Plant Nuclear Genome Composition

Abstract

The plant nuclear genome consists of deoxyribonucleic acid (DNA) divided among the chromosomes within the cell nucleus. Plant genomes contain coding and regulatory sequences for genes and repetitive DNA. They are evolutionarily dynamic and analysis provides insights into the evolution of genes and genomes, supporting studies of species phylogeny and plant breeding. The amount of DNA present in plant genomes, nearly constant within one species, varies over some 2300 times between species; the majority of the difference is accounted for genome duplication, or by various classes of repetitive DNA which may be dispersed widely along chromosomes or located in arrays at a small number of loci. Bioinformatics and genome sequence analysis show conservation of many gene sequences across all plants. Repetitive DNA motifs may be conserved over large taxonomic groupings or evolve rapidly. Repetitive DNA plays an important role as a structural component of plant chromosomes (e.g. telomeres and centromeres) and affects gene regulation.

Key Concepts:

  • Plant nuclear genome sizes, constant in a species, vary from 60 000 000 base pairs of DNA (written as 60 Mbp) to 150 000 Mbp, a range of 2300 times.

  • The DNA of plant nuclear genomes is wrapped around the histone proteins to form nucleosomes, and the resulting chromatin is organised into linear chromosomes with characteristic numbers, sizes and morphology in each species.

  • Genomes contain coding sequences, typically for 25 000–40 000 genes, and regulatory sequences, as shown by genome sequencing and bioinformatics.

  • Size variation comes from polyploidisation, genome or chromosome duplication, and particularly amplification of DNA motifs to give repetitive DNA.

  • Repetitive DNA consists of sequences that amplify via RNA intermediates (retrotransposons), through copying and reinsertion of DNA (DNA transposable elements), or other mechanisms (satellite and microsatellite DNA).

  • Some repetitive DNA encodes genes, in particular the 45S and the 5S ribosomal RNA genes (rDNA); other repetitive DNA has structural roles at the telomeres or chromosomal ends and the centromeres where chromosomes attach to microtubules during segregation. In most species, much of the repetitive DNA has no known function.

Keywords: tandemly repeated DNA; transposable elements; in situ hybridisation; chromosomes; genomes; nucleus; retrotransposons; repetitive DNA; satellite DNA; heterochromatin

Figure 1.

Nuclei from a hybrid cereal plant at various stages of cell division showing many circular interphase nuclei with decondensed chromatin and internal structures including lighter areas (the nucleoli with rDNA gene expression) and some chromatin fibres. The DNA has been stained with a molecule called 4′ 6′‐diamidino‐2‐phenylindole (DAPI) which fluoresces blue when excited by ultraviolet light in an epifluorescence light microscope. Chromosomes condense from prophase (P), and metaphase chromosomes (M), separating into the chromatids at anaphase (A) before decondensing during telophase (T) of the cell cycle. Arrow shows the nucleolus where rRNA genes are transcribed.

Figure 2.

Metaphase chromosomes from bread wheat (Triticum aestivum) next to two interphase nuclei photographed under the epifluorecence light microscope. The DNA in the 2n=42 chromosomes in this hexaploid (6x) species are seen stained with the fluorochrome DAPI (see Figure ) in the left panel, with some differentiation reflecting differences in chromatin density and base composition along the chromosomes. Two different tandemly repeated sequences, labelled in red and green (right), have been hybridised to the chromosomes to show the locations of large arrays of satellite DNA at terminal and some intercalary (green) locations while the red array is clustered near some centromeres on the chromosomes (scale bar 10 μm).

Figure 3.

Diagrams of the plant nuclear genome at various scales. The genome is divided among chromosomes within the cell nucleus, and consists of various classes of repetitive and single‐copy DNA sequence. The linear DNA is packaged with histone proteins to form nucleosomes which are packaged into the interphase and metaphase chromosomes.

Figure 4.

Major DNA components of the plant nuclear genome and their relationships.

close

References

Bennett MD and Leitch IJ (2011) Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Annals of Botany 107(3): 467–590. http://dx.doi.org/10.1093/aob/mcq258.

Cullis CE, Vorster BJ, van der Vyver C and Kunert KJ (2009) Transfer of genetic material between the chloroplast and nucleus: how is it related to stress in plants? Annals of Botany 103(4): 625–633. http://dx.doi.org/10.1093/aob/mcn173.

Hu TT, Pattyn P, Bakker EG et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43(5): 476–481. doi: 10.1038/ng.80.

Ma X‐F and Gustafson JP (2008) Allopolyploidization‐accommodated genomic sequence changes in Triticale. Annals of Botany 101(6): 825–832. http://www.dx.doi.org/10.1093/aob/mcm331.

Neumann P, Pozarkova D and Macas J (2003) Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced. Plant Molecular Biology 53: 399–410.

Schranz ME, Mohammadin M and Edger PP (2012) Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag‐Time Model. Current Opinion in Plant Biology 15: 147–153. http://dx.doi.org/10.1016/j.pbi.2012.03.011.

Further Reading

Feschotte C and Pritham EJ (2009) A cornucopia of Helitrons shapes the maize genome. Proceedings of the National Academy of Sciences of the USA 106(47): 19747–19748. http://dx.doi.org/10.1073/pnas.0910273106.

Heslop‐Harrison JS and Schwarzacher T (2011) Organization of the plant genome in chromosomes. Plant Journal 66: 18–33. http://dx.doi.org/10.1111/j.1365‐313x.2011.04544.x.

Schmidt T (1999) LINEs, SINEs and repetitive DNA: non‐LTR retrotransposons in plant genomes. Plant Molecular Biology 40(6): 903–910. http://dx.doi.org/10.1023/A:1006212929794.

Schmidt T and Heslop‐Harrison JS (1998) Genomes, genes and junk: the large‐scale organization of plant chromosomes. Trends in Plant Science 3: 195–199. http://dx.doi.org/10.1016/S1360‐1385(98)01223‐0.

Wicker T, Sabot F, Hua‐Van A et al. (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8: 973–982. http://dx.doi.org/10.1038/nrg2165.

Many chapters in the ELS are relevant and up to date.

Our understanding of plant genomes continues to develop rapidly as DNA sequence information is gained. Recent papers presenting complete genome sequences often put into context and expand the general findings of all previous sequences published; see, e.g. Wang X, Wang H, Wang J et al. (2011) The genome of the mesopolypoid crop species Brassica rapa. Nature Genetics 43(10): 1035–1039. http://dx.doi.org/10.1038/ng.919

Web Links

As well as the sequences and functional annotation of proteins in the Genbank/EMBL/DDJB databases, many species have genomic databases where much of the current information about plant genomes is described. These include Arabidopsis: The Arabidopsis Information Resource, TAIR, www.arabidopsis.org (see particularly ‘education and outreach’) and The Institute for Genome Research, TIGR www.tigr.org (many genome projects).

The US National Science Foundation (the grant body funding major plant genome projects in the United States) has the ‘National Plant Genome Initiative’ and their website, www.nsf.gov, includes accessible, accurate and current information and reports.

Genome sizes of plants are given in the database at http://www.rbgkew.org.uk/cval/

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Heslop‐Harrison, JS (Pat), and Schmidt, Thomas(Aug 2012) Plant Nuclear Genome Composition. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002014.pub2]