Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012;7(12):e51687.
doi: 10.1371/journal.pone.0051687. Epub 2012 Dec 14.

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia Pinnata

Affiliations
Free PMC article

Capturing the Biofuel Wellhead and Powerhouse: The Chloroplast and Mitochondrial Genomes of the Leguminous Feedstock Tree Pongamia Pinnata

Stephen H Kazakoff et al. PLoS One. .
Free PMC article

Abstract

Pongamia pinnata (syn. Millettia pinnata) is a novel, fast-growing arboreal legume that bears prolific quantities of oil-rich seeds suitable for the production of biodiesel and aviation biofuel. Here, we have used Illumina® 'Second Generation DNA Sequencing (2GS)' and a new short-read de novo assembler, SaSSY, to assemble and annotate the Pongamia chloroplast (152,968 bp; cpDNA) and mitochondrial (425,718 bp; mtDNA) genomes. We also show that SaSSY can be used to accurately assemble 2GS data, by re-assembling the Lotus japonicus cpDNA and in the process assemble its mtDNA (380,861 bp). The Pongamia cpDNA contains 77 unique protein-coding genes and is almost 60% gene-dense. It contains a 50 kb inversion common to other legumes, as well as a novel 6.5 kb inversion that is responsible for the non-disruptive, re-orientation of five protein-coding genes. Additionally, two copies of an inverted repeat firmly place the species outside the subclade of the Fabaceae lacking the inverted repeat. The Pongamia and L. japonicus mtDNA contain just 33 and 31 unique protein-coding genes, respectively, and like other angiosperm mtDNA, have expanded intergenic and multiple repeat regions. Through comparative analysis with Vigna radiata we measured the average synonymous and non-synonymous divergence of all three legume mitochondrial (1.59% and 2.40%, respectively) and chloroplast (8.37% and 8.99%, respectively) protein-coding genes. Finally, we explored the relatedness of Pongamia within the Fabaceae and showed the utility of the organellar genome sequences by mapping transcriptomic data to identify up- and down-regulated stress-responsive gene candidates and confirm in silico predicted RNA editing sites.

Conflict of interest statement

Competing Interests: This reasearch was funded in part by BioEnergy Plantation Australia and BES Pty Ltd. BioEnergy Plantation Australia is developing critical technology platforms for the genetic, genomic and biotechnology application to the legume tree Pongamia pinnata. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Map of the Pongamia cpDNA (152,968 bp).
The innermost circle indicates the locations of the IRs (IRA and IRB, 25,528 bp), which separate the LSC (83,401 bp) and SSC (18,511 bp) regions. Genes on the outermost of the map are transcribed in a counter-clockwise direction and those on the inside clockwise. The graphs plotted between these circles represent the percentage synonymous (blue) and non-synonymous (red) divergence of each protein-coding gene, between Pongamia and V. radiata, and, Pongamia and L. japonicus. The red arrow indicates the position of the replication origin, oriC. Genes marked with a red asterisk are genes in the Pongamia unique inversion event (the bounds of this region have been marked out in red). Genes underlined in red are pseudogenes.
Figure 2
Figure 2. Mauve alignment of the Pongamia cpDNA LSC to representatives of the flowering plants (Arabidopsis thaliana) and Fabaceae (G. max) showing a 50 kb inversion that is a unique event in the evolution of the Fabaceae (green and gold blocks) as well as a 6.5 kb inversion that is unique to the Pongamia cpDNA (gold and blue blocks).
Plots of similarity can be found inside of each element.
Figure 3
Figure 3. Map of the Pongamia mtDNA (425,718 bp).
The innermost circle indicates the locations of two sets of inverted repeats (IR1A and IR1B, 6,229 bp; IR2A and IR2B, 2,274 bp) and two sets of direct repeats (DR1A and DR1B, 13,319 bp; DR2A and DR2B, 3,919 bp). Furthermore, IR1B and DR2A share an overlap of 669 bp. Genes on the outside of the map are transcribed in a counter-clockwise direction and those on the inside clockwise. The graphs plotted between these circles represent the percentage synonymous (blue) and non-synonymous (red) divergence of each protein-coding gene, between Pongamia and V. radiata, and, Pongamia and L. japonicus. Genes underlined in red are pseudogenes.
Figure 4
Figure 4. Map of the L. japonicus mtDNA (380,861 bp).
The innermost circle indicates the locations of a set of inverted repeats (IRA and IRB, 4,460 bp) and a set of direct repeats (DRA and DRB, 18,971 bp). Genes on the outermost of the map are transcribed in a counter-clockwise direction and those on the inside clockwise. The graphs plotted between these circles represent the percentage synonymous (blue) and non-synonymous (red) divergence of each protein-coding gene, between L. japonicus and V. radiata, and, L. japonicus and Pongamia. Genes underlined in red are pseudogenes.

Similar articles

See all similar articles

Cited by 29 articles

See all "Cited by" articles

References

    1. Murphy HT, O’Connell DA, Seaton G, Raison RJ, Rodriguez LC, et al. .. (2012) A common view of the opportunities, challenges, and research actions for Pongamia in Australia. BioEnergy Research. doi:10.1007/s12155-012-9190-6.
    1. Scott PT, Pregelj L, Chen N, Hadler JS, Djordjevic MA, et al. .. (2008) Pongamia pinnata: an untapped resource for the biofuels industry of the future. BioEnergy Res. doi:10.1007/s12155-008-9003-0.
    1. Biswas B, Scott PT, Gresshoff PM (2011) Tree legumes as feedstock for sustainable biofuel production: Opportunities and challenges. J. Plant Physiol. doi:10.1016/j.jclepro.2009.04.004. - PubMed
    1. Mike Imelfort website. Available: http://www.sassy.mikeimelfort.com. Accessed 2012 Nov 12.
    1. Bally J, Job C, Belghazi M, Job D (2011) Metabolic adaptation in transplastomic plants massively accumulating recombinant proteins. PLoS ONE. doi:10.1371/journal.pone.0025289. - PMC - PubMed

Publication types

Grant support

The authors thank BioEnergy Plantation Australia for research support in Pongamia, BES Pty Ltd. for university liaison. Research was also funded by an Australian Research Council Centre of Excellence grant to PMG. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

LinkOut - more resources

Feedback