Plant genomics general overview

Introduction
History
First model organism(Arabidopsis thaliana)
Studying plant genome
Plant nuclear genome composition
Organization of plant genome
Transposable elements
Chloroplast genome & its evolution
Mapping plant genomes
Plant genome project
Application
Conclusion
References

1. PLANT GENOMICS By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )

2. CONTENTS:   Introduction History First model organism(Arabidopsis thaliana) Studying plant genome Plant nuclear genome composition Organization of plant genome Transposable elements Chloroplast genome & its evolution Mapping plant genomes Plant genome project Application Conclusion References

3. Introduction Genomics - the study of genomes. Genome -The word ‘’genome’’describes the total repertoire of DNA in a particular organelle. Plant genomes dramatically vary in size and in function.  Plant chloroplasts and mitochondria maintain plant genomes, and plant mitochondrial genomes are large, variable and enormously interesting.   Plant nuclear genomes have been sculpted by interspecific hybridization ,polyploidy, transposition, retro-transposition and translocation events.

4. History : Formal research into the function of the plant genome started with mendel in 1866 . Arabidopsis thaliana (a dicot) was the first plant chosen for genome sequencing, Rice was the second genome sequenced and was the first monocot.  A small number of plant genomes have been studied in great detail in the 1990s and early in the twenty-first century and the DNA of their genomes has been sequenced.  

5. First eukaryotic model organism( Arabidopsis thaliana )   One of the first eukaryotic organisms that will be completely sequenced is the small mustard species Arabidopsis thaliana .  During the past decade, Arabidopsis has emerged as one of the most widely used model organisms for studying the biology of higher plants. It was chosen for sequencing because it has a highly compact genome of about 130 Mb with little interspersed repetitive DNA.  

6. Fig.: Functional classification of predicted genes in a 1.9-Mb region of the Arabidopsis genome.

7. Studying Plant genome: Plant genomes are more complex than other eukaryotic genomes, and analysis reveals many evolutionary flips and turns of the DNA sequences over time.   Plant nuclear genome range in size from less than 100million base pairs to more than 100 billion base pairs.   Plants show widely different chromosome numbers and varied ploidy levels . Overall, the size of plant genomes (both number of chromosomes and total nucleotide base-pairs) exhibits the greatest variation of any kingdom in the biological world. For example, tulips contain over 170 times as much DNA as the small weed Arabidopsis thaliana .

8. The DNA of plants, like animals, can also contain regions of sequence repeats, sequence inversions, or transposable element insertions, which further modify their genetic content. Traditionally, variation in chromosome inversions and ploidy has been used to build up a picture of how plant species have evolved .   Increasingly,researchers are turning to studying the organization of plant DNA sequences to obtain important information about the evolutionary history of a plant species.  

9. FIGURE : Chromosome numbers possible in plant genomes.

10. Nuclear Genomes and their Size The nuclear genome of rice consists of 450 million base pairs (Mbp) of DNA divided among the 12 chromosome pairs, and includes the genes that encode some 38 000 proteins. Along with their controlling sequences, these genes represent less than 10% of the total amount of DNA, and about half of all the DNA consists of repetitive motifs that are present thousands of times in the genome. Another fully sequenced plant genome, Arabidopsis ( Arabidopsis thaliana ) has a total of 157Mbp with about 31 000 genes on five chromosome pairs.

11. It is currently anticipated that the complete genome sequence of Arabidopsis will be available by the end of the year 2000.   Because Arabidopsis is only distantly related to the cereal crops that provide the bulk of the world’s food supply, the genome of rice will also be sequenced during the next decade .   Rice was chosen because, in addition to its importance as a food source for about one-quarter of the human population, it has one of the most compact genomes among the cereals. It contains about 3.5 times as much DNA as Arabidopsis but only about 20% as much DNA as maize and about 3% as much DNA as wheat .

12. All higher plants, at the diploid level, require approximately the same number of genes and regulatory DNA sequences for physiological processes like seed germination,growth, flowering and reproduction. However, nuclear genome sizes, measured by the number of base pairs of DNA, of different plant species vary enormously between species, although each species has a characteristic and relatively constant genome size. The amount of nuclear DNA can be given as an absolute weight of the DNA (in pg, picograms) or converted into the number of base pairs represented by that weight.

13. Plant Nuclear Genome Composition   The plant nuclear genome consists of DNA divided among the chromosomes within the cell nucleus.   Plant genomes contain coding and regulatory sequences for the genes and repetitive DNA.   Genomes are evolutionarily dynamic and analysis provides insights into the evolution of genes, sequence families and genomes, and supports studies of species phylogeny and relationships.

14. The plant nuclear genome consists of deoxyribonucleic acid (DNA) and is contained within the nucleus, an organelle encased by a double membrane in each cell.   During cell division, mitosis, the genome condenses into a characteristic number of metaphase chromosomes, the nuclear membranes break down, and the chromosomes divide, moving into the two daughter cells before the nuclei reform.  

15. Organization of Plant Genomes:-   Most seed plants contain quantities of DNA that greatly exceed their needs for coding and regulatory function. Hence, for plants, a very small percentage of the genome may actually encode genes involved in the production of protein. This portion of the genome which encodes most of the transcribed genes is often referred to as “low-copy number DNA,” because the DNA sequences comprising these genes are present in single or small numbers of copies.  

