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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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Fruits form from a mature flower ovary. As seeds develop from the ovules contained within, the ovary wall undergoes a series of complex changes to form fruit. In some fruits, such as soybeans, the ovary wall dries; in other fruits, such as grapes, it remains fleshy. In some cases, organs other than the ovary contribute to fruit formation; such fruits are called accessory fruits.
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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Recombinant DNA technology called transgenesis is often used to add a foreign gene or remove a detrimental gene from an organism. Such genetically modified organisms are called transgenic organisms.
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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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Updated: Jul 4, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Passionfruit Genomic Database (PGD): a comprehensive resource for passionfruit genomics.

Chaowei Yu1, Peng Wang1, Shengjie Zhang2

  • 1MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), Yangtze University, Jingzhou, 434025, China.

BMC Genomics
|February 8, 2024
PubMed
Summary

Researchers developed the first passionfruit genome database (PGD) to integrate and analyze omics data. This user-friendly platform enhances passionfruit research by providing comprehensive genomic information and analysis tools.

Keywords:
Functional genomicsPassiflora edulisPassionfruit genomic databaseTranscriptomicsWeb server

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Area of Science:

  • Agricultural Science
  • Genomics
  • Bioinformatics

Background:

  • Passionfruit (Passiflora edulis) is a commercially important crop with significant nutritional and medicinal value.
  • High-throughput sequencing has generated extensive passionfruit omics data, including genome and transcriptome information under various stress conditions.
  • Efficient integration and analysis of this large-scale data are crucial for advancing passionfruit research.

Purpose of the Study:

  • To develop the first comprehensive passionfruit genome database (PGD).
  • To provide a user-friendly platform for integrating, storing, and analyzing passionfruit omics data.
  • To enhance the utilization value of passionfruit genomic data for researchers.

Main Methods:

  • Development of the Passionfruit Genome Database (PGD) platform.
  • Integration of diverse omics data, including genome sequences and transcriptomes.
  • Implementation of functional modules such as a genome browser, search functions, heatmaps, gene expression analysis, sequence alignment, and batch download.
  • Inclusion of supplementary tools for gene family analysis, Gene Ontology (GO) term enrichment, and pathway analysis.

Main Results:

  • The PGD offers a user-friendly interface with multiple functional modules for data exploration and analysis.
  • Supplementary tools enhance the utility of the data for in-depth analysis and mining.
  • The database is designed for scalability to accommodate future passionfruit omics data integration.

Conclusions:

  • The PGD serves as a centralized resource for passionfruit omics data.
  • It significantly facilitates efficient data integration, storage, and analysis for researchers.
  • The PGD aims to provide comprehensive support for advancing passionfruit research and breeding efforts.