ArticleGenome research2004
Analysis of segmental duplications and genome assembly in the mouse.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed.
- Diversification of Cellulose Synthase (CESA) Genes in Mosses Suggests Both Ancient and Recent Gene duplications.Journal of molecular evolution · 2026Article
- Acquisition of ampliconic sequences marks a selfish mouse t-haplotype.Nature communications · 2025Article
- Genome organization and botanical diversity.The Plant cell · 2024Review
- A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.BMC biology · 2022Article
- The Complexity of the Ovine and Caprine Keratin-Associated Protein Genes.International journal of molecular sciences · 2021Review
- The Taxus genome provides insights into paclitaxel biosynthesis.Nature plants · 2021Article
- Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications.Nucleic acids research · 2020Article
- Article
- Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary.Molecular ecology resources · 2019Article
- Extended regions of suspected mis-assembly in the rat reference genome.Scientific data · 2019Article
- Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals.BMC genomics · 2017Article
- Gene Duplication Analysis Reveals No Ancient Whole Genome Duplication but Extensive Small-Scale Duplications during Genome Evolution and Adaptation ofFrontiers in cellular and infection microbiology · 2017Article
- Article
- Article
- Global copy number analyses by next generation sequencing provide insight into pig genome variation.BMC genomics · 2014Article
- Article
- Sequence, structural and expression divergence of duplicate genes in the bovine genome.PloS one · 2014Article
- A survey of innovation through duplication in the reduced genomes of twelve parasites.PloS one · 2014Article
- Segmental duplications in the silkworm genome.BMC genomics · 2013Article
- The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family.BMC evolutionary biology · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications. The extent of segmental duplications in other mammalian genomes is unknown and confounded by methodological differences in genome assembly. Here, we present a detailed analysis of recent duplication content within the mouse genome using a whole-genome assembly comparison method and a novel assembly independent method, designed to take advantage of the reduced allelic variation of the C57BL/6J strain. We conservatively estimate that approximately 57% of all highly identical segmental duplications (>or=90%) were misassembled or collapsed within the working draft WGS assembly. The WGS approach often leaves duplications fragmented and unassigned to a chromosome when compared with the clone-ordered-based approach. Our preliminary analysis suggests that 1.7%-2.0% of the mouse genome is part of recent large segmental duplications (about half of what is observed for the human genome). We have constructed a mouse segmental duplication database to aid in the characterization of these regions and their integration into the final mouse genome assembly. This work suggests significant biological differences in the architecture of recent segmental duplications between human and mouse. In addition, our unique method provides the means for improving whole-genome shotgun sequence assembly of mouse and future mammalian genomes.
Indexed as
Identifiers
What OpenQuestion holds
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.