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Genomics02:02

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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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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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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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PGD: Pineapple Genomics Database.

Huimin Xu1,2, Qingyi Yu3, Yan Shi1

  • 11Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.

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|September 25, 2018
PubMed
Summary
This summary is machine-generated.

A new Pineapple Genomics Database (PGD) centralizes genomic and transcriptomic data for Ananas comosus. This open-access resource aids research into pineapple evolution and crassulacean acid metabolism (CAM) photosynthesis.

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Area of Science:

  • Plant genomics
  • Evolutionary biology
  • Photosynthesis research

Background:

  • Pineapple (Ananas comosus) is crucial for studying Bromeliaceae family evolution and crassulacean acid metabolism (CAM) photosynthesis.
  • A comprehensive genomic resource is needed to facilitate research on pineapple biology and evolution.

Purpose of the Study:

  • To develop a central online platform for pineapple genomic, transcriptomic, functional annotation, and genetic marker data.
  • To provide researchers with tools for comparative genomics, gene expression, and gene annotation studies.

Main Methods:

  • Development of the Pineapple Genomics Database (PGD).
  • Integration of genomic, transcriptomic, functional annotation, and genetic marker data.
  • Implementation of search tools, a genomic browser, and data download functionalities.

Main Results:

  • The PGD provides integrated datasets and tools for studying Ananas comosus.
  • Features include interactive genomic visualization, bulk data download, and a user manual.
  • An email-based helpdesk is available for user support and data requests.

Conclusions:

  • The PGD serves as a long-term, open-access resource for pineapple research.
  • It will facilitate studies on pineapple biology, distribution, and evolution.
  • The database is designed for future data integration and expansion.