Mechanisms of Functional and Physical Genome Reduction in Photosynthetic and Nonphotosynthetic Parasitic Plants of the Broomrape Family
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Cites background from "Mechanisms of Functional and Physic..."
...6-kb plastome of Conopholis americana (Orobanchaceae) is the smallest published plastid genome to date (Colwell 1994; Wicke et al. 2013)....
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...The 45.6-kb plastome of Conopholis americana (Orobanchaceae) is the smallest published plastid genome to date (Colwell 1994; Wicke et al. 2013)....
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...The evolution of the chloroplast genome in parasitic plants, particularly nonphotosynthetic holoparasites, can lead to significantly reconfigured plastomes (Wicke et al. 2013)....
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...The fates of other essential plastid genes, such as the clpP and ycf2 loci (Wicke et al. 2013), are unknown, and must await detailed genomic and biochemical studies on these parasitic plant species....
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...In these plants many photosystem and energy production genes are lost from the plastome (Krause 2008; Li et al. 2013; Wicke et al. 2013)....
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Cites background from "Mechanisms of Functional and Physic..."
...…Chang et al. 2006; Funk et al. 2007; McNeal et al. 2007; Braukmann et al. 2009; Blazier et al. 2011; Braukmann and Stefanovic 2012; Braukmann et al. 2013; Iles et al. 2013; Peredo et al. 2013; Wicke et al. 2013), including some of the leafy, photosynthetic orchid plastomes included in figure 3....
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...Chlorophyll has been detected in other strictly heterotrophic plants (Cummings and Welschmeyer 1998), including members of Orobanchaceae and the monotropoid Ericaceae....
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...3 and references therein, including discussion in Wicke et al. 2013)....
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...Examples of heterotrophic taxa for which plastome evolution has been studied include various Orobanchaceae (e.g., Epifagus, Wolfe et al. 1992; Conopholis, Wimpee et al. 1991; Hyobanche/Harveya, Wolfe and dePamphilis 1998; Randle and Wolfe 2005; family-wide representative genera, Wicke et al. 2013), Convolvulaceae (Cuscuta, Funk et al. 2007; McNeal et al. 2007; Braukmann et al. 2013), monotropoid Ericaceae (Braukmann and Stefanovic 2012; Broe M and Freudenstein J, personal communication), and monocots including Orchidaceae (Delannoy et al. 2011; Logacheva et al. 2011, 2014; Barrett and Davis 2012)....
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...Orobanchaceae range from 38.08% GC in the hemiparasitic Schwalbea to 31.09% in the holoparasitic Phelipanche purpurea....
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References
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"Mechanisms of Functional and Physic..." refers methods in this paper
...1 (Darling et al., 2010) using a seed weight of 21 and a custom gap open penalty of 2200 to account for (relatively) small gaps....
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...To circumvent this problem, we determined the maximum amount of locally colinear blocks among all sequenced Orobanchaceae genomes with progressive Mauve 2.3.1 (Darling et al., 2010) using a seed weight of 21 and a custom gap open penalty of 2200 to account for (relatively) small gaps....
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2,754 citations
"Mechanisms of Functional and Physic..." refers methods in this paper
...CAP3 contigs were preannotated using DOGMA, manually joined, and checked for incongruences with MIRA contigs....
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...Contigs were preannotated using DOGMA (Wyman et al., 2004) and then overlapped manually....
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...Annotation of finished plastid chromosome sequences was performed using DOGMAwith somemanual refinement....
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...Positive matches were extracted and postassembled gene by gene with high stringency in SeqMan I. Contigs were preannotated using DOGMA (Wyman et al., 2004) and then overlapped manually....
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2,184 citations
1,643 citations
"Mechanisms of Functional and Physic..." refers methods in this paper
...effect of branch lengths upon trait changes (Pagel, 1994); significance was again assessed by a LRT....
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...…versus punctuated) by constraining the BayesTraits-specific parameter kappa (k) to k = 0 to measure the effect of branch lengths upon trait changes (Pagel, 1994); significance was again assessed by a LRT. Correlation of traits was further tested by constraining the covariance to zero and then…...
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