GRCr8: A new rat reference assembly is released!
GRCr8 (GCA_036323735.1), the latest version of the rat reference genome assembly, is now available. GRCr8 is an evolution of mRatBN7.2 (GCA_015227675.2), the Vertebrate Genomes Project-generated rat assembly that was the first reference for this species to be adopted by the GRC for stewardship. mRatBN7.2 was an assembly of a Brown Norway (BN) male rat from the same colony at the Medical College of Wisconsin that supplied the female rat used in the 2004 RGSC_v3.4 assembly (AABR00000000.3/GCF_000001895.1). While the assembly of mRatBN7.2 was a substantial improvement over prior versions (https://pubmed.ncbi.nlm.nih.gov/37214...
Source: GenomeRef - February 2, 2024 Category: Genetics & Stem Cells Source Type: blogs
GRCh38.p14 is now released!
GRCh38.p14 (GCA_000001405.29/GCF_000001405.40), the latest update to the human reference assembly, has been released! It adds 69 new patch scaffolds, 51 of which are FIX patches that update sequences on the GRCh38 reference chromosomes or alternate loci, while 18 are NOVEL patches, providing new alternate representations for complex genomic regions that are inadequately represented by a single sequence. Two previously released FIX patches were also updated. With this release, the reference assembly contains a total of 250 patch scaffolds (164 FIX, 90 NOVEL).30 of the patches included in this release include genome updates ...
Source: GenomeRef - May 9, 2022 Category: Genetics & Stem Cells Source Type: blogs
One of these things doesn't belong: efforts to exclude problematic sequences in GRCh38
Since the release of GRCh38, the GRC has received a number of user reports alerting us to a potential false duplication involving chr 21p and 21q. Users noted that reads were aligning to both regions in GRCh38, but not GRCh37/hg19, resulting in a decreased mapping score and difficulties in variant calling throughout. Additionally, user analyses involving Multiplex Ligation-dependent Probe Amplification (MLPA), a technique for gene copy number detection, and exome studies indicated potential false duplications. The implicated regions contained several genes, including CBS (Gene ID: 875), U2AF1 (Gene ID: 7307) and KCNE1B (Ge...
Source: GenomeRef - July 21, 2021 Category: Genetics & Stem Cells Source Type: blogs
A New Rat Genome Assembly Sparks Membership of Rat and RGD in the Genome Research Consortium
TheRat Genome Database RGD is very pleased to announce the release of mRatBN7.1, the new rat genome assembly! The mRatBN7 assembly, generated by theDarwin Tree of Life Project at theWellcome Sanger Institute, is significantly improved over the Rnor6.0 and previous assemblies. mRatBN7 was derived from a male BN/NHsdMcwi rat that is a direct descendent from the female BN rat previously sequenced. The new BN rat reference genome was generated using multiple technologies including PacBio long reads, 10X linked reads, Bionano maps and Arima Hi-C. Its quality is a substantial improvement compared to any of the pre...
Source: GenomeRef - November 30, 2020 Category: Genetics & Stem Cells Source Type: blogs
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A New Rat Genome Assembly Sparks Membership of Rat and RGD in the Genome Research ConsortiumTheRat Genome Database RGD is very pleased to announce the release of mRatBN7.1, the new rat genome assembly! The mRatBN7 assembly, generated by theDarwin Tree of Life Project at theWellcome Sanger Institute, is significantly improved over the Rnor6.0 and previous assemblies. mRatBN7 was derived from a male BN/NHsdMcwi rat that is a direct descendent from the female BN rat previously sequenced. The new BN rat reference genome was generated using multiple technologies including PacBio long reads, 10X linked reads, Bion...
Source: GenomeRef - November 30, 2020 Category: Genetics & Stem Cells Source Type: blogs
GRCm39: the new mouse reference genome assembly
The GRC is pleased to announce the release of GRCm39 (GCA_000001635.9), the latest version of the mouse reference genome assembly. GRCm39 is the first coordinate-changing update to the mouse reference since the 2012 release of GRCm38. More than 400 reported issues were resolved in the production of the new assembly, which also incorporates the sequence edits released as scaffolds in the six GRCm38 patch releases.The new reference assembly exhibits substantial improvements in contiguity. As shown in Fig 1, the scaffold N50 has increased by 95% to 106.1 Mb in GRCm39, and 1.9 Mb of non-N bases were added to the assembly....
Source: GenomeRef - July 22, 2020 Category: Genetics & Stem Cells Source Type: blogs
ZFIN and the GRC: Supporting the zebrafish reference genome assembly
ZFIN is a member of The Genome Reference Consortium (GRC), an international collaboration consisting of NCBI, the Wellcome Trust Sanger Institute, the McDonnell Genome Institute at Washington University, the European Bioinformatics Institute (EBI) and ZFIN. This consortium is tasked with ensuring that the reference assemblies for human, mouse, zebrafish and chicken are updated and improved through new data and analysis from genome centers and the research community.Thezebrafish-specific GRC webpage (Fig. 1) provides an overview of the zebrafish genome, including an ideogram of the latest zebrafish assembly (GRCz11) that hi...
