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SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping

Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangem...

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Autores principales: Feng, Yi, Beh, Leslie Y, Chang, Wei-Jen, Landweber, Laura F
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7586852/
https://www.ncbi.nlm.nih.gov/pubmed/32790832
http://dx.doi.org/10.1093/gbe/evaa147
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author Feng, Yi
Beh, Leslie Y
Chang, Wei-Jen
Landweber, Laura F
author_facet Feng, Yi
Beh, Leslie Y
Chang, Wei-Jen
Landweber, Laura F
author_sort Feng, Yi
collection PubMed
description Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.
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spelling pubmed-75868522020-10-30 SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping Feng, Yi Beh, Leslie Y Chang, Wei-Jen Landweber, Laura F Genome Biol Evol Letter Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements. Oxford University Press 2020-08-13 /pmc/articles/PMC7586852/ /pubmed/32790832 http://dx.doi.org/10.1093/gbe/evaa147 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Letter
Feng, Yi
Beh, Leslie Y
Chang, Wei-Jen
Landweber, Laura F
SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title_full SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title_fullStr SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title_full_unstemmed SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title_short SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping
title_sort sigar: inferring features of genome architecture and dna rearrangements by split-read mapping
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7586852/
https://www.ncbi.nlm.nih.gov/pubmed/32790832
http://dx.doi.org/10.1093/gbe/evaa147
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