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Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

• Authors : Greenham, Kathleen; Sartor, Ryan C; Zorich, Stevan ...

• Source: eLife ; volume 9 ; ISSN 2050-084X

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Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

• Authors : Greenham, Kathleen; Guadagno, Carmela Rosaria; Gehan, Malia A ...

• Source: eLife ; volume 6 ; ISSN 2050-084X

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Decision letter: Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

• Authors : Hardtke, Christian S

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Author response: Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns

• Authors : Greenham, Kathleen; Sartor, Ryan C; Zorich, Stevan

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Decision letter: Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

• Authors : Bohlmann, Joerg

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Author response: Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

• Authors : Greenham, Kathleen; Guadagno, Carmela Rosaria; Gehan, Malia A

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Figure 1. Experimental design for evaluation of early effects of mild drought treatment on Brassica rapa R500 plants and soil water potential during the experiment. ; (A) Schematic illustration of the experimental design with days of the experiment and collection/measurement times. Top: The time of the experiment in days after sowing (DAS) is plotted with the orange shade representing the days of mild drought treatment starting at the end of 15 DAS. Center: Purple shade (between 18 and 20 DAS) indicates the 2 days of continuous collection/measurements. The x-axis represents the 48 hr of the experiment in Zeitgeber Time (ZT0 = lights on in the growth chambers). The dotted yellow lines represent the ZT times for collection and measurements of both well-watered and droughted plants. Bottom: White and black bars represent the photoperiod in the growth chambers (14 hr/10 hr; Day/Night) for Days 3 and 4. (B) Soil water potential (Ψs) progression for well-watered (solid symbols) and mild droughted (open symbols) B. rapa R500 plants (n = at least 6) after the start of the drought treatment during the physiology (triangles) and RNA-seq (circles) time-course experiments.

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Figure 7—figure supplement 1. Sequence Alignment of FKF1/ZTL family members in plants. ; ZTL/FKF1/LKP2 homologs from dicots; (Arabidopsis thaliana (At), Brassica rapa (Bra), Glycine max (Gm), Cucumis sativus (Cs), Citrus clementine (Cc), Gossypium hirsutum (Gh), Avena sativa (As), monocots; Oryza sativa japonica (Os), Setaria italica (Si), Zea mays (Zm), Brachypodium distachyon (Bd), Liverwort; Marchantia polymorpha (Mp) and Spikemoss; Selaginella moellendorffii (Sm). ZTL and FKF1 cluster in reference to conserved CGF and QFF motifs. See Figure 7 for corresponding accession numbers. All ZTL proteins conserve G46 and V48 (blue). In FKF1 the position corresponding to G46 contain Ala (FKF1-like monocots) or Ser (FKF1-like dicots) (red); Phototropins contain an Asn at the equivalent position (green). * denote conserved residues through all proteins. All proteins conserve the canonical GXNCRFLQ motif (magenta) as well as residues leading into the E-F loop. The FKF1 species differ in the residues immediately following the LOV consensus sequence in the beginning of the E-F loop (ZTL: C87 and G89; FKF1: F87 and D89). Liverwort and spikemoss sequences diverge containing elements consistent with both ZTL and FKF1 (G46 and ZTL E-F loop but I48 for Mp; S46 and F87 but G89 for Sm), indicating an evolutionary transition. The QFF (blue) motif is more divergent. All ZTL/FKF1 contain a Phe at position 156 that occupies an alternative buried position compared to solvent exposed hydrophilic residues in other LOV proteins.

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Figure 7. Phylogenetic Analysis of FKF1/ZTL family members in plants. ; Residue identity at position 46 (Colored Bar) distinguishes ZTL-like, LKP2-like and FKF1-like proteins consistent with evolutionary diversification of signaling mechanisms. LKP2 is isolated to a clade containing Brassica rapa members that all contain a Q154L substitution. Al ZTL members contain G46 which is necessary to promote the alternative conformation of Q154. Spikemoss and liverwort FKF1’s are isolated indicating a possible intermediate function. Accession numbers for all sequences are shown after the protein name. The evolutionary history was inferred using the Minimum Evolution method (Rzhetsky and Nei, 1992). The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches (Felsenstein, 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method (Zuckerkandl and Pauling, 1965) and are in the units of the number of amino acid substitutions per site. The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm (Nei and Kumar, 2000) at a search level of 1. The Neighbor-joining algorithm (Saitou and Nei, 1987) was used to generate the initial tree. The analysis involved 28 amino acid sequences. All positions containing gaps and missing data were eliminated. There were a total of 535 positions in the final dataset. Evolutionary analyses were conducted in MEGA7 (68). (Figure 7—figure supplement 1).

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Figure 2. Permutations can be observed in various species with spiral phyllotaxis. ; A schema in the bottom right corner of each image indicates the rank and azimuthal directions of the lateral branches. The first number (in yellow, also displayed on the picture) indicates the approximate azimuthal angle as a multiple of the plant’s divergence angle (most of the times close to 137° or 99°). The second number (in red) corresponds to the rank of the branch on the main stem. (A) Brassica napus (Inflorescence) (B) Muscari comosum (Inflorescence) (C) Alliara petiolata (D) Aesculus hippocastanum (Inflorescence) (E) Hedera Helix (F) Cotinus Dummeri.

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