T2T-MFA8

T2T-MFA8, is pronounced T2T-macfallite.

We generated a parthenogenesis cell line, MFA582-1, from a crab-eating macaque, from which we produced 53× PacBio HiFi, 77× ONT, 32× Illumina WGS, and 156× Hi-C data. Then, we constructed a telomere-to-telomere assembly of the crab-eating macaque (T2T-MFA8). All resources are available on this site.

Resources

NCBI Genome

• T2T-MFA8v1.0: GCF_037993035.1/GCA_037993035.1 (chrY is under processing)

The UCSC Genome Browser

All tracks are available on the UCSC Genome Browser.

Assembly

• T2T-MFA8v1.1: unmasked, 20 autosomes + chrX + chrMT + chrY from MFA0214
• T2T-MFA8v1.1: soft-masked (segmental duplications, tandem repeats and RepeatMasker), 20 autosomes + chrX + chrMT + chrY from MFA0214
• T2T-MFA8v1.1: soft-masked T2T-MFA8v1.1 + hard-masked chrY PAR

Sequencing data

• MFA582-1
  • PacBio WGS: SRX22719293
  • Oxford Nanopore Technology WGS: SRX22719294
  • Illumina WGS: SRX22702646
  • Hi-C: SRX22702647
• MFA0214
  • PacBio WGS: SRX22874566 and SRX25542261
  • Oxford Nanopore Technology WGS: SRX22874568
  • Illumina WGS: SRX22874666 and SRX25542262

Gene annotation

• Curated gene annotation: LiftOff result from Mmul _10 RefSeq and lso-Seq transcripts annotated by GeneMarkS-T, with manual curation
• GeneMarkS-T: annotated Iso-Seq FLNC transcripts (autosomes + chrX)
• LiftOff from Mmul_10 RefSeq

Mappability

• 21-mer with no error: produced by GenMap
• 24-mer with no error: produced by GenMap

Repeat annotation

• Centromere
• CenSat: the 500-kbp extended regions of centromeres
• Segmental duplications: native bed format or merged bed format
• Tandem repeats: bed format or merged bed format
• RepeatMasker: native out format or bed format or merged bed format
• WindowMasker (with SDust)
• Centromere suprachromosomal family annotation
• rDNA models
• chrY annotations
  • PAR
  • Sequence classes
  • Palindromes
  • Non-B-DNA

Epigenetic profile

• CpG islands
• CpG methylation from ONT: autosomes + chrX or chrY, identified by Nanopolish v0.14.0

Non-syntenic regions

• Crab-eating macaque assemblies
  • macFas6
  • MFA1912RKSv2
• Rhesus macaque assemblies
  • Mmul_10
  • rheMacS

Previous versions

To avoid confusion, previous versions are not displayed on this page, but you can still access them through the links.

Citation

We would appreciate if you would acknowledge and cite our paper:

Zhang, S. et al. Comparative genomics of macaques and integrated insights into genetic variation and population history. bioRxiv (2024).

License

All data is released to the public domain (CC0).