Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

Wicke, Susann; Müller, Kai; Pamphilis, Claude W. de; Quandt, Dietmar; Wickett, Norman J.; Zhang, Yan; Renner, Susanne S.; Schneeweiss, Gerald M.

doi:10.1105/tpc.113.113373

Cited by 273 publications

(425 citation statements)

References 84 publications

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“…The Hawaiian mint genome did not demonstrate any rearrangements or inversions, which have been found in Jasmin nudiflorum, Schwalbea americana, and a few other species (Welch et al, 2016) (Lee et al, 2007;Wicke et al, 2013). The lengths of the mint chloroplast genomes, including lengths of the inverted repeat and small single copy region, were similar to other species in this family, such as Origanum vulgare and Salvia miltiorrhiza (Lukas and Novak, 2013;Qian et al, 2013), with most of the differences in length being due to short indels within the long single copy region.…”

Section: Mint Chloroplast Genome Structure and Variabilitymentioning

confidence: 58%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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Section: Mint Chloroplast Genome Structure and Variabilitymentioning

confidence: 58%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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“…The overall A-T contents of two genomes are 62.0% which is similar with general angiosperms and other cp genomes of Lamiaceae and some genus of Orobanchaceae (Shinozaki et al 1986;Kim & Lee 2004;Yi & Kim 2012;Wicke et al 2013;Zhu et al 2014;Welch et al 2016). In both of two genomes, the A-T content in the non-coding (64.6%) is higher than in the coding (60.1%) regions.…”

mentioning

confidence: 53%

Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa

Kim

2016

Mitochondrial DNA Part B

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The nucleotide sequence of the two chloroplast (cp) genomes from Paulownia coreana and P. tomentosa are the first to be completed in genus Paulownia of family Paulowniaceae. The structure of two Paulownia cp genomes shows similar characteristic with general cp genome of angiosperms. The lengths of two cp genomes are 154,545 bp and 154,540 bp, respectively. The cp genomes are divided into LSC region (85,241 bp and 85,236 bp) and SSC region (17,736 bp and 17,736 bp) by two IR regions (25,784 bp and 25,784 bp). Both of two cp genomes contain 113 genes (79 protein coding genes, 30 tRNA genes and 4 rRNA genes), eight protein-coding genes, seven tRNA genes and four rRNA genes duplicated in the IR regions. Similar to the general cp genome of angiosperms, 18 of the genes in the two cp genomes have one or two introns. The overall A-T contents of two genomes are 62.0% which is similar with general angiosperms. The A-T content in the non-coding (64.6%) is higher than in the coding (60.1%) regions. Seventy-one and seventy simple sequence repeat (SSR) loci were identified in the P. coreana and P. tomentosa cp genomes, respectively. In phylogenetic analysis, genus Paulownia shows closed relationship with Lindenbergia philippensis of Orobanchaceae.

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“…Parasitic plants are an excellent system for studying genome evolution under altered selective constraints because of lifestyle changes such as the transition from an autotrophic to a parasitic way of life (5). These plants directly connect to their host plants through a specialized organ to steal water and nutrients.…”

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confidence: 99%

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

Wicke

Müller²,

dePamphilis

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Because novel environmental conditions alter the selection pressure on genes or entire subgenomes, adaptive and nonadaptive changes will leave a measurable signature in the genomes, shaping their molecular evolution. We present herein a model of the trajectory of plastid genome evolution under progressively relaxed functional constraints during the transition from autotrophy to a nonphotosynthetic parasitic lifestyle. We show that relaxed purifying selection in all plastid genes is linked to obligate parasitism, characterized by the parasite's dependence on a host to fulfill its life cycle, rather than the loss of photosynthesis. Evolutionary rates and selection pressure coevolve with macrostructural and microstructural changes, the extent of functional reduction, and the establishment of the obligate parasitic lifestyle. Inferred bursts of gene losses coincide with periods of relaxed selection, which are followed by phases of intensified selection and rate deceleration in the retained functional complexes. Our findings suggest that the transition to obligate parasitism relaxes functional constraints on plastid genes in a stepwise manner. During the functional reduction process, the elevation of evolutionary rates reaches several new rate equilibria, possibly relating to the modified protein turnover rates in heterotrophic plastids.parasitism | relaxed selection | evolutionary rates | plastid genomes | Orobanchaceae L ineages change over time as they adapt to new environments. Novel conditions determine the selection in genes or cellular genomes and shape their functional and structural evolution. A system well suited to study the evolution of genomic traits in the context of altered selective regimes that is also tractable technically (due to its small size and high copy number) is the plastid genome (plastome). The prime function of plastids is photosynthesis, but this essential plant organelle also produces starch, lipids, amino acids, sulfur compounds, and pigments. As a result of the strong selective pressure on plastid gene function, plastid genomes have a conserved gene content (1; but see ref.2) and their genes functioning in photosynthesis (atp, ndh, pet, psa, psb, ccsA, cemA, ycf3/4, rbcL), transcription, transcript maturation or translation (rpo, matK, rpl, rps, infA), and other pathways (accD, clpP, ycf1, and ycf2) evolve at lower evolutionary rates than nuclear genes (3). However, in eukaryotic lineages such as Apicomplexan pathogens and nongreen plants that independently made the transition from an autotrophic to a parasitic way of life, plastomes have experienced convergent reductions and accelerations of evolutionary rates (4). Although there is a general understanding of the association of the nonphotosynthetic lifestyle with plastome degradation and rate acceleration, the precise trajectory of plastome evolution under progressively reduced function along the way from being a full autotroph to an obligate nonphotosynthetic parasite remains unknown.Parasitic plants are an excellent system for stu...

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Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family

Cited by 273 publications

References 84 publications

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Two complete chloroplast genome sequences of genus Paulownia (Paulowniaceae): Paulownia coreana and P. tomentosa

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

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