Description

This track represents the gene models for the T2T CHM13 assembly generated using the CAT (Comparative Annotation Toolkit) software with genes that CAT could not be mapped as well as novel paralogs, filled in from the LiftOff mappings. The reference annotations are from GENCODE V35.

Display Conventions and Configuration

This track follows the display conventions for gene prediction tracks. The exons for putative non-coding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker. Gene names are displayed in 'pack' or 'full' mode. More information about each gene can be found by clicking on the specific gene/transcript model.

The following color key is used:

• Blue: protein coding
• Green: non-coding
• Pink: pseudogenes

Methods

This tracks combines gene annotations generated by two methods. First the Comparative Annotation Toolkit (CAT) was used to Liftoff was then used as a second annotation method to map genes missed by CAT and additional gene paralogs.

Comparative Annotation Toolkit

Genome annotation for T2T CHM13 assembly was performed using Comparative Annotation Toolkit (CAT). CAT leverages whole-genome alignments generated by Cactus to transfer annotations from one source genome to one or more target genomes. For this annotation set, CAT lifted over the reference GENCODE v35 annotations onto the T2T genome. CAT also incorporated Iso-Seq data, first assembled into transcripts with StringTie2, to make the final consensus annotation set.

Liftoff

Liftoff uses Minimap2 to align reference gene DNA sequences to the target genome and selects the alignment(s) concordant with the intron/exon structure with the highest sequence identity. A minimum sequence identity of 95% was required to annotate gene paralogs. After running Liftoff, we identified genes that did not overlap any CAT annotations using bedtools intersect. These were combined with the CAT annotation to create the final annotation.

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can also be accessed from scripts through our REST API, where the track name is catLiftOffGenesV1.

For automated analysis, the data may be downloaded from our download server as a bigGenePred file. The file for this track is called catLiftOffGenesV1.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, for example:

Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

This track was provide by Marina Haukness <mhauknes@ucsc.edu> of UC Santa Cruz and Alaina Shumate <ashumat2@jhmi.edu> of Johns Hopkins University.

References

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. PMID: 29884752; PMC: PMC6028123

Stanke M, Diekhans M, Baertsch R, Haussler D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 2008 Mar 1;24(5):637-44. PMID: 18218656

Stanke M, Steinkamp R, Waack S, Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W309-12. PMID: 15215400; PMC: PMC441517

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. PMID: 33177663; PMC: PMC7673649

Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics. 2020 Dec 15;. PMID: 33320174; PMC: PMC8289374