Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. Here, we present EquCab3. The count of non-N bases in the incorporated chromosomes is improved from 2.33 Gb in EquCab2 to 2.41 Gb in EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5 Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240028 | PMC |
| http://dx.doi.org/10.1038/s42003-018-0199-z | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A cost-effective oligo-based barcode system for chromosome identification in longan and lychee.
Hortic Res
January 2025
Key Laboratory of Tropical Fruit Biology (Ministry of Agriculture), South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Mazhang District, Zhanjiang 524091, China.
Oligonucleotide (Oligo)-based fluorescence hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan ( Lour.
View Article and Find Full Text PDFThe Darwin Tree of Life (DToL) project aims to generate high-quality reference genomes for all eukaryotic organisms in Britain and Ireland. At the time of writing, PacBio HiFi reads are generated for all samples using the Sequel IIe systems by the Wellcome Sanger Institute's Scientific Operations teams, however we expect lessons from this work to apply directly to the Revio system too, as core principles of SMRT sequencing remain the same. We observed that HiFi yield is highly variable for DToL samples.
View Article and Find Full Text PDFTrends and advances in , a bibliometric analysis.
Front Microbiol
January 2025
Department of Intensive Care Unit, The Peoples Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
Background: Leptospirosis is an acute zoonotic disease caused by pathogenic , primarily transmitted to humans through contact with water or soil contaminated by the bacteria. It is globally distributed, with heightened prevalence in tropical regions. While prior studies have examined the pathophysiology, epidemiology, and risk factors of leptospirosis, few have explored trends and emerging topics in the field.
View Article and Find Full Text PDFComprehensive genomic analysis and selection signature detection in endangered Beigang pigs using whole-genome sequencing data.
Anim Genet
February 2025
Hainan Yazhou Bay Seed Lab, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya, China.
The Beigang pig was recently identified as one of the endangered breeds during a Chinese indigenous pig genetic resource survey. The Beigang breed is notable for its remarkable roughage tolerance and high reproductive capacity according to historical records. Morphologically, the Beigang pig resembles many indigenous pigs in eastern China, especially in its large ears.
View Article and Find Full Text PDFSpatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity.
Cell Biosci
January 2025
Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Erheng Road, Guangzhou, 510655, Guangdong, China.
Background: Intratumoral heterogeneity emerges from accumulating genetic and epigenetic changes during tumorigenesis, which may contribute to therapeutic failure and drug resistance. However, the lack of a quick and convenient approach to determine the intratumoral epigenetic heterogeneity (eITH) limit the application of eITH in clinical settings. Here, we aimed to develop a tool that can evaluate the eITH using the DNA methylation profiles from bulk tumors.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!