scispace - formally typeset
Search or ask a question
Topic

Genome

About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.


Papers
More filters
Journal ArticleDOI
TL;DR: A comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions provides evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor.
Abstract: The histories of crop domestication and breeding are recorded in genomes. Although tomato is a model species for plant biology and breeding, the nature of human selection that altered its genome remains largely unknown. Here we report a comprehensive analysis of tomato evolution based on the genome sequences of 360 accessions. We provide evidence that domestication and improvement focused on two independent sets of quantitative trait loci (QTLs), resulting in modern tomato fruit ∼100 times larger than its ancestor. Furthermore, we discovered a major genomic signature for modern processing tomatoes, identified the causative variants that confer pink fruit color and precisely visualized the linkage drag associated with wild introgressions. This study outlines the accomplishments as well as the costs of historical selection and provides molecular insights toward further improvement.

678 citations

Journal ArticleDOI
24 Apr 2020-PLOS ONE
TL;DR: The method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, suggesting that this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.
Abstract: The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 virus genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 virus genomes. The proposed method combines supervised machine learning with digital signal processing (MLDSP) for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman’s rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp, including the 29 COVID-19 virus sequences available on January 27, 2020. Our results support a hypothesis of a bat origin and classify the COVID-19 virus as Sarbecovirus, within Betacoronavirus. Our method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.

676 citations

Journal ArticleDOI
TL;DR: A genome-wide search in 140 families with ≥2 asthmatic sibs, from three racial groups and report evidence for linkage to six novel regions, including 5p15 (P= 0.0008) and 17p11.1–q11.2 (/> = 0.0015) in African Americans and 11p15 and 19q13 (P =0.0013) in Caucasians and Hispanics.
Abstract: Asthma is an inflammatory airwaysdisease associated with intermittent respiratory symptoms, bronchial hyperresponsiveness (BHR) and reversible airflow obstruction and is phenotypically heterogeneous1,2. Patterns of clustering and segregation analyses in asthma families have suggested a genetic component to asthma3–6. Previous studies reported linkage of BHR and atopy to chromosomes 5q (refs 7–9), 6p (refs 10–12), 11q (refs 13–15), 14q (ref. 16), and 12q (ref. 17) using candidate gene approaches. However, the relative roles of these genes in the pathogenesis of asthma or atopy are difficult to assess outside of the context of a genome-wide search. One genome-wide search in atopic sib pairs has been reported18, however, only 12% of their subjects had asthma. We conducted a genome-wide search in 140 families with ≥2 asthmatic sibs, from three racial groups and report evidence for linkage to six novel regions: 5p15 (P= 0.0008) and 17p11.1–q11.2 (/> = 0.0015) in African Americans; 11p15 (P = 0.0089) and 19q13 (P = 0.0013) in Caucasians; 2q33 (P = 0.0005) and 21q21 (P = 0.0040) in Hispanics. Evidence for linkage was also detected in five regions previously reported to be linked to asthma-associated phenotypes: 5q23–31 (P = 0.0187), 6p21.3–23 (P = 0.0129), 12q14–24.2 (P = 0.0042), 13q21.3–qter (P = 0.0014), and 14q11.2–13 (P = 0.0062) in Caucasians and 12q14–24.2 (P = 0.0260) in Hispanics.

676 citations

Journal ArticleDOI
TL;DR: In screening over 14,000 mice for a large number of clinically relevant parameters, 182 mouse mutants are recovered and this mutagenesis screen leads to a significant increase in the number of mouse models available to the scientific community.
Abstract: In the post-genome era, the mouse will have a major role as a model system for functional genome analysis. This requires a large number of mutants similar to the collections available from other model organisms such as Drosophila melanogaster and Caenorhabditis elegans. Here we report on a systematic, genome-wide, mutagenesis screen in mice. As part of the German Human Genome Project, we have undertaken a large-scale ENU-mutagenesis screen for dominant mutations and a limited screen for recessive mutations1. In screening over 14,000 mice for a large number of clinically relevant parameters, we recovered 182 mouse mutants for a variety of phenotypes. In addition, 247 variant mouse mutants are currently in genetic confirmation testing and will result in additional new mutant lines. This mutagenesis screen, along with the screen described in the accompanying paper2, leads to a significant increase in the number of mouse models3 available to the scientific community. Our mutant lines are freely accessible to non-commercial users (for information, see http://www.gsf.de/ieg/groups/enu-mouse.html ).

676 citations

Journal ArticleDOI
19 May 2006-Science
TL;DR: Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties and led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains.
Abstract: With the use of synthetic biology, we reduced the Escherichia coli K-12 genome by making planned, precise deletions. The multiple-deletion series (MDS) strains, with genome reductions up to 15%, were designed by identifying nonessential genes and sequences for elimination, including recombinogenic or mobile DNA and cryptic virulence genes, while preserving good growth profiles and protein production. Genome reduction also led to unanticipated beneficial properties: high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Eradication of stress-induced transposition evidently stabilized the MDS genomes and provided some of the new properties.

675 citations


Network Information
Related Topics (5)
Gene
211.7K papers, 10.3M citations
96% related
Transcription (biology)
56.5K papers, 2.9M citations
92% related
RNA
111.6K papers, 5.4M citations
91% related
Regulation of gene expression
85.4K papers, 5.8M citations
91% related
Gene expression
113.3K papers, 5.5M citations
90% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20242
20237,313
202214,209
20214,955
20205,080
20194,839