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
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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.
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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.
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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
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Journal ArticleDOI
Phylogeny and origins of holoparasitism in Orobanchaceae.
TL;DR: There is a single origin of parasitism, and from within the hemiparasites, holoparasitism has originated three times.
Journal ArticleDOI
Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana
TL;DR: Sizing and sequencing of cDNAs generated by reverse transcriptase-PCR for three genes, rps12, rpl2, and clpP, show that their transcripts are properly cis-and/or trans-spliced at the same five group II intron insertion sites used in photosynthetic plants.
Journal ArticleDOI
Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis.
Norman J. Wickett,Yan Zhang,S. Kellon Hansen,J. M. Roper,Jennifer V. Kuehl,Sheila A. Plock,Paul G. Wolf,Claude W. dePamphilis,Jeffrey L. Boore,Bernard Goffinet +9 more
TL;DR: A pattern of genome evolution congruent with functional gene losses in parasitic angiosperms is observed but it is suggested that A. mirabilis' plastid genome represents a genome in the early stages of decay following the relaxation of selection pressures.
Journal ArticleDOI
The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured
TL;DR: The convergence of plastid genome structure in Helicosporidium and the Apicomplexa raises the interesting possibility that there are common forces that shape plastids genomes, subsequent to the loss of photosynthesis in an organism.
Journal ArticleDOI
Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia Nidus-Avis
Maria D. Logacheva,Maria D. Logacheva,Mikhail I. Schelkunov,Mikhail I. Schelkunov,Aleksey A. Penin,Aleksey A. Penin +5 more
TL;DR: The complete sequence of a plastid genome of nonphotosynthetic mycoheterotrophic orchid Neottia nidus-avis is determined using 454 pyrosequencing technology and was found to be reduced in both genome size and gene content; this reduction is however not as drastic as in the other nonphotosynthesis orchid, R. gardneri.