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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 comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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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Crop pangenomes.

A Yu Pronozin1, M K Bragina2, E A Salina2

  • 1Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

Vavilovskii Zhurnal Genetiki I Selektsii
|December 13, 2021
PubMed
Summary

Agricultural plant pangenomics reveals extensive genomic variation beyond single reference genomes. Understanding these gene copy number variations (CNVs) and presence/absence variations (PAVs) is crucial for crop breeding and functional genomics.

Keywords:
agricultural plantsbioinformatics analysiscomputational pipelinesevolutiongenesgenomespangenomes

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Area of Science:

  • Agricultural genomics
  • Plant biology
  • Bioinformatics

Background:

  • Genome sequencing advances enable detailed study of agricultural plants.
  • Published genomes aid in understanding gene functions and selection strategies.
  • Crops exhibit significant genomic variations like copy number variations (CNVs) and presence/absence variations (PAVs).

Purpose of the Study:

  • To review agricultural plant pangenome studies.
  • To analyze pangenome structural features and bioinformatic analysis methods.
  • To highlight the importance of pangenomes for understanding crop diversity and breeding.

Main Methods:

  • Review of current literature on agricultural plant pangenome studies.
  • Description of pangenome structural features.
  • Overview of bioinformatic methods and programs for pangenomic data analysis.

Main Results:

  • Single reference genomes inadequately represent species diversity due to prevalent genomic variations.
  • The pangenome concept encompasses all genes within a taxon, including common and variable ones.
  • Pangenome analysis offers insights into genomic variation, evolutionary research, and crop improvement.

Conclusions:

  • Pangenome sequencing is essential for capturing the full genetic diversity within crop species.
  • Understanding pangenomes facilitates functional genomics and accelerates marker-assisted and genomic selection in crop breeding.
  • This review synthesizes current knowledge on agricultural plant pangenomes, providing a foundation for future research.