This track is part of the Structural Variation collection of the zebra finch telomere-to-telomere hub.
This track marks the sequence that the new assembly resolves and the previous zebra finch reference, bTaeGut1.4, did not contain or had collapsed. These regions are where most of the newly annotated genes are found, and they are strongly enriched for satellite DNA and other repeats. The track contains about 27,000 regions longer than 1 kb.
Plain blocks, one per region. Regions shorter than 1 kb were filtered out by the authors, so the track shows the substantial gains rather than every base of difference.
The new diploid assembly was aligned to the previous reference GCF_003957565.2 (bTaeGut1.4) with FastGA, and the resulting unassembled-region intervals were filtered to keep only those longer than 1 kb. Each gene was then classified by how it sits relative to these regions, and genes lying entirely inside one, or overlapping one over at least 75 percent of their length, were called putative novel or improved genes; novelty was checked by aligning the gene sequence back to bTaeGut1.4. The manuscript reports 2,710 genes gained this way, and a per-chromosome Fisher test of which feature types are enriched in these regions.
The file was taken from GenomeArk at https://genomeark.s3.amazonaws.com/species/Taeniopygia_guttata/bTaeGut7/manuscript/annotations/PUR/bTaeGut7v0.4_MT_rDNA.PUR.fastga.v0.1.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=newRegions.
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/newRegions.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
Myers G, Durbin R, Zhou C. FastGA: fast genome alignment. Bioinform Adv. 2025;5(1):vbaf238. PMID: 41262969; PMC: PMC12624442
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.