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1. The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data

   https://doi.org/10.1038/s41598-019-54488-1  

   Thompson, Max C. ; Feng, Honglin ; Wuchty, Stefan ; Wilson, Alex C. C. ( December 2019 , Scientific Reports)

   Like all organisms, aphids, plant sap-sucking insects that house a bacterial endosymbiont calledBuchnera, are members of a species interaction network. Ecological interactions across such networks can result in phenotypic change in network members mediated by molecular signals, like microRNAs. Here, we interrogated small RNA data from the aphid,Myzus persicae, to determine the source of reads that did not map to the aphid orBuchneragenomes. Our analysis revealed that the pattern was largely explained by reads that mapped to the host plant,Brassica oleracea, and a facultative symbiont,Regiella. To start elucidating the function of plant small RNA in aphid gut, we annotated 213 uniqueB. oleraceamiRNAs; 32/213 were present in aphid gut as mature and star miRNAs. Next, we predicted targets in theB. oleraceaandM. persicaegenomes for these 32 plant miRNAs. We found that plant targets were enriched for genes associated with transcription, while the distribution of targets in the aphid genome was similar to the functional distribution of all genes in the aphid genome. We discuss the potential of plant miRNAs to regulate aphid gene expression and the mechanisms involved in processing, export and uptake of plant miRNAs by aphids.

    

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2. Temporal and spatial transcriptomic and micro RNA dynamics of CAM photosynthesis in pineapple

   https://doi.org/10.1111/tpj.13630  

   Wai, Ching M. ; VanBuren, Robert ; Zhang, Jisen ; Huang, Lixian ; Miao, Wenjing ; Edger, Patrick P. ; Yim, Won C. ; Priest, Henry D. ; Meyers, Blake C. ; Mockler, Todd ; et al ( August 2017 , The Plant Journal)

   The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in an up to 80% higher water‐use efficiency than C₃photosynthesis in plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA(miRNA) expression patterns in the obligateCAMplant pineapple [Ananas comosus(L.) Merr.]. The high‐resolution transcriptome atlas allowed us to distinguish betweenCAM‐related and non‐CAMgene copies. A differential gene co‐expression network across green and white leaf diel datasets identified genes with circadian oscillation,CAM‐related functions, and source‐sink relations. Gene co‐expression clusters containingCAMpathway genes are enriched with clock‐associatedcis‐elements, suggesting circadian regulation ofCAM. About 20% of pineapple microRNAs have diel expression patterns, with several that target keyCAM‐related genes. Expression and physiology data provide a model forCAM‐specific carbohydrate flux and long‐distance hexose transport. Together these resources provide a list of candidate genes for targeted engineering ofCAMinto C₃photosynthesis crop species.

    

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3. The Sarracenia alata pitcher plant system and obligate arthropod inquilines should be considered an evolutionary community

   https://doi.org/10.1111/jbi.13498  

   Satler, Jordan D. ; Carstens, Bryan C. ( January 2019 , Journal of Biogeography)

   TheSarracenia alatapitcher plant and inquiline species comprise an ecological community. These inquilines span the continuum in their ecological association with the host pitcher plant, from species that contain little‐to‐no interaction with the plant to species that are completely dependent on the plant for their entire life cycle. We are interested in testing if degree of ecological dependence is positively correlated with a shared evolutionary history, and in identifying members of this community that display concordant phylogeographic structure.

   Southeastern United States.

   We collected genome‐wide sequence data from a set of arthropods that are ecologically associated with the plant to estimate comparative phylogeographic patterns among the species. We estimated species tree distributions from biallelic unlinkedSNPdata and used phylogeographic concordance factors (PCFs) to test degree of phylogeographic concordance among community members. In addition, for each species we conducted an analysis of molecular variance and calculatedF_STvalues to identify population genetic structure across the landscape, and compared these traditional values to the tree‐based approach.

