title: Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata.
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.
authors.affiliation: Australian Research Council Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane, Queensland, Australia.
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Kazakoff
authors.forename: Michael
authors.initials: M
authors.lastname: Imelfort
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.forename: Jasper
authors.initials: J
authors.lastname: Koehorst
authors.forename: Bandana
authors.initials: B
authors.lastname: Biswas
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.forename: Paul T
authors.initials: PT
authors.lastname: Scott
authors.forename: Peter M
authors.initials: PM
authors.lastname: Gresshoff
mesh_terms: D003062:Codon; D007887:Fabaceae / Q000235:genetics / Q000378:metabolism; D023061:Gene Order; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D033641:Millettia / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016366:Open Reading Frames; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D017393:RNA Editing; D018749:RNA, Plant
chemical_list: D003062:Codon; D018749:RNA, Plant