Plant Genome Projects

Abstract

A genome project aims to discover all genes and their function in a particular species. Plant genome projects initially focused on a few model organisms that are characterised by small genomes or their amenability to genetic studies. Since sequencing technologies have moved on, sequencing cost have dropped and bioinformatics tools advanced, the genomes of many plant species including the enormous genome of bread wheat have been assembled. Genome sequencing projects have been carried out on all three plant genomes: the nuclear, chloroplast and mitochondrial genomes and have opened venues for advanced molecular breeding and manipulation of plant species, but also have accelerated phylogenetics studies amongst species. Several excellent curated plant genome databases, besides the general nucleotide data base archives, allow public access of plant genomes.

Key Concepts

  • Plant genomes have been extensively studied at the cytological, genetic and molecular level.
  • Plant cells have their genetic information distributed in three locations: nucleus, mitochondria and chloroplasts.
  • The main location of genetic information is the nuclear genome.
  • Nuclear genomes vary greatly in size and complexity.
  • Although many mitochondrial and chloroplast genes were already transferred to the nucleus since the incorporation of both organelles in the plant cell, a core of around 110 genes is retained in chloroplasts and of 35 genes in mitochondria.
  • Mitochondrial genomes are of special interest in plant breeding because they are involved in cytoplasmic male sterility.
  • The first entire plant genome sequenced was the genome of the model plant for plant genetics and plant physiology, Arabidopsis thaliana.
  • The list of sequenced plant genomes is continuously increasing due to drop in sequencing costs, advances in sequencing and bioinformatics technologies.
  • Comparative genomics approaches are useful to help along other non‐finished plant genomes.
  • Most sequenced plant genomes are from crop plants with an intention of making these genome sequencing efforts useful towards breeding of improved cultivars and for use of basic discoveries in plant biology.

Keywords: genome; genome size; genome sequence; crops; sequencing technologies

Figure 1. Circular structure of the chloroplast genome of Lolium perenne. Genes written on the outside are transcribed clockwise, genes on the inside counter‐clockwise, annotated genes are colour coded according to their function, genes containing introns are highlighted with an asterisk; LSC, large single copy region; SSC, small single copy region; IR, inverted repeat. Reproduced with permission from Diekmann et al. 2009 © Oxford University Press.
Figure 2. Conceptual representation of different genomic structural variations to a single region of the reference genome. Structural variations are large (>1 kbp) rearrangements of DNA that frequently result in phenotypic differences. These variations include insertions, deletions, inversions, duplications and translocations. By comparing genomes of different species, large chromosomal changes can be identified. Reproduced with permission from Chaney et al. 2016 © Elsevier.
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Further Reading

Further plant genome databases and resources can be accessed at: (1) http://www.gramene.org, a curated, open‐source, integrated data resource for comparative functional genomics in crops and model plant species; (2) Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute. Phytozome provides a hub for accessing, visualising and analysing JGI and non‐JGI‐sequenced plant genomes. As of release v12.1, Phytozome hosts 77 assembled and annotation genomes, from 74 viridiplantae species. Forty‐three of these genomes have been sequenced, assembled and annotated with JGI Plant Science program resources (http://www.phytozome.net); (3) various PLAZA platforms to accelerate comparative genomics (http://bioinformatics.psb.ugent.be/plaza/); (4) the Plant DB database aims to provide a data and information resource for individual plant species and to provide a platform for integrative and comparative plant genome research (http://mips.helmholtz‐muenchen.de/plant/genomes.jsp); (5) MaizeGDB is a community‐oriented and long‐term informatics service to researchers focused on the crop plant and model organism Zea mays (http://www.maizegdb.org); (6) the Sol Genomics Networks provides sequences and annotation information for the sequenced members of the Solanaceae, including potato, tomato and pepper (http://solgenomics.net/).

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How to Cite close
Barth, Susanne(Sep 2017) Plant Genome Projects. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002018.pub3]