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Related Concept Videos

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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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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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croFGD: Catharanthus roseus Functional Genomics Database.

Jiajie She1, Hengyu Yan1, Jiaotong Yang1

  • 1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China.

Frontiers in Genetics
|April 11, 2019
PubMed
Summary
This summary is machine-generated.

This study developed the Catharanthus roseus Functional Genomics Database (croFGD) by analyzing 53 RNA-seq datasets to map gene functions. The database aids research into this medicinal plant

Keywords:
Catharanthus roseusco-expression networkfunctional modulegene functionmonoterpene indole alkaloid

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Area of Science:

  • Plant Genomics and Bioinformatics
  • Functional Genomics
  • Medicinal Plant Research

Background:

  • Catharanthus roseus is a vital medicinal plant producing valuable monoterpene indole alkaloid (MIA) metabolites like vinblastine and vincristine.
  • The availability of the C. roseus genome sequence necessitates comprehensive gene function annotation at the whole-genome level.
  • Existing public RNA-seq datasets offer a rich resource for exploring gene expression across various tissues and treatments.

Purpose of the Study:

  • To construct a comprehensive co-expression network for Catharanthus roseus using multi-dimensional gene expression data.
  • To integrate miRNA-target and protein-protein interaction (PPI) data to enhance functional predictions.
  • To develop an accessible online database (croFGD) for facilitating functional genomics research in C. roseus.

Main Methods:

  • Utilized a data processing pipeline combining Pearson Correlation Coefficient (PCC) and Mutual Rank (MR) algorithms to build a gene co-expression network.
  • Analyzed gene expression across multiple dimensions: global, tissue-preferential, and treatment responses (MeJA, PnWB, yeast elicitor).
  • Integrated predicted miRNA-target and PPI pairs, and implemented tools for gene set, functional module, and motif enrichment analysis.

Main Results:

  • Successfully constructed a multi-layered co-expression network revealing global, tissue-specific, and treatment-responsive gene expression patterns.
  • Integrated omics data and analytical tools to provide robust functional predictions for co-expressed genes.
  • Developed and launched the Catharanthus roseus Functional Genomics Database (croFGD) as a centralized resource.

Conclusions:

  • The croFGD database provides a valuable platform for the scientific community to explore C. roseus functional genomics.
  • The integrated network and analytical tools facilitate the identification of key genes involved in important biological processes.
  • This resource is expected to accelerate novel discoveries regarding the biosynthesis of valuable compounds and other plant functions.