16. “Medium-copy-number DNA” is composed largely of DNA sequences that encode ribosomal RNA (rRNA), a key element of the cellular machinery that translates transcribed messenger RNA (mRNA) into protein.  In plant genomes, rRNA genes may be repeated several hundred to several thousand times.  Plant cells may also contain excess DNA in their genomes in the form of highly repetitive sequences, or “high-copy-number DNA.” At present, the function of this high-copy-number DNA in plant genomes is unknown.

17. Sequence Replication and Inversion High-copy-number DNA sequences in the plant genome may be short, such as the nucleotide sequence “GAA,” or much longer, involving up to several hundred nucleotides.   Moreover, the number of copies of an individual high copy repetitive DNA sequence can total from 10,000 to 100,000. There are several possibilities for how high-copy repetitive DNA sequences may be organized within a plant genome.   Several copies of a single repetitive DNA sequence may be present together in the same orientation, in a pattern called “simple tandem array.”

18. Alternatively, repetitive DNA sequences can be dispersed among single-copy DNA in the same orientation (“repeat/single-copy interspersion”) or the opposite orientation (“inverted repeats”).   In addition, groups of repetitive DNA sequences can also occur together in plant genomes in a variety of possible arrangements, such as a“compound tandem array” or a “repeat/repeat interspersion.”   The presence of repetitive DNA can vastly increase the size of a plant genome, making it difficult to find and characterize individual single-copy genes.   A variety of mechanisms can account for the presence of highly repetitive DNA sequences in plant genomes.  

19. Transposable Elements:   Transposable elements, are special sequences of DNA with the ability to move from place to place in the genome.   They can excise from one site at unpredictable times and reinsert in another site. For this reason, transposable elements have been called “jumping genes.   Transposable elements often insert into coding regions or regulatory regions of a gene and so affect expression of that gene, resulting in a mutation that may or may not be detectable.   Barbara McClintock won the Nobel Prize in 1983 for her work describing transposable elements in corn.

20. FIGURE : Organization of repeated DNA sequences and the mechanism of transposable elements in altering gene function.

21. Chloroplast Genome and Its Evolution   The chloroplast is a plant organelle that functions in photosynthesis,and it can independently replicate in the plant cell.   Plant chloroplasts have their own specific DNA, which is separate from that present in the nucleus.   This DNA is maternally inherited and encodes unique chloroplast proteins.   Many of the proteins encoded by chloroplast DNA are involved in photosynthesis.  

22. Chloroplast DNA is present as circular loops of double-stranded DNA similar to prokaryotic chromosomal DNA.   Moreover, chloroplast DNA contains genes for ribosomes that are very similar to those present in prokaryotes. The DNA in chloroplasts of all land plants has about the same number of genes (~100), and they are present in about the same order .

23. FIGURE :Chloroplast genome.

24. Mapping plant genomes:   RFLP and AFLP as Tools to Map Genomes and Detect Polymorphisms Genome mapping is a widely-Aplicable approach to scanning the genetic information of an organism for genes that are responsible for a specific trait.   Higher plants are thought to have 25,000 or more genes,the vast majority of which remain of unknown function.   A particular strenghth of genome mapping.is that it facilitates isolation of genes based simply on measurement of their effects(s)on phenotype requiring no a priori knowledge of the biochemical function performed by a gene.

25. Much more of the genome can be mapped using RFLPs (restriction fragment length polymorphisms) which need not have a macroscopic phenotype. This approach, involves analysis of the RFLP map, or the pattern of DNA fragments, produced when DNA is treated with restriction enzymes that cleave at specific sites.  RFLP mapping can identify important regions of the genome at a glance, while sequence data require sophisticated computer- based searching and matching systems. A comparison of the RFLP maps of parents and progeny can give an indication of the heritability of gene traits and of heritable loci that are characteristic of traits.  

26. Another tool that utilizes sequence variability is AFLPs, or amplified fragment length polymorphisms.  Hybridizing DNA primers with genomic DNA fragments that have been cut with restriction enzymes, usually Eco RI and Mse I, and then subsequently amplified using the polymerase chain reaction (PCR) generates AFLP maps. The resulting PCR products, which represent each piece of DNA cut by a restriction enzyme, are separated by size via gel electrophoresis. The band sizes on an AFLP gel tend to show more polymorphisms than those found with RFLP mapping because the entire genome is visible on the gel .  

27. Applications: Genomics research will lead to new and innovative ways to achieve such trait improvement. Clearly,genomics can help in issues related to food safety, food quality,and food diversity.   Genomics provides objectivity in breeding as never before possible; it allows hypothesis testing of quantitative genetics applications in plant improvement.   It is useful to increase crop productivity, improve crop quality, and maintain the environment.  

28. Conclusion:   Genomic organization is much more varied in plants than in animals. The completely sequenced Arabidopsis genome will have far-reaching uses in agricultural breeding and evolutionary analysis. Plant genome research is more than biology; it is also about producing food for our planet.

29. References Plant genomics and proteomics-Christopher A.Cullis, A. Jhon & Sons,Inc.Publication (pdf). Biotechnology –vol-VII plant genome mapping strategies & application – Andrew H.Peterson(pdf).