Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions.
Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions.
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DOI：
10.1101/gr.275325.121
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发表时间：
2022-01
期刊：
影响因子：
7
通讯作者：
Kissinger JC
中科院分区：
文献类型：
--
作者：
Baptista RP;Li Y;Sateriale A;Sanders MJ;Brooks KL;Tracey A;Ansell BRE;Jex AR;Cooper GW;Smith ED;Xiao R;Dumaine JE;Georgeson P;Pope BJ;Berriman M;Striepen B;Cotton JA;Kissinger JC
隐孢子虫病是全球水传播腹泻疾病的主要原因，也是婴儿和免疫抑制者死亡的重要原因。尽管它的重要性，隐孢子虫社区只获得了一个良好的，但不完整的，小隐孢子虫爱荷华州参考基因组序列。不完整的参考序列妨碍了注释、实验设计和解释。在PacBio和Oxford Nanopore长读技术的支持下，我们生成了一个新的细小孢子虫（C. parvum） IOWA基因组序列，并对三个密切相关的物种：细小孢子虫（C. parvum）、人隐孢子虫（crypsporidium hominis）和tyzzeri隐孢子虫（Cryptosporidium tyzzeri）进行了新的比较和一致的基因组注释。我们根据实验证据对1926年小弧菌的注释进行了更新。它们包括新的转运体、ncrna、内含子和改变的基因结构。新的组装和注释揭示了一个完整的Dnmt2甲基化酶同源物。对细小C.、人猿C.和C. tyzzeri的比较注释发现，大多数缺失的同源物都被发现，这表明物种之间的生物学差异可能是由基因拷贝数变异、基因调控差异和单核苷酸变异（snv）造成的。利用新的组装和注释作为参考，鉴定出190个基因在正选择下进化，包括许多以前未检测到的基因。新的小孢子虫IOWA参考基因组组装更大，无间隙，缺乏模糊的碱基。这个染色体组装恢复所有16条染色体末端，其中13条是连续组装的。剩下的三个染色体末端被暂时放置。这些末端代表了包括亚端粒区域在内的整个染色体末端的重复，揭示了基因组可塑性的新水平，这将为未来的研究提供信息和影响。
Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design, and interpretation. We have generated a new C. parvum IOWA genome assembly supported by Pacific Biosciences (PacBio) and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species: C. parvum, Cryptosporidium hominis, and Cryptosporidium tyzzeri. We made 1926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns, and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis, and C. tyzzeri revealed that most “missing” orthologs are found, suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation, and single-nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free, and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.
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影响因子：
12.3
作者：
Buels R;Yao E;Diesh CM;Hayes RD;Munoz-Torres M;Helt G;Goodstein DM;Elsik CG;Lewis SE;Stein L;Holmes IH
通讯作者：
Holmes IH
影响因子：
7
作者：
Bankier, AT;Spriggs, HF;Dear, PH
通讯作者：
Dear, PH
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
9.2
作者：
Ansell, Brendan R. E.;Pope, Bernard J.;Jex, Aaron R.
通讯作者：
Jex, Aaron R.
影响因子：
56.9
作者：
Goll, MG;Kirpekar, F;Bestor, TH
通讯作者：
Bestor, TH