ArticleGenes2022
Initial Analysis of Structural Variation Detections in Cattle Using Long-Read Sequencing Methods.
Article in Genes, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Deciphering the Evolution Pattern of Structural Variations Overlapped With Repetitive Sequence During Cattle Evolution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Detection and evaluation of copy number variation using both linked-read and short-read sequencing in New Zealand dairy cattle.Frontiers in genetics · 2026Article
- Systematic benchmarking of tools for structural variation detection using short- and long-read sequencing data in pigs.iScience · 2025Article
- A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle.Animals : an open access journal from MDPI · 2024Article
- When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications.Genes · 2024Review
- In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants.Genetics, selection, evolution : GSE · 2023Review
- Nanopore Sequencing for De Novo Bacterial Genome Assembly and Search for Single-Nucleotide Polymorphism.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural variations (SVs), as a great source of genetic variation, are widely distributed in the genome. SVs involve longer genomic sequences and potentially have stronger effects than SNPs, but they are not well captured by short-read sequencing owing to their size and relevance to repeats. Improved characterization of SVs can provide more advanced insight into complex traits. With the availability of long-read sequencing, it has become feasible to uncover the full range of SVs. Here, we sequenced one cattle individual using 10× Genomics (10 × G) linked read, Pacific Biosciences (PacBio) continuous long reads (CLR) and circular consensus sequencing (CCS), as well as Oxford Nanopore Technologies (ONT) PromethION. We evaluated the ability of various methods for SV detection. We identified 21,164 SVs, which amount to 186 Mb covering 7.07% of the whole genome. The number of SVs inferred from long-read-based inferences was greater than that from short reads. The PacBio CLR identified the most of large SVs and covered the most genomes. SVs called with PacBio CCS and ONT data showed high uniformity. The one with the most overlap with the results obtained by short-read data was PB CCS. Together, we found that long reads outperformed short reads in terms of SV detections.
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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.