Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family
Susann Wicke,Kai F. Müller,Claude W. de Pamphilis,Dietmar Quandt,Norman J. Wickett,Yan Zhang,Susanne S. Renner,Gerald M. Schneeweiss +7 more
TLDR
The authors report the complete plastomes of 10 photosynthetic and nonphotosynthetic parasites plus their nonparasitic sister from the broomrape family (Orobanchaceae), finding that the establishment of obligate parasitism triggers the relaxation of selective constraints.Abstract:
Nonphotosynthetic plants possess strongly reconfigured plastomes attributable to convergent losses of photosynthesis and housekeeping genes, making them excellent systems for studying genome evolution under relaxed selective pressures. We report the complete plastomes of 10 photosynthetic and nonphotosynthetic parasites plus their nonparasitic sister from the broomrape family (Orobanchaceae). By reconstructing the history of gene losses and genome reconfigurations, we find that the establishment of obligate parasitism triggers the relaxation of selective constraints. Partly because of independent losses of one inverted repeat region, Orobanchaceae plastomes vary 3.5-fold in size, with 45 kb in American squawroot (Conopholis americana) representing the smallest plastome reported from land plants. Of the 42 to 74 retained unique genes, only 16 protein genes, 15 tRNAs, and four rRNAs are commonly found. Several holoparasites retain ATP synthase genes with intact open reading frames, suggesting a prolonged function in these plants. The loss of photosynthesis alters the chromosomal architecture in that recombinogenic factors accumulate, fostering large-scale chromosomal rearrangements as functional reduction proceeds. The retention of DNA fragments is strongly influenced by both their proximity to genes under selection and the co-occurrence with those in operons, indicating complex constraints beyond gene function that determine the evolutionary survival time of plastid regions in nonphotosynthetic plants.read more
Citations
More filters
Journal ArticleDOI
Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.
TL;DR: The mitochondrial genome of an aerobic parasitic plant, the mistletoe Viscum scurruloideum, is presented, which is miniaturized, shows clear signs of rapid and degenerative evolution, and lacks all genes for complex I of the respiratory electron-transfer chain.
Journal ArticleDOI
Possible Loss of the Chloroplast Genome in the Parasitic Flowering Plant Rafflesia lagascae (Rafflesiaceae)
Jeanmaire Molina,Khaled M. Hazzouri,Daniel L. Nickrent,Matt Geisler,Rachel S. Meyer,Melissa M. Pentony,Jonathan M. Flowers,Jonathan M. Flowers,Pieter B. Pelser,Julie F. Barcelona,Samuel Alan Inovejas,Iris Diana Uy,Wei Yuan,Olivia Wilkins,Claire Iphanise Michel,Selina Locklear,Gisela P. Concepcion,Michael D. Purugganan,Michael D. Purugganan +18 more
TL;DR: The inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastids genome, or if present is found in cryptic form at very low levels.
Journal ArticleDOI
Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots.
Craig F. Barrett,Craig F. Barrett,William J. Baker,Jason R. Comer,John G. Conran,Sean Lahmeyer,Jim Leebens-Mack,Jeff Li,Gwynne S. Lim,Dustin Mayfield-Jones,Dustin Mayfield-Jones,Leticia Perez,Jesus C. Medina,J. Chris Pires,Cristian Santos,Dennis W. Stevenson,Wendy B. Zomlefer,Jerrold I. Davis +17 more
TL;DR: This study represents the most comprehensively sampled matrix of plastomes assembled for monocot angiosperms, providing genome-scale support for phylogenetic relationships of monocots, and lays the phylogenetic groundwork for comparative analyses of the drivers and correlates of such drastic differences in substitution rates across a diverse and significant clade.
Book ChapterDOI
The plastid genomes of flowering plants.
TL;DR: This chapter presents an overview of some of the seminal and contemporary research that has contributed to the current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and tools ofplastid genetic engineering.
Journal ArticleDOI
Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms
Craig F. Barrett,John V. Freudenstein,Jeff Li,Dustin Mayfield-Jones,Leticia Perez,J. Chris Pires,Cristian Santos +6 more
TL;DR: Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastsome evolution in heterotrophic angiosperms.
References
More filters
Journal ArticleDOI
Piecing together the puzzle of parasitic plant plastome evolution.
TL;DR: The collective loss of larger sets of functionally related genes like those for the plastid NADH–dehydrogenase complex and concomitant losses of RNA polymerase genes together with their target promoters point to “domino effects” where an initial loss might have triggered others.
Journal ArticleDOI
Nucleus-Encoded Genes for Plastid-Targeted Proteins in Helicosporidium: Functional Diversity of a Cryptic Plastid in a Parasitic Alga
TL;DR: Overall, the metabolic diversity of the Helicosporidium cryptic plastid exceeds that of the Plasmodium plastids, as it includes representatives of most of the pathways known to operate in theplastid as well as many others.
Journal ArticleDOI
Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants.
TL;DR: A line of transplastomic tobacco was identified containing an antibiotic resistance gene unlinked from the intended transgene insertion as a result of an unintended recombination event, indicating that the homologous recombination events described here may hinder efficient recovery of plastid transformants containing the desired transgenes.
Journal ArticleDOI
Extensive homologous chloroplast DNA recombination in the pt14 Nicotiana somatic hybrid
E. Fejes,D. Engler,Pal Maliga +2 more
TL;DR: Physical mapping revealed six recombination sites in the 11.4-kb SalI fragment alone, only one of which has been previously identified, which is located in the large unique region.
Journal ArticleDOI
The rbcL genes of two Cuscuta species, C. gronovii and C. subinclusa, are transcribed by the nuclear-encoded plastid RNA polymerase (NEP).
TL;DR: It is shown that despite high sequence conservation of the coding region of rbcL among different Cuscuta species and tobacco, the 5′ non-coding regions of C. gronovii and C. subinclusa have suffered extensive deletions encompassing the PEP promoter that is present in C. reflexa.