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Engineering bacteriocin-mediated resistance against plant pathogenic bacteria in plants

Pseudomonas syringae (Ps) and related plant pathogenic bacteria are responsible for losses in diverse crops such as tomato, kiwifruit, pepper, olive and soybean. Current solutions, involving the use of chemicals and the introduction of resistance genes, have enjoyed only limited success and may have adverse environmental impacts. Consequently, there is a pressing need to develop alternative technologies to address the problem of bacterial disease in crops. An alternative strategy is to utilise the narrow spectrum protein antibiotics (bacteriocins) used by diverse bacteria for competition against closely related species. Here, we demonstrate that active putidacin L1 (PL1) can be expressed at high levels in planta and expression of PL1 provides effective resistance against diverse pathovars of Ps. Furthermore, we found that strains which evolve to become insensitive to PL1; lose their O-antigen, exhibit reduced motility and are less virulent in PL1 transgenic plants. Our results provide proof-of-principle that transgene-mediated expression of a bacteriocin in planta is an effective strategy for providing disease resistance against bacterial pathogens. Genetically modified (GM) crops expressing insecticidal proteins have proved extremely successful as a strategy for pest management; expressing bacteriocins to control bacterial disease may have a similar potential. Crucially, nearly all genera of bacteria, including many plant pathogenic species, produce bacteriocins, providing an extensive source of these antimicrobial agents.\n\nSIGNIFICANCEWith the global population to surpass 9 billion by 2050 there is a huge demand to make industrial farming as efficient as possible. A disadvantage of industrial farming is the lack of genetic diversity within crop monocultures, which make them highly susceptible to diseases caused by plant pathogenic bacteria like Pseudomonas syringae. Bacteriocins are narrow spectrum protein antibiotics which are produced by all major bacterial lineages. Their main purpose is to eliminate competitor strains to establish dominance within a niche. By arming plants with bacteriocins we can increase the genetic toolbox used to engineer crops to be resistant to specific bacterial plant pathogens.

plant biology

Cyanogenic glucoside production in cassava: The comparable influences of varieties, soil moisture content and nutrient supply

Varieties and soil moisture content are the two agronomic factors mostly pointed out as influencers of cyanogenic glucoside production in cassava. The role of soil nutrient supply is however often overlooked or minimised, despite its known influence on cyanogenic glucoside production. A pot experiment was hence carried out to determine whether soil nutrient supply had an equal influence on cyanogenic glucoside production in cassava, as varieties and soil moisture content. The cassava varieties, Kiroba (a sweet cassava variety) and Salanga (a bitter cassava variety), were used in the experiment, together with three soil moisture treatments that respectively induced severe moisture stress, moderate moisture stress and no moisture stress (optimal soil moisture conditions where plants were kept well-watered). The soil nutrient treatments used depicted conditions of low (no fertiliser), moderate (25 N mg, 5 P mg, 25 K mg /kg) and high (25 N mg, 5 P mg, 25 K mg /kg) nutrient supply. A sole K treatment was also included (25 K mg/kg). Total hydrogen cyanide (HCN) levels in cassava leaves were used to indicate the effects of the three factors on cyanogenic glucoside production. The results of the study showed that nutrient supply had a significantly (p < 0.001) equal influence on cyanogenic glucoside production, as varieties (p < 0.001) and soil moisture content (p < 0.001). Cyanogenic glucoside production was however found to be differently influenced by soil moisture content (M) and nutrient supply (N) in both Salanga (MxN, p = 0.002) and Kiroba (MxN, p < 0.001). Leaf HCN levels of unfertilised Salanga and Kiroba were respectively increased by 1.8 times and 2.7 times their levels under optimal soil moisture conditions. Thus, under severe moisture stress, low soil fertility was found to have an increasing effect on leaf HCN levels in both varieties. A high supply of N, P and K, however also had an increasing effect on leaf HCN in both varieties regardless of soil moisture conditions. Leaf HCN levels in Salanga ranged from 95.5 mg/kg to 334.5 mg/kg and in Kiroba they ranged from 39.3 mg/kg to 161.5 mg/kg, on a fresh weight basis. The study managed to demonstrate that soil fertility had an equally important influence on cyanogenic glucoside production, just like varieties and soil moisture content. The study also showed that the effects of nutrient supply on cyanogenic glucoside production in various cassava varieties is dependent on changes in soil moisture content and vice versa.

