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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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SpudDB: a database for accessing potato genomic data.

John P Hamilton1,2, Julia Brose2, C Robin Buell1,2,3,4

  • 1Department of Crop & Soil Sciences, University of Georgia, Athens, GA 30602, USA.

Genetics
|December 10, 2024
PubMed
Summary
This summary is machine-generated.

The SpudDB database now offers a comprehensive potato genome resource, featuring phased assemblies and gene annotations. This platform aids researchers in understanding potato genetics and improving this vital food crop.

Keywords:
annotationco-expressiondiversitypotato

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Crop science

Background:

  • The potato (Solanum tuberosum) possesses a complex, polyploid genome, posing challenges for genetic research.
  • Recent advancements in sequencing and assembly have facilitated the creation of high-quality, chromosome-scale genome assemblies for cultivated potato.

Purpose of the Study:

  • To establish a centralized database (SpudDB) for potato genome sequence and annotation data.
  • To provide tools and resources for exploring potato gene function, expression, and synteny.

Main Methods:

  • Generation of phased, chromosome-scale genome assemblies for cultivated tetraploid potato.
  • Development of the SpudDB database, including gene annotation and expression profiling across 438 samples.
  • Construction of 65 gene co-expression modules to identify co-regulated genes.
  • Identification of syntelogs across 25 cultivated potato genomes.

Main Results:

  • SpudDB provides access to the reference doubled monoploid DM 1-3 516 R44 (DM) genome and haplotype.
  • Gene Report Pages offer diverse annotation data, including gene expression profiles.
  • Co-expression modules reveal gene regulation patterns during development and stress responses.
  • Genome browser views and syntelog identification facilitate comparative genomics.

Conclusions:

  • SpudDB serves as a valuable resource for potato biologists, geneticists, and breeders.
  • The database enables deeper understanding of potato genome structure and function.
  • Facilitates continued improvement of potato as a key global food crop.