Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly
| العنوان: | Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly |
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| المؤلفون: | Ivan Alexandrov, A. A. Alexandrov, V. A. Shepelev, Yu. B. Yurov, Evgeny I. Rogaev, Lev Uralsky |
| المصدر: | Genomics Data, Vol 5, Iss C, Pp 139-146 (2015) Genomics Data |
| بيانات النشر: | Elsevier BV, 2015. |
| سنة النشر: | 2015 |
| مصطلحات موضوعية: | lcsh:QH426-470, Hybrid genome assembly, hg38 human genome assembly, Computational biology, Genome browser, Biology, Biochemistry, Genome, 03 medical and health sciences, Annotation, 0302 clinical medicine, Data in Brief, Centromere, Genetics, Higher-order repeats, Alpha satellite, 030304 developmental biology, Sequence (medicine), Centromeres, 0303 health sciences, Contig, Suprachromosomal families, lcsh:Genetics, Molecular Medicine, Human genome, 030217 neurology & neurosurgery, Biotechnology |
| الوصف: | Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly. The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2. |
| تدمد: | 2213-5960 0000-0140 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0beb7bb7437a65fd2820a858c44ad6e https://doi.org/10.1016/j.gdata.2015.05.035 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....f0beb7bb7437a65fd2820a858c44ad6e |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 22135960 00000140 |
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