This track is part of the Centromeres and Telomeres collection of the zebra finch telomere-to-telomere hub.
Bird centromeres are built from long arrays of satellite repeat, and in the zebra finch two families dominate: Tgut716A and Tgut191A. Because these arrays are hundreds of kilobases of nearly identical sequence, they collapsed in every earlier assembly of this species, and resolving them is one of the main results of this genome. This track shows about 7,000 satellite array segments placed with a curated centromere satellite library.
Each segment is drawn in the color that the source annotation gives its satellite family, so one array appears as a run of features in a single color. The family is in the item name, for example Motif:Tgut716A, and the full annotation attributes are on the details page.
Centromeric satellite repeats were localized with RepeatMasker using the curated satellite library published for the zebra finch by Takki et al. Adjacent hits to the same family were merged. The similarity of Tgut716A to crowSat1 was assessed with Censor.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/centromeres/bTaeGut7v0.4_MT_rDNA.RM.Takki2022.v0.1.colored.merged.gff. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. The GFF is a flat feature annotation rather than a gene annotation, so each line became one BED feature, with the color attribute kept as itemRgb and the remaining attributes as an extra field. The conversion, and the whole hub, is reproduced by the commands in src/hg/makeDb/doc/contrib/bTaeGut7.txt of the UCSC kent source tree.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=centroSat.
For automated download and analysis, this annotation is a bigBed file inside the hub. Individual regions or the whole annotation can be obtained with bigBedToBed, which can be compiled from source or downloaded as a precompiled binary; instructions are here. The tool also fetches a range, for example bigBedToBed <hubUrl>/GCF_048771995.1/centroSat.bb -chrom=NC_133024.1 -start=0 -end=100000 stdout, where <hubUrl> is the directory this hub was loaded from.
The original annotation files are on GenomeArk, in the bTaeGut7 annotations directory.
Formenti G, Jain N, Medico JA, Sollitto M, Antipov D, Barcellos S, Biegler M, Borges I, Chang JK, Chen Y et al. The complete genome of a songbird. Cell. 2026 Aug 6;189(16):4922-4945.e12. PMID: 42561917
Takki O, Komissarov A, Kulak M, Galkina S. Identification of Centromere-Specific Repeats in the Zebra Finch Genome. Cytogenet Genome Res. 2022;162(1-2):55-63. PMID: 35279659
The assembly and all of these annotations were produced by the Vertebrate Genome Laboratory at The Rockefeller University and their collaborators, and released through GenomeArk. Thanks to Giulio Formenti and Erich D. Jarvis and their co-authors for making the data available before and after publication. The analysis code is at github.com/gf777/T2T-zebra-finch. This hub was assembled at UCSC from the IGV session distributed with the annotations, using hubtools.