Abstract:
BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundreds of breeds make cattle ideally suited to investigate the optimal composition of variation-aware references. RESULTS:We augment the bovine linear reference sequence (ARS-UCD1.2) with variants filtered for allele frequency in dairy (Brown Swiss, Holstein) and dual-purpose (Fleckvieh, Original Braunvieh) cattle breeds to construct either breed-specific or pan-genome reference graphs using the vg toolkit. We find that read mapping is more accurate to variation-aware than linear references if pre-selected variants are used to construct the genome graphs. Graphs that contain random variants do not improve read mapping over the linear reference sequence. Breed-specific augmented and pan-genome graphs enable almost similar mapping accuracy improvements over the linear reference. We construct a whole-genome graph that contains the Hereford-based reference sequence and 14 million alleles that have alternate allele frequency greater than 0.03 in the Brown Swiss cattle breed. Our novel variation-aware reference facilitates accurate read mapping and unbiased sequence variant genotyping for SNPs and Indels. CONCLUSIONS:We develop the first variation-aware reference graph for an agricultural animal ( https://doi.org/10.5281/zenodo.3759712 ). Our novel reference structure improves sequence read mapping and variant genotyping over the linear reference. Our work is a first step towards the transition from linear to variation-aware reference structures in species with high genetic diversity and many sub-populations.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Crysnanto D,Pausch Hdoi
10.1186/s13059-020-02105-0subject
Has Abstractpub_date
2020-07-27 00:00:00pages
184issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-020-02105-0journal_volume
21pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Some years ago we established an N-ethyl-N-nitrosourea screen for modifiers of transgene variegation in the mouse and a preliminary description of the first six mutant lines, named MommeD1-D6, has been published. We have reported the underlying genes in three cases: MommeD1 is a mutation in SMC hinge domain ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-12-r182
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1848-3
更新日期:2019-11-26 00:00:00
abstract::A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-016-0898-z
更新日期:2016-02-27 00:00:00
abstract:BACKGROUND:Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detec...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-12-r96
更新日期:2004-01-01 00:00:00
abstract::We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show tha...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1773-5
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1746-8
更新日期:2019-07-15 00:00:00
abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-020-02221-x
更新日期:2021-01-08 00:00:00
abstract:BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02192-z
更新日期:2020-11-23 00:00:00
abstract::CRISPR guide RNA libraries have been iteratively improved to provide increasingly efficient reagents, although their large size is a barrier for many applications. We design an optimised minimal genome-wide human CRISPR-Cas9 library (MinLibCas9) by mining existing large-scale gene loss-of-function datasets, resulting ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-021-02268-4
更新日期:2021-01-21 00:00:00
abstract:BACKGROUND:Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying me...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1457-6
更新日期:2018-07-17 00:00:00
abstract::A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-5-315
更新日期:2012-05-25 00:00:00
abstract::The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1646-y
更新日期:2019-03-04 00:00:00
abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-11-132
更新日期:2011-11-21 00:00:00
abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01998-1
更新日期:2020-04-29 00:00:00
abstract::The circadian clock determines the rhythmic expression of many different genes throughout a 24-hour period. A recent study investigating the circadian regulation of liver proteins reveals multiple levels of regulation, including transcriptional, post-transcriptional and post-translational mechanisms. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-9-234
更新日期:2006-01-01 00:00:00
abstract::The majority of people in the developed world spend more than 90% of their lives indoors. Here, we examine our understanding of the bacteria that co-inhabit our artificial world and how they might influence human health. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2013-14-2-202
更新日期:2013-02-28 00:00:00
abstract::Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02096-y
更新日期:2020-08-06 00:00:00
abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2009-10-1-301
更新日期:2009-01-01 00:00:00
abstract::Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the princi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-10-reviews2002
更新日期:2001-01-01 00:00:00
abstract::Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1267-2
更新日期:2017-07-27 00:00:00
abstract:BACKGROUND:Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. RESULTS...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-4-r40
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r11
更新日期:2012-02-20 00:00:00
abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-6-r69
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-6-r79
更新日期:2014-06-19 00:00:00
abstract::A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-3-reviews1007
更新日期:2002-01-01 00:00:00
abstract::A genomic analysis of heterogeneous colorectal tumor samples has uncovered interactions between immunophenotype and various aspects of tumor biology, with implications for informing the choice of immunotherapies for specific patients and guiding the design of personalized neoantigen-based vaccines. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0631-3
更新日期:2015-03-31 00:00:00
abstract:BACKGROUND:Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA patho...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1002-4
更新日期:2016-06-23 00:00:00
abstract:BACKGROUND:Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30% to 40% of patients failing to be cured with available primary therapy. microRNAs (miRNAs) are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 ben...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0568-y
更新日期:2015-01-29 00:00:00
abstract:BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r218
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV detection algorithms can detect many types of SVs using whole genome sequencing (WGS) data, no single a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1720-5
更新日期:2019-06-03 00:00:00