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1. H v 1 Proton Channels in Dinoflagellates: Not Just for Bioluminescence?

   https://doi.org/10.1111/jeu.12627  

   Kigundu, Gabriel ; Cooper, Jennifer L. ; Smith, Susan M. E. ( May 2018 , Journal of Eukaryotic Microbiology)

   Bioluminescence in dinoflagellates is controlled byH_V1 proton channels. Database searches of dinoflagellate transcriptomes and genomes yielded hits with sequence features diagnostic of all confirmedH_V1, and show thatH_V1 is widely distributed in the dinoflagellate phylogeny including the basal speciesOxyrrhis marina. Multiple sequence alignments followed by phylogenetic analysis revealed three major subfamilies ofH_V1 that do not correlate with presence of theca, autotrophy, geographic location, or bioluminescence. These data suggest that most dinoflagellates express aH_V1 which has a function separate from bioluminescence. Sequence evidence also suggests that dinoflagellates can contain more than oneH_V1 gene.

    

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2. Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation

   https://doi.org/10.1111/mec.14348  

   Calla, Bernarda ; Noble, Katherine ; Johnson, Reed M. ; Walden, Kimberly K. O. ; Schuler, Mary A. ; Robertson, Hugh M. ; Berenbaum, May R. ( October 2017 , Molecular Ecology)

   Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely.CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by co‐evolution between herbivores and their chemically defended hostplants. Alternatively, variation inCYPome size may be due to random “birth‐and‐death” processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examinedCYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella).CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, familiesCYP6,CYP9 andCYP321 are most diverse andCYP6AB,CYP6AE,CYP6B,CYP9A andCYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization (“P450 blooms”), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm,Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defences, consistent with an adaptive, nonrandom process driven by ecological interactions.

    

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3. High‐efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR /Cas9

   https://doi.org/10.1111/tpj.13446  

   Gil‐Humanes, Javier ; Wang, Yanpeng ; Liang, Zhen ; Shan, Qiwei ; Ozuna, Carmen V. ; Sánchez‐León, Susana ; Baltes, Nicholas J. ; Starker, Colby ; Barro, Francisco ; Gao, Caixia ; et al ( February 2017 , The Plant Journal)

   The ability to edit plant genomes through gene targeting (GT) requires efficient methods to deliver both sequence‐specific nucleases (SSNs) and repair templates to plant cells. This is typically achieved usingAgrobacteriumT‐DNA, biolistics or by stably integrating nuclease‐encoding cassettes and repair templates into the plant genome. In dicotyledonous plants, such asNicotinana tabacum(tobacco) andSolanum lycopersicum(tomato), greater than 10‐fold enhancements inGTfrequencies have been achieved usingDNAvirus‐based replicons. These replicons transiently amplify to high copy numbers in plant cells to deliver abundantSSNs and repair templates to achieve targeted gene modification. In the present work, we developed a replicon‐based system for genome engineering of cereal crops using a deconstructed version of the wheat dwarf virus (WDV). In wheat cells, the replicons achieve a 110‐fold increase in expression of a reporter gene relative to non‐replicating controls. Furthermore, replicons carryingCRISPR/Cas9 nucleases and repair templates achievedGTat an endogenousubiquitinlocus at frequencies 12‐fold greater than non‐viral delivery methods. The use of a strong promoter to express Cas9 was critical to attain these highGTfrequencies. We also demonstrate gene‐targeted integration by homologous recombination (HR) in all three of the homoeoalleles (A, B and D) of the hexaploid wheat genome, and we show that with theWDVreplicons, multiplexedGTwithin the same wheat cell can be achieved at frequencies of ~1%. In conclusion, high frequencies ofGTusingWDV‐basedDNAreplicons will make it possible to edit complex cereal genomes without the need to integrateGTreagents into the genome.

    

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4. Transcriptome and phenotyping analyses support a role for chloroplast sigma factor 2 in red‐light‐dependent regulation of growth, stress, and photosynthesis

   https://doi.org/10.1002/pld3.43  

   Oh, Sookyung ; Strand, Deserah D. ; Kramer, David M. ; Chen, Jin ; Montgomery, Beronda L. ( February 2018 , Plant Direct)

   Sigma factor (SIG) proteins contribute to promoter specificity of the plastid‐encodedRNApolymerase during chloroplast genome transcription. All six members of theSIGfamily, that is,SIG1–SIG6, are nuclear‐encoded proteins targeted to chloroplasts. Sigma factor 2 (SIG2) is a phytochrome‐regulated protein important for stoichiometric control of the expression of plastid‐ and nuclear‐encoded genes that impact plastid development and plant growth and development. AmongSIGfactors,SIG2 is required not only for transcription of chloroplast genes (i.e., anterograde signaling), but also impacts nuclear‐encoded, photosynthesis‐related, and light signaling‐related genes (i.e., retrograde signaling) in response to plastid functional status. AlthoughSIG2 is involved in photomorphogenesis in Arabidopsis, the molecular bases for its role in light signaling that impacts photomorphogenesis and aspects of photosynthesis have only recently begun to be investigated. Previously, we reported thatSIG2 is necessary for phytochrome‐mediated photomorphogenesis specifically under red (R) and far‐red light, thereby suggesting a link between phytochromes and nuclear‐encodedSIG2 in light signaling. To explore transcriptional roles ofSIG2 in R‐dependent growth and development, we performedRNAsequencing analysis to compare gene expression insig2‐2mutant and Col‐0 wild‐type seedlings at two developmental stages (1‐ and 7‐day). We identified a subset of misregulated genes involved in growth, hormonal cross talk, stress responses, and photosynthesis. To investigate the functional relevance of these gene expression analyses, we performed several comparative phenotyping tests. In these analyses, strongsig2mutants showed insensitivity to bioactiveGA₃, high intracellular levels of hydrogen peroxide (H₂O₂) indicative of a stress response, and specific defects in photosynthesis, including elevated levels of cyclic electron flow (CEF) and nonphotochemical quenching (NPQ). We demonstrated thatSIG2 regulates a broader range of physiological responses at the molecular level than previously reported, with specific roles in red‐light‐mediated photomorphogenesis.

    

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5. Rolling‐circle amplification of centromeric Helitrons in plant genomes

   https://doi.org/10.1111/tpj.13314  

   Xiong, Wenwei ; Dooner, Hugo K. ; Du, Chunguang ( October 2016 , The Plant Journal)

   The unusual eukaryoticHelitrontransposons can readily capture host sequences and are, thus, evolutionarily important. They are presumed to amplify by rolling‐circle replication (RCR) because some elements encode predicted proteins homologous toRCRprokaryotic transposases. In support of this replication mechanism, it was recently shown that transposition of a batHelitrongenerates covalently closed circular intermediates. Another strong prediction is thatRCRshould generate tandemHelitronconcatemers, yet almost allHelitronsidentified to date occur as solo elements in the genome. To investigate alternative modes ofHelitronorganization in present‐day genomes, we have applied the novel computational tool HelitronScanner to 27 plant genomes and have uncovered numerous tandem arrays of partially decayed, truncatedHelitronsin all of them. Strikingly, most of theseHelitrontandem arrays are interspersed with other repeats in centromeres. Many of these arrays have multipleHelitron5′ ends, but a single 3′ end. The number of repeats in any one array can range from a handful to several hundreds. We propose here anRCRmodel that conforms to the presentHelitronlandscape of plant genomes. Our study provides strong evidence that plantHelitronsamplify byRCRand that the tandemly arrayed replication products accumulate mostly in centromeres.

    

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