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Related Concept Videos

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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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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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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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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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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DRDB: An Online Date Palm Genomic Resource Database.

Zilong He1, Chengwei Zhang1,2,3, Wanfei Liu1,4,5

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.

Frontiers in Plant Science
|December 7, 2017
PubMed
Summary

This study improved the date palm genome assembly and identified numerous short sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). These genomic resources aid in date palm cultivar classification and molecular breeding.

Keywords:
cultivar classificationdate palmgenome variationshort sequence repeatsingle nucleotide polymorphism

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Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Breeding

Background:

  • Date palm (Phoenix dactylifera L.) is an agriculturally and economically significant woody plant.
  • Advancements in next-generation sequencing have enabled the release of numerous date palm genome sequences.
  • Short Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) are valuable biomarkers for plant genome analysis and breeding.

Purpose of the Study:

  • To improve the date palm genome assembly.
  • To identify and annotate SSRs and SNPs within the improved genome assembly.
  • To reconstruct phylogenetic relationships and develop resources for cultivar classification and molecular breeding.

Main Methods:

  • Improved date palm genome assembly using 130X HiSeq data.
  • Annotation of SSRs and SNPs, including quality filtering and PCR primer design.
  • Phylogenetic analysis and principal component analysis of 62 cultivars using identified variants.

Main Results:

  • Annotated 246,445 SSRs (58.92% mononucleotide) and 6,375,806 SNPs.
  • Designed PCR primers for 70.81% of SSRs and 65.53% of SNPs.
  • Reconstructed phylogenetic relationships, dividing 62 cultivars into North Africa, Egypt-Sudan, and Middle East-South Asian clusters.

Conclusions:

  • The Date Palm Resource Database (DRDB) is a comprehensive genomic resource.
  • DRDB serves as a bioinformatics platform for date palm genomics, genetics, and molecular breeding.
  • The identified SSRs and SNPs facilitate cultivar identification, comparison, and breeding applications.