ArticleMolecular biology and evolution2014
Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed, 310 citations in OpenAlex.
- Deciphering the genetic basis of nodule number through integrative analysis of host genotype and endophytes.Journal of advanced research · 2026Article
- Vestigial Plastids in Parasitic Plants: Evolutionary Remnants or Adaptive Innovations?Plant, cell & environment · 2026Review
- The Effects of Rapid Mitochondrial Gene Loss on Organellar Proteomes.Genome biology and evolution · 2026Article
- Progress and prospects of parasitic plant biodiversity genomics.Plant & cell physiology · 2026Review
- Evolutionary mobility and genetic dynamics of MORFFO genes: shuttling among ancient plant lineages.The New phytologist · 2026Article
- Reshaping organellar translation and tRNA metabolism: the consequences of photosynthesis loss and massive horizontal gene transfer.Molecular biology and evolution · 2026Article
- Mycoheterotrophy and plastid genome evolution in the early-diverging epidendroid orchid tribe Nervilieae: independent transitions inAoB PLANTS · 2026Article
- Recombination and Retroprocessing in Broomrapes Reveal RNA-Mediated Gene Transfer Mechanism and a Generalizable Model for Mitochondrial Evolution in Heterotrophic Plants.Genome biology and evolution · 2026Article
- Gene loss and positively selected genes in chloroplast genomes reveal adaptive evolution in Styracaceae.BMC plant biology · 2026Article
- A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes.BMC biology · 2025Article
- Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms.The New phytologist · 2025Review
- Genome analysis of dark-adapted variants identifies the phosphatase gene phsP involved in the regulation of photosynthetic and dark-heterotrophic growth in the cyanobacterium Leptolyngbya boryana.Plant & cell physiology · 2025Article
- A composite universal DNA signature for the tree of life.Nature ecology & evolution · 2025Article
- Chloroplast Functionality at the Interface of Growth, Defense, and Genetic Innovation: A Multi-Omics and Technological Perspective.Plants (Basel, Switzerland) · 2025Review
- The evolution of the plastid genomes in the holoparasitic Balanophoraceae.Proceedings. Biological sciences · 2025Article
- Elucidating the evolutionary dynamics of parasitism in Cuscuta: in-depth phylogenetic reconstruction and extensive plastomes reduction.BMC genomics · 2025Article
- Article
- Organellar phylogenomics at the epidendroid orchid base, with a focus on the mycoheterotrophic Wullschlaegelia.Annals of botany · 2024Article
- Photosynthetic demands on translational machinery drive retention of redundant tRNA metabolism in plant organelles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Reduced plastid genomes of colorless facultative pathogens Prototheca (Chlorophyta) are retained for membrane transport genes.BMC biology · 2024Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 8 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches--despite success in identifying and developing a draft assembly of the much larger mitochondrial genome--suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.