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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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Genomic Imprinting and Inheritance02:30

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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.
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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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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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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.
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The ITS2 Database
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CeleryDB: a genomic database for celery.

Kai Feng1, Xi-Lin Hou1, Meng-Yao Li1

  • 1State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.

Database : the Journal of Biological Databases and Curation
|July 12, 2018
PubMed
Summary
This summary is machine-generated.

Researchers have sequenced the whole genome of celery (Apium graveolens L.), a popular vegetable, and created CeleryDB, an accessible online database for genomic data. This resource aids global celery research by providing gene and protein sequences.

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Agricultural science

Background:

  • Celery (Apium graveolens L.) is a globally significant vegetable crop within the Apiaceae family, valued for its nutritional and medicinal properties.
  • Despite its importance, comprehensive genomic data for celery has been lacking, hindering in-depth genetic and molecular studies.
  • The increasing demand for genomic resources underscores the need for a publicly accessible celery genome database.

Purpose of the Study:

  • To sequence the whole genome of a specific celery inbred line ('Q2-JN11').
  • To establish an online database, CeleryDB, for easy access to celery genomic information.
  • To facilitate future research in celery genetics, breeding, and functional genomics.

Main Methods:

  • Whole-genome sequencing of the 'Q2-JN11' celery line utilizing HiSeq 2000 technology.
  • Bioinformatic analysis to predict gene and protein sequences from the assembled genome.
  • Development of an online database (CeleryDB) with user-friendly interfaces for data retrieval and analysis.

Main Results:

  • The complete genome sequence of 'Q2-JN11' celery was successfully obtained and assembled.
  • CeleryDB was constructed, providing access to whole-genome sequences, predicted gene nucleotide sequences, and predicted protein amino acid sequences.
  • The database features integrated tools, including Basic Local Alignment Search Tool (BLAST) and a Genome Browser, for efficient data querying.

Conclusions:

  • The availability of the celery whole genome sequence and the CeleryDB database represents a significant advancement for the scientific community.
  • CeleryDB offers a valuable, centralized resource for researchers worldwide studying celery genetics and improvement.
  • Future updates to CeleryDB will ensure its continued utility and support for ongoing celery research endeavors.