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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Genomics02:02

Genomics

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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...
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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Genome-wide Association Studies-GWAS01:11

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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.
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Related Experiment Video

Updated: Aug 24, 2025

An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants
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CuGenDBv2: an updated database for cucurbit genomics.

Jingyin Yu1, Shan Wu1, Honghe Sun1,2

  • 1Boyce Thompson Institute, Ithaca, NY 14853, USA.

Nucleic Acids Research
|October 22, 2022
PubMed
Summary
This summary is machine-generated.

The Cucurbit Genomics Database (CuGenDBv2) now integrates 34 cucurbit genomes, enhancing analysis of genetic variations and gene expression for these important crops.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • The Cucurbitaceae family includes numerous vital fruit and vegetable crops.
  • Recent advancements have generated extensive genomic and transcriptomic data for cucurbits.
  • Existing databases require updates to effectively manage and analyze this growing data.

Purpose of the Study:

  • To develop an updated Cucurbit Genomics Database (CuGenDBv2) for efficient data mining and dissemination.
  • To provide a centralized resource for analyzing cucurbit genomes, variomes, and transcriptomes.
  • To support research on economically important cucurbit species.

Main Methods:

  • Integrated 34 reference genomes from 27 cucurbit species across 10 genera.
  • Annotated protein-coding genes using public protein and domain databases.
  • Developed new 'Genotype' and 'Expression' modules for variome and transcriptome analysis.
  • Performed 595 pair-wise genome comparisons to identify synteny blocks.

Main Results:

  • CuGenDBv2 hosts 34 reference genomes with comprehensive gene annotations.
  • The 'Genotype' module facilitates analysis of SNPs and indels.
  • The 'Expression' module offers a detailed gene expression atlas for cucurbits.
  • Identified and visualized synteny blocks across multiple cucurbit genomes.

Conclusions:

  • CuGenDBv2 is a valuable, updated resource for cucurbit genomics research.
  • The database enables efficient exploration of genetic diversity and gene function.
  • Facilitates comparative genomics and understanding of cucurbit evolution.