The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat.
The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat.
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易中风的自发性高血压大鼠的组装基因组。
DOI：
10.1161/hypertensionaha.122.20140
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Doris
中科院分区：
文献类型：
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作者：
Kalbfleisch,TheodoreS;HussienAbouElEla,NahlaA;Li,Kai;Brashear,WesleyA;Kochan,KelliJ;Hillhouse,AndrewE;Zhu,Yaming;Dhande,IshaS;Kline,EricJ;Hudson,ElizabethA;Murphy,TerenceD;Thibaud-Nissen,Françoise;Smith,MelissaL;Doris
BackgroundWe报告了自发性高血压大鼠基因组从头组装的创建和评估，自发性高血压大鼠是人类心血管疾病最广泛使用的模型。MethodsThe基因组是从长读段测序（PacBio HiFi和连续长读段数据[100]）组装的，并与从Bionano光学图谱和基因组的邻近连接测序邻近分析获得的长距离结构信息一起构建。用Illumina短读段对基因组组装进行抛光。使用基准通用单拷贝直系同源物分析研究组装的完整性。还使用NCBI自动化方案用大鼠参考基因集评估基因组组装。我们还从8种组织中产生了正交单分子转录物序列读数（Iso-Seq），并使用它们来验证编码组装，用代表每个基因独特的全长转录物同种型的RNA转录物注释组装，并确定RefSeq序列和组装之间的分歧是否归因于组装错误或多态性。这意味着与当前大鼠参考组装的邻近性和完整性，而HiFi测序的使用产生在单个碱基水平上更正确的组装。进行同线性分析，以揭示同线性的程度和染色体重排的存在和分布之间的参考和此assembly.ConclusionThe产生的基因组组装是参考质量和捕获显着的结构变异。
BackgroundWe report the creation and evaluation of a de novo assembly of the genome of the spontaneously hypertensive rat, the most widely used model of human cardiovascular disease.MethodsThe genome is assembled from long read sequencing (PacBio HiFi and continuous long read data [CLR]) and scaffolded with long-range structural information obtained from Bionano optical maps and proximity ligation sequencing proximity analysis of the genome. The genome assembly was polished with Illumina short reads. Completeness of the assembly was investigated using Benchmarking Universal Single Copy Orthologs analysis. The genome assembly was also evaluated with the rat reference gene set, using NCBI automated protocols. We also generated orthogonal single molecule transcript sequence reads (Iso-Seq) from 8 tissues and used them to validate the coding assembly, to annotate the assembly with RNA transcripts representing unique full length transcript isoforms for each gene and to determine whether divergences between RefSeq sequences and the assembly were attributable to assembly errors or polymorphisms.ResultsThe assembly analysis indicates that this assembly is comparable in contiguity and completeness to the current rat reference assembly, while the use of HiFi sequencing yields an assembly that is more correct at the single base level. Synteny analysis was performed to uncover the extent of synteny and the presence and distribution of chromosomal rearrangements between the reference and this assembly.ConclusionThe resulting genome assembly is reference quality and captures significant structural variation.