ArticleHypertension (Dallas, Tex. : 1979)2023
The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat.
Article in Hypertension (Dallas, Tex. : 1979), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 13 citations in OpenAlex.
- Telomere-to-telomere genome assembly and a pangenome for the rat.Cell genomics · 2026Article
- Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats.Nature communications · 2025Article
- Incidence and characterization of spontaneous pituitary neuroendocrine tumors in aged spontaneously hypertensive rats.Scientific reports · 2025Article
- Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats.bioRxiv : the preprint server for biology · 2025Article
- The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region.bioRxiv : the preprint server for biology · 2025Article
- NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.Nucleic acids research · 2025Article
- Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding.Genome research · 2024Article
- Four-week inhibition of the renin-angiotensin system in spontaneously hypertensive rats results in persistently lower blood pressure with reduced kidney renin and changes in expression of relevant gene networks.Cardiovascular research · 2024Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.Cell genomics · 2024Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.bioRxiv : the preprint server for biology · 2023Article
- Polygenic genetic variation affecting antibody formation underlies hypertensive renal injury in the stroke-prone spontaneously hypertensive rat.American journal of physiology. Renal physiology · 2023Article
- The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species.Current protocols · 2023Review
- 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource.Genetics · 2023Article
Corrections and comments
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Authors and funding
14 authors at 6 institutions in 1 country.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.