plant biology

Pyrenophora teres and Rhynchosporium secalis infections in malt barley as influenced by genotype, spatial and temporal effects and nitrogen fertilization

Net form net blotch (NFNB) and barley leaf scald are among the most important barley diseases worldwide and particularly in Greece. Their occurrence in malt barley can exert a significant negative effect on malt barley grain yield and quality. An experimental trial across two growing seasons was implemented in Greece in order i) to assess the epidemiology of NFNB and leaf scald in a barley disease free area when the initial inoculation of field occurs through infected seeds, and ii) to further explore the relationship among nitrogen rate, grain yield, quality variables (i.e. grain protein content and grain size) and disease severity and epidemiology. It was demonstrated that both NFNB and leaf scald can be carried over from one season to the next on infected seed under Mediterranean conditions. However, disease severity was more pronounced after barley tillering phase when soil had been successfully inoculated first. When nitrogen rate and genotype were the main sources of variation the epidemiology assessment was implemented with hotspot and Anselin Local Morans I analysis. It was found that the location of hotspots was modified during growing season. Soil and plant variables were assessed for the explanation of this variability. According to commonality analysis the effect of distance from the locations with the highest disease infections was a better predictor of disease severity (for both diseases) compared to nitrogen rate during pre-anthesis period. However, disease severity after anthesis was best explained by nitrogen rate only for the most susceptible cultivars to NFNB. The effect of disease infections on yield, grain size and grain protein content varied in relation to genotype, pathogen and stage of crop development. The importance of crop residues on the evolution of both diseases was also highlighted.

plant biology

Molecular Cloning and Functional Analysis of the UV-B Photoreceptor Gene ZmUVR8 (UVR8 Response locus), from Zea Mays.

Low UV-B fluence is a signaling stimulus that regulates various physiological processes and induces photomorphogenic responses in plants. The specific UV-B receptor UVR8 is a key component in these processes. Although UVR8 sequence is conserved, few homologs have been cloned and reported to be functional. Here we show the cloning and functional analysis of Zea mays UVR8 (ZmUVR8). ZmUVR8 presents 73% of identity with AtUVR8, maintaining the key tryptophan responsible of UV-B perception. ZmUVR8 also contains the VP domain, involved in the interaction with the proteins CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and REPRESSOR OF UV-B PHOTOMOPHOGENESIS 1 (RUP1). Whereas UVR8 was expressed in non-irradiated Arabidopsis and maize leaves, after 2h of UV-B irradiation, its expression was reduced. The expression of chalcone synthase (CHS), involved in flavonoid biosynthesis and regulated by UVR8, was increased in irradiated Arabidopsis and maize leaves. Arabidopsis uvr8-1 null mutant was complemented with ZmUVR8 driven by the CaMV-35S promoter and fused to eGFP. ZmUVR8-eGFP fusion was mainly localized in nuclei of transgenic lines, irrespective of UV-B treatments. UV-B suppressed hypocotyl elongation in WT Arabidopsis plants, whereas in uvr8-1 hypocotyl growth was observed. However, hypocotyl elongation was reduced in UV-B irradiated transgenic lines complemented with ZmUVR8. Moreover, CHS and transcription factor HY5 (ELONGATED HYPOCOTYL 5) expression were also restored in these plants. These results confirm that ZmUVR8 is similar enough to AtUVR8 to restore UV-B perception and signaling in Arabidopsis mutant uvr8-1, thus being a functional UV-B photoreceptor.

plant biology

Evolution of vascular plants through redeployment of ancient developmental regulators

