Genomics is defined as the study of genes and their functions, and related techniques (WHO, 2002 and WHA, 2004). The main difference between genomics and genetics is that genetics scrutinizes the functioning and composition of the single gene where as genomics addresses all genes and their inter relationships in order to identify their combined influence on the growth and development of the organism.

Mitochondria and chloroplasts are eukaryotic organelles that evolved from bacterial ancestors and harbor their own genomes. The gene products of these genomes work in concert with those of the nuclear genome to ensure proper organelle metabolism and biogenesis. Organelle genomes occur in a variety of sizes and topologies.

MAMMALIAN Human 16.5 circular
FUNGAL S. cerevisiae 74-85 circular
P. anserina linear
Candida rhagii linear
PARAMECIA - - linear
PLANT B. campestris 218 multiple circles
Z. mays 570 multiple circles
Muskmelon 2500 multiple circles
Most range 130-150 circles
Objectives of organelle genomics:

  • Describe the organization and coding content of modern-day organelle genomes
  • Reconcile any discrepancies between observed DNA structures and the physical maps
  • Describe how evolution has shaped and changed modern-day organelle genome coding content compared to ancestral prokaryotic genomes
  • Consider the possible reasons that plant organelles retain genomes at all
  • Explain the challenges and experimental opportunities associated with genetic transformation of the plastid genome
Salient features of organelle genomics:

  • Small but essential for functional advantages
  • Multiple organelles per cell, multiple genomes per organelle
    • 20 - 20,000 genomes per cell depending on cell type
  • Organized in nucleo-protein complexes called Nucleoids
  • Non-Mendelian inheritance pattern
    • Maternal inheritance is followed but not always
  • Necessary but not sufficient to elaborate a functional organelle
    • Nuclear gene products required for their function
    • Genes of these organelles are translated on cytosolic ribosomes
    • Then imported into the organelles
    • Plant mitochondria also import tRNAs
The plastid is a nearly autonomous organelle because it contains the biochemical machinery necessary to replicate and transcribe its own genome and carry out protein synthesis. Within angiosperms the plastid genome includes approximately 120 to 130 genes and usually ranges in size from 120 to 170 kilobases (kb) (Palmer, 1991; Roubeson and Jansen,2005). Of the estimated 3000 or so distinct proteins found in the higher plant plastid (Colas and Surek, 2004) only a small fraction are encoded by the plastid genome (Shimada and Sugiura, 1991). The bulk of the plastid proteome is nuclear encoded, translated on cytosolic ribosomes and subsequently translocated across the plastid envelopes (Zerges, 2000). The circular plastid genome is divided into four regions: large single copy (LSC), small single copy (SSC) and the inverted repeat (IR) which is present in exact duplicate separated by the two single copy regions.

The availability of the complete plastid genome sequence should facilitate improved transformation efficiency and foreign gene expression in crops through utilization of endogenous flanking sequences and regulatory elements (Ruhlman et al, 2006 ).

The advantages of plastid transformation for bioengineering are several-fold

  • Integration of multiple genes in a single transformation event (Lossl et al., 2003),
  • Lack of gene silencing (Dhingra et al., 2004),
  • Position effect due to site-specific transgene integration (Daniell et al., 2002)
  • Minimization of pleiotropic effects due to compartmentalization of recombinant proteins (Daniell et al., 2001)
Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders.

Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement (Brozynska et al., 2016). In addition to improving our understanding of plant biology and evolution, chloroplast genomics research has important translational applications, such as conferring protection against biotic or abiotic stress and the development of vaccines and biopharmaceuticals in edible crop plants (Daniell, 2016). Genome analysis results in discovery of useful alleles in and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.


1. Brozynska, M., Furtado, A. and Henry, R. J. 2016. Genomics of crop wild relatives: expanding the gene pool for crop improvement. Plant Biotechnol J, 14: 1070-1085. doi:10.1111/pbi.12454
2. Colas des Francs-Small C, Szurek B, Small I. 2004. Proteomics, bioinformatics and genomics applied to plant organelles. Molecular Biology and Biotechnology of Plant Organelles: Chloroplast and Mitochondria. Edited by: Daniell H, Chase C. Dordrecht, The Netherlands: Springer, 179
3. Daniell H, Khan MS, Allison L. 2002. Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology. Trends Plant Sci., 7: 84-10.1016/S1360-1385(01)02193-8.
4. Daniell H, Lee SB, Panchal T, Wiebe PO. 2001. Expression of the native cholera toxin B subunit gene and assembly as functional oligomers in transgenic tobacco chloroplasts. J Mol Biol. 311: 1001-1009. 10.1006/jmbi.2001.4921.
5. Daniell, H.; Lin, C.-S.; Yu, M. & Chang, W.-J. 2016. Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biology, 17: 134
6. Dhingra A, Portis AR, Daniell H. 2004. Enhanced translation of a chloroplast-expressed rbcS gene restores small subunit levels and photosynthesis in nuclear rbcS antisense plants. Proc Natl Acad Sci USA, 101: 6315-10.1073/pnas.0400981101.
7. Lossl A, Eibl C, Harloff HJ, Jung C, Koop HU 2003. Polyester synthesis in transplastomic tobacco (Nicotiana tabacum L.): significant contents of polyhydroxybutyrate are associated with growth reduction. Plant Cell Rep. 21: 891
8. Palmer JD. 1991: Plastid chromosomes: structure and evolution. The Molecular Biology of Plastids. Edited by: Bogorad L, Vasil K., San Diego: Academic Press, 5:53.
9. Raubeson LA, Jansen RK 2005. Chloroplast genomes of plants. Diversity and Evolution of Plants-Genotypic and Phenotypic Variation in Higher Plants. Edited by: Henry H Wallingford. CABI Publishing, 45-68.
10. Ruhlman, T.; Lee, S. B.; Jansen, R. K.; Hostetler, J. B.; Tallon, L. J.; Town, C. D. & Daniell, H. 2006. Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics, 7 .
11. Shimada H, Sugiura M. 1991. Fine structural features of the chloroplast genome: comparison of the sequenced chloroplast genomes. Nucl Acids Res. 19: 983
12. WHA . 2004. Genomics and World Health, Fifty Seventh World Health Assembly Resolution.
13. WHO. 2002. Genomics and World Health: Report of the Advisory Committee on Health research, Geneva.
14. Zerges W. 2000. Translation in chloroplasts. Biochimie. 82: 583-10.1016/S0300-9084(00)00603-9.

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Research Scholar at Genetics and Plant Breeding, BHU