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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Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer
Dale Zhang,Dale Zhang,Jinfeng Qi,Jipei Yue,Jipei Yue,Jinling Huang,Jinling Huang,Ting Sun,Suoping Li,Jian-Fan Wen,Christian Hettenhausen,Jinsong Wu,Lei Wang,Huifu Zhuang,Jianqiang Wu,Guiling Sun +15 more
TL;DR: This study strongly supports that parasitic plants can gain novel nuclear genes from distantly related host species by HGT and the foreign genes may execute certain functions in the new hosts.
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AliTV—interactive visualization of whole genome comparisons
TL;DR: The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures.
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Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication
TL;DR: The size of mimosoid plastomes was found significantly affected by a IR-SC boundary shift, and also associated with repeat content, while linear regression analysis showed decreased synonymous substitution rates of genes relocating from SSC into IR.
Journal ArticleDOI
Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants
TL;DR: In this article, the chloroplast genomes of three zygnematophycean chloroplasts of the freshwater charophytes Klebsormidium flaccidum, Mesotaenium endlicherianum, and Roya anglica were reconstructed.
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The Highly Reduced Plastome of Mycoheterotrophic Sciaphila (Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection.
TL;DR: This study confirms the utility of whole plastid genome data in phylogenetic studies of highly modified heterotrophic plants, even when they have substantially elevated rates of substitution.
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