Source: GenomeRef - June 8, 2020 Category: Genetics & Stem Cells Source Type: blogs
Readying the release of GRCm39
GRCm38, the current mouse reference assembly, whose chromosomes represent the C57BL/6J strain, supports a broad range of research activities. Despite being one of the highest quality mammalian genome assemblies ever produced, it still has more than 600 gaps and includes sub-optimal representations for some genes. To address these issues and provide the murine research community with an improved substrate for their work, the GRC has been applying new technologies, such as optical/genome mapping, and using new sequence resources to curate an update to the reference genome assembly. The public release of the updated assembly,...
Source: GenomeRef - May 23, 2019 Category: Genetics & Stem Cells Source Type: blogs
Shining a light on human acrocentric p-arms
The GRC is excited to announce that representations for the p-arms of the human acrocentric chromosomes can now be found in theGRCh38.p13 patch update of the reference genome, thanks to work done inBrian McStay ' s lab. These sequences are included on the following scaffolds:ML143366.1,ML143367.1,ML143372.1,ML143377.1, andML143380.1.The p-arms of the human acrocentric chromosomes HSA13-15, 21 and 22 each bear ribosomal gene arrays (Figure 1) termed nucleolar organiser regions (NORs). These are the most transcriptionally active regions of the genome and direct formation of nucleoli, the largest structures in the nuclei of a...
Source: GenomeRef - March 26, 2019 Category: Genetics & Stem Cells Source Type: blogs
GRCh38.p13 has been released
The GRC is pleased to announce that GRCh38.p13 is now available! This release adds 45 new scaffolds: 43 FIX patches and 2 NOVEL patches. The FIX patch scaffolds provide assembly corrections while the NOVEL patch scaffolds deliver new alternate sequence representations. A valuable contribution to this patch release comes in the addition of the Nucleolus Organiser Region (NOR) sequences for the short arms of the acrocentric chromosomes (13, 14, 15, 21, and 22) as provided by Brian McStay ' s group (PMID: 23990606). The NOR additions will be discussed in detail in a separate blog.With access to an ever-increasing pool of...
Source: GenomeRef - March 20, 2019 Category: Genetics & Stem Cells Source Type: blogs
GRCg6: Curation of the chicken reference genome assembly transfers to the GRC
The GRC announces the release of the latest chicken reference genome assembly,GRCg6.The chicken reference assembly defines a standard upon which other avian whole genome studies are based. Providing the best representation of the chicken genome is essential for facilitating continued progress in understanding and improving human health as this species serves as a model organism similar to mouse, zebrafish and other vertebrates.The chicken reference genome project began as an international research collaboration coordinated by the McDonnell Genome Institute with past funding from the National Institutes of Health (NIH) and ...
Source: GenomeRef - February 23, 2018 Category: Genetics & Stem Cells Source Type: blogs
New technique closes gaps in GRCm38.p6
Ongoing efforts to close gaps and to correct clone problems remaining in the GRCm38 mouse reference assembly have proved difficult. The available clone library resources have been exhausted, and the remaining gaps are recalcitrant to cloning, with either no clones available or gap-spanning clones deleted for the expected genomic sequence. The GRC has previously used contigs from publicly available whole genome shotgun assemblies to provide sequence at some of these gaps, and in some cases have been able to close gaps entirely with this approach. Nonetheless, several hundred sequence gaps, many of which are k...
Source: GenomeRef - February 9, 2018 Category: Genetics & Stem Cells Source Type: blogs
GRCh38.p11: Clinically Relevant Updates to SLC39A4
The GRCh38.p11 patch release includes the fix patch scaffold KZ208914.1/NW_018654716.1 that updates two bases in SLC39A4, a change prompted by user request and that has implications for clinically-relevant variant analyses of this gene. This GRCh38 fix patch restores the gene to the same representation found in GRCh37.SLC39A4, solute carrier family 39 member 4 (NCBI Gene ID: 55630), encodes a protein that is required for dietary zinc absorption in the intestine. In GRCh37, the BAC cloneAF205589.5 (CTA-393G12) provided the sequence for SLC39A4 on chromosome 8. In GRCh38,AC23...
Source: GenomeRef - September 13, 2017 Category: Genetics & Stem Cells Source Type: blogs
GRCh38.p11: Update to GCNT2
The GRC prioritizes curation efforts that improve gene representation in the human reference genome assembly. In some cases, such curation takes the form of base-pair level edits. The recent GRCh38.p11 patch release includes a new, curated, representation for the GCNT2 gene. The representation of the GCNT2 gene in the GRCh38 reference assembly contains the " C " allele for SNP rs539351 on chromosome 6 (NC_000006.12) at position 10,586,805, which reflects the sequence from the underlying component AL358777.12 (RP11-421M1) (Figure 1, top). During human development, the fetal blood group ant...
Source: GenomeRef - July 11, 2017 Category: Genetics & Stem Cells Source Type: blogs
Improvements in the 5S rRNA gene cluster on chromosome 1q42.11-q42.13
Sequence updates that improve gene representation in the human reference genome assembly are priorities for the GRC. The recentGRCh38.p11 patch release includes a newly curated representation of the 5S RNA gene cluster (RN5S1@) located on chromosome 1q42.11-q42.13. The 5S ribosomal RNA (rRNA) is a component of the large subunit of the ribosome in all organisms. In humans, the 5S rRNA cluster is comprised of individual rRNA genes repeated in head-to-tail orientation with non-rRNA sequences in the spacer regions. The number of 5S rRNA repeats per haploid human genome is highly polymorphic, in a range of 35-175 (1).The r...
Source: GenomeRef - June 28, 2017 Category: Genetics & Stem Cells Source Type: blogs