Vascular plants provide most of the biomass, food and feed on earth; yet the molecular innovations that led to the evolution of their conductive tissues are unknown. Here, we reveal the evolutionary trajectory for the heterodimeric TMO5/LHW transcription factor complex, which is rate-limiting for vascular cell proliferation in Arabidopsis thaliana. Both regulators have origins predating vascular tissue emergence, and even terrestrialization. We further show that TMO5 evolved its modern function, including dimerization with LHW, at the origin of land plants. A second innovation in LHW, coinciding with vascular plant emergence, conditioned obligate heterodimerization and generated the critical function in vascular development. In summary, our results suggest that division potential of vascular cells may have been a major driver in the evolution of vascular plants.

plant biology

Unfolded protein-independent IRE1 activation contributes to multifaceted developmental processes in Arabidopsis

As an initial step for the unfolded protein response (UPR) pathway, the luminal domain of inositol requiring enzyme 1 (IRE1) senses unfolded proteins in the endoplasmic reticulum (ER). Recent findings in yeast and metazoans suggest alternative IRE1 activation without the sensor domain, although its mechanism and physiological significance remain to be elucidated. In Arabidopsis, the IRE1A and IRE1B double mutant (ire1a/b) is unable to activate cytoplasmic splicing of bZIP60 mRNA and regulated IRE1-dependent decay (RIDD) under ER stress, while the mutant does not exhibit severe developmental defects and is fertile under non-stress conditions. In this study, we focused on a third Arabidopsis IRE1 gene, designated as IRE1C, whose product lacks a sensor domain. We found that even though ire1c and ire1a/c mutants did not exhibit defective bZIP60 splicing and RIDD under ER stress, the ire1a/b/c triple mutant is lethal. Heterozygous IRE1C (ire1c/+) mutation in the ire1a/b mutants resulted in growth defects and reduction of the number of pollen grains. Genetic analysis revealed that IRE1C is required for male gametophyte development in the ire1a/b mutant background. Expression of a mutant form of IRE1B that lacks the luminal sensor domain ({Delta}LD) in the ire1a/b mutant did not complement defects in ER stress-dependent bZIP60 splicing and RIDD. Nevertheless, expression of {Delta}LD complemented a developmental defect in the male gametophyte in ire1a/b/c haplotype. In vivo, the {Delta}LD protein was activated by glycerol treatment that increases the composition of saturated lipid and was able to activate RIDD but not bZIP60 splicing. Phenotypes of IRE1B mutants lacking the sensor domain produced by CRISPR/Cas9-mediated gene editing in the ire1a/c mutant background were essentially same as those of {Delta}LD-expressing ire1a/b mutant. These observations suggest that IRE1 contributes to plant development, especially male gametogenesis, using an alternative activation mechanism that bypasses the unfolded protein-sensing luminal domain.

plant biology

Inhibition of jasmonate-mediated plant defences by the fungal metabolite higginsianin B

Infection of Arabidopsis thaliana by the ascomycete fungus Colletotrichum higginsianum is characterised by an early symptomless biotrophic phase followed by a destructive necrotrophic phase. The fungal genome contains 77 secondary metabolism-related biosynthetic gene clusters (BGCs), and their expression during the infection process is tightly regulated. Deleting CclA, a chromatin regulator involved in repression of some BGCs through H3K4 trimethylation, allowed overproduction of 3 families of terpenoids and isolation of 12 different molecules. These natural products were tested in combination with methyl jasmonate (MeJA), an elicitor of jasmonate responses, for their capacity to alter defence gene induction in Arabidopsis. Higginsianin B inhibited MeJA-triggered expression of the defence reporter VSP1p:GUS, suggesting it may block bioactive JA-Ile synthesis or signalling in planta. Using the JA-Ile sensor Jas9-VENUS, we found that higginsianin B, but not three other structurally-related molecules, suppressed JA-Ile signalling by preventing degradation of JAZ proteins, the repressors of JA responses. Higginsianin B likely blocks the 26S proteasome-dependent degradation of JAZ proteins because it inhibited chymotrypsin- and caspase-like protease activities. The inhibition of target degradation by higginsianin B also extended to auxin signalling, as higginsianