ArticlePloS one2012
Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 79 citations in OpenAlex.
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- Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection.bioRxiv : the preprint server for biology · 2026Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- Mitogenome ofInternational journal of molecular sciences · 2025Article
- The complete mitochondrial genome and phylogenetic analysis ofFrontiers in plant science · 2025Article
- The complete plastid genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Comparative Analysis ofBiology · 2023Article
- Analysis of the Chloroplast Genome ofCurrent issues in molecular biology · 2023Article
- The complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2023Article
- Comparative analysis of the complete mitogenome ofFrontiers in genetics · 2023Article
- Comparative analysis of mitochondrial genomes of two alpine medicinal plants of Gentiana (Gentianaceae).PloS one · 2023Article
- A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms.International journal of molecular sciences · 2022Article
- Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis ofFrontiers in plant science · 2022Article
- The Multipartite Mitochondrial Genome of Marama (Frontiers in plant science · 2021Article
- Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species.PloS one · 2021Article
- Unraveling the Chloroplast Genomes of TwoInternational journal of molecular sciences · 2020Article
- Comparative Mitogenome Analysis of the GenusInternational journal of molecular sciences · 2020Article
- Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of TwoBioMed research international · 2020Article
- The Role of Transposable Elements in Pongamia Unigenes and Protein Diversity.Molecular biotechnology · 2020Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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