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Results for “segmental duplication reconstruction”

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PubMed2025

SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids.

Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification, and the emergence of novel functions. The detection of segmental duplications is challenging due to heterogeneous amelioration of sequence similarity among duplicates, which hinders the reconstruction of continuous sequence alignment. Here we introduce SegMantX, a novel approach for the identification of diverged segmental duplications in prokaryote genomes using local alignment chaining. In this approach, local alignments resulting from a preliminary sequence similarity search (e.g. BLASTn) are chained into continuous segments. Evaluating the performance of SegMantX using simulated sequences shows that the tool can detect diverged duplications beyond the sensitivity limits of standard alignment-based methods. Applying SegMantX to 6,784 enterobacterial plasmids, we find that 65% plasmids contain duplicated regions and gene duplications, most of which correspond either to dispersed, noncoding regions or duplicated mobile genetic elements (MGEs; e.g. transposons and insertion sequences). Furthermore, we demonstrate the applicability of SegMantX for the identification of diverged gene transfers between replicons and plasmid hybridization events. Our findings highlight MGEs as drivers of segmental duplications in plasmid evolution, leading to the amplification of their cargo genes, including antibiotic resistance genes. SegMantX provides a powerful framework for reconstructing diverged segmental duplications and other alignment problems.

Plasmids↗

PubMedDate not supplied

[Duplication of the colon in the adult (author's transl)].

The authors describe 2 cases of duplication of the colon. One was discovered by accident and not treated. The other occurred in a patient with a long story of abdominal pain and had been operated twice with signs of intestinal obstruction. A partial resection of the duplication with the adjoining bowel segment was performed and the digestive tract was reconstructed bij and end-to-end anastomosis. The different forms of duplication are described with their specific features and the current theories about their mode of formation. Finally a brief description of the symptoms and of the available surgical techniques is given.

Adolescent↗

PubMed2025

GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.

MOTIVATION: The emergence of the 'telomere-to-telomere' genomics brought the challenge of identifying segmental duplications (SDs) in complete genomes. It further opened a possibility for identifying the differences in SDs across individual human genomes and studying the SD evolution. These newly emerged challenges require algorithms for reconstructing SDs in the most complex genomic regions that evaded all previous attempts to analyze their architecture, such as rapidly evolving immunoglobulin loci. RESULTS: We describe the GenomeDecoder algorithm for inferring SDs and apply it to analyzing genomic architectures of various loci in primate genomes. Our analysis revealed that multiple duplications/deletions led to a rapid birth/death of immunoglobulin genes within the human population and large changes in genomic architecture of immunoglobulin loci across primate genomes. Comparison of immunoglobulin loci across primate genomes suggests that they are subjected to diversifying selection. AVAILABILITY AND IMPLEMENTATION: GenomeDecoder is available at https://github.com/ZhangZhenmiao/GenomeDecoder. The software version and test data used in this paper are uploaded to https://doi.org/10.5281/zenodo.14753844.

Humans↗

PubMed1978

A comprehensive examination of protein sequences for evidence of internal gene duplication.

We have implemented a routine procedure for screening protein sequences for evidence of intragenic duplications. We tested 163 protein sequences representing 116 superfamilies of unrelated proteins. Twenty superfamilies contain proteins with internal gene duplications. The intragenic duplications detected can be divided into two major types. (1) One or more duplications of all or part of a gene produce a protein with two or several detectable regions of sequence homology. Sequences from 18 superfamilies contained this type of duplication. (2) Repeated reduplication of a small DNA segment can produce a protein that is repetitive over most of its length. Three superfamilies contain such repetitive sequences. We also investigated the limits of detection of ancient duplications using sequences derived by random mutation of a model sequence consisting of ten 10-residue repeats. The original repetitive nature of the sequence was usually detected after 250 point mutations even though the ancestral segment could not be accurately reconstructed.

Amino Acid Sequence↗

PubMed2026

Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes.

Complex karyotype changes are widespread in cancer genomes. A major gap in cancer genome characterization is the resolution of rearranged chromosomes with chromosome-length continuity. Here, we describe a two-tiered approach to determine the segmental composition of rearranged chromosomes with haplotype resolution. First, we present refLinker, a bioinformatic method for robust determination of chromosomal haplotypes using cancer Hi-C data. By contrast with existing methods, refLinker is insensitive to the presence of large-scale DNA deletions, duplications, and high-level amplification in cancer genomes. Second, we demonstrate a computational strategy to determine the segmental structure of rearranged chromosomes using haplotype-specific Hi-C contacts. We apply these methods to breast cancer genomes and provide direct evidence for long-range transcriptional changes associated with rearrangements of the inactive X chromosome. Together, these results highlight refLinker's broad utility for studying the functional consequences of chromosomal rearrangements.

Humans↗

PubMed1978

Facial duplication -- the unique case of Antonio.

A case of facial duplication with its surgical correction in childhood and the consequences on facial growth is reported. It is a unique case in the duration of observation. The following structures were fully duplicated: the nose, the premaxilla, the cribriform plate, the crista galli. In addition there was an enormous facial cleft including lip, alveolus and palate. Additionally there were two rudimentary eye sockets, eyes, and two supplementary eyebrows. The monstrous hypertelorism with the facial duplication was corrected at the age of ten. The surgical procedure is described and the postoperative complications are discussed. Gross lack of growth of the middle third of the facial skeleton was observed. This was probably the consequence of the initial corrective surgery. Overgrowth of the mandible created a gorilla-like appearance by the end of the growth period. This was corrected in one operation by advancement of the middle third in three sections and repositioning of the mandible as a whole together with the mandibular anterior alveolar segment. Finally all parts of the lower half of the nose had to be enlarged, both soft tissues as well as the cartilaginous framework. A pharyngoplasty in addition to the correction of the intermaxillary abnormalities did much to improve the speech quality of the patient. A large secondary cranial defect was successfully reconstructed with the use of 14 halved ribs. In spite of the removal of four ribs from one side and three ribs from the other, there were no postoperative respiratory problems. Spontaneous rib regeneration was found where ribs had been removed one year earlier.

Adolescent↗