This track is part of the Centromeres and Telomeres collection of the zebra finch telomere-to-telomere hub.
Before assemblies could span a centromere, centromere positions were located genetically, by following which markers failed to recombine. This track places the primer pairs from one such study onto the assembly, so the earlier genetic map of zebra finch centromeres can be compared directly with the satellite arrays now visible in the sequence. It contains 225 mapped primer positions.
Each item is one mapped primer, named after the marker it belongs to and whether it is the forward or reverse primer of the pair, together with the position class assigned in the original study.
64 previously described primer pairs were queried against both haplotype assemblies with blastn -task blastn-short. Hits from the two haplotypes were combined and filtered to keep only chromosome-specific hits whose forward and reverse partners lay less than 1 kb apart. Because the assembly has diverged from the reference the primers were designed on, primers without a surviving pair were rescued by taking the single highest scoring match per chromosome. Final coordinates were checked by hand.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/centromeres/bTaeGut7v0.4_MT_rDNA.BLAST.Knief2016.v0.2.bed. It is a text format that a track hub cannot use directly, so it was converted to a binary indexed file. 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=centroMarkers.
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/centroMarkers.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
Knief U, Forstmeier W. Mapping centromeres of microchromosomes in the zebra finch (Taeniopygia guttata) using half-tetrad analysis. Chromosoma. 2016 Sep;125(4):757-68. PMID: 26667931; PMC: PMC5023761
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.