;Berriman M;Boothroyd JC;Pfefferkorn ER;Dubey JP;Ajioka JW;Roos DS;Wootton JC;Sibley LD
通讯作者：
Sibley LD
影响因子：
16.6
作者：
Bowden, Rory;Davies, Robert W.;Donnelly, Peter
通讯作者：
Donnelly, Peter
影响因子：
14.2
作者：
Edvinsson, B;Lappalainen, M;Evengård, B
通讯作者：
Evengård, B