   Obligate members of the pitcher plant community display concordant phylogeographic patterns, suggesting their ecological dependence has manifested itself into a shared evolutionary history. In contrast, two spider species do not contain significant population genetic structure or similar phylogeographic histories, highlighting their loose association with the host pitcher plant.

   TheS. alatapitcher plant system should be considered an evolutionary community, where multiple members sharing strong ecological interactions also display concordant phylogeographic structure. This work demonstrates thatPCFs provide an important quantitative measure into assessing community structure and illustrates how simulations can be used to assess significance of shared patterns of phylogeographic structure across the landscape.

    

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4. Divergent expression of cytokinin biosynthesis, signaling and catabolism genes underlying differences in feeding sites induced by cyst and root‐knot nematodes

   https://doi.org/10.1111/tpj.13647  

   Dowd, Carola D. ; Chronis, Demosthenis ; Radakovic, Zoran S. ; Siddique, Shahid ; Schmülling, Thomas ; Werner, Tomáš ; Kakimoto, Tatsuo ; Grundler, Florian M. W. ; Mitchum, Melissa G. ( August 2017 , The Plant Journal)

   Cyst and root‐knot nematodes are obligate parasites of economic importance with a remarkable ability to reprogram root cells into unique metabolically active feeding sites. Previous studies have suggested a role for cytokinin in feeding site formation induced by these two types of nematodes, but the mechanistic details have not yet been described. Using Arabidopsis as a host plant species, we conducted a comparative analysis of cytokinin genes in response to the beet cyst nematode (BCN),Heterodera schachtii, and the root‐knot nematode (RKN),Meloidogyne incognita. We identified distinct differences in the expression of cytokinin biosynthesis, catabolism and signaling genes in response to infection byBCNandRKN, suggesting differential manipulation of the cytokinin pathway by these two nematode species. Furthermore, we evaluated Arabidopsis histidine kinase receptor mutant linesahk2/3,ahk2/4andahk3/4in response toRKNinfection. Similar to our previous studies withBCN, these lines were significantly less susceptible toRKNwithout compromising nematode penetration, suggesting a requirement of cytokinin signaling inRKNfeeding site formation. Moreover, an analysis ofahkdouble mutants usingCycB1;1:GUS/ahkintrogressed lines revealed contrasting differences in the cytokinin receptors mediating cell cycle activation in feeding sites induced byBCNandRKN.

    

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5. Effects of predation pressure and prey density on short‐term indirect interactions between two prey species that share a common predator

   https://doi.org/10.1111/een.12855  

   Emery, Sara E. ; Mills, Nicholas J. ( March 2020 , Ecological Entomology)

   1. Generalist predators are important contributors to reliable conservation biological control. Indirect interactions between prey species that share a common generalist predator can influence both community dynamics and the efficacy of biological control.

   2. Laboratory cage experiments investigated the impact of the combined consumptive and non‐consumptive effects of predation by adultHippodamia convergensas a shared predator on the population growth and relative abundance ofAcyrthosiphon pisumandAphis gossypiias prey species. Predation pressure and prey density were varied.

   3. At low predation pressure the indirect interaction between aphid species was asymmetrical with a proportionally greater negative impact of predation onA. gossypiithan onA. pisum. At intermediate predation pressure, the indirect interaction became symmetrical. At high predation pressure and higher levels of prey density, it was asymmetrical with greater negative impact onA. pisum, often driven to local extinction whileA. gossypiipopulations persisted.

   4. A linear mixed‐effects model including early population growth of both aphid species and predation pressure explained 96% and 92% of the variation in the population growth ofA. pisumandA. gossypii, respectively, over an 8‐day period. The overall effect of shared predation on the indirect interaction between the two aphid species is best described as apparent commensalism, whereA. pisumbenefited from early population growth ofA. gossypii, whileA. gossypiiwas unaffected by early population growth ofA. pisum. Considering these indirect interactions is important for conservation biological control efforts to be successful.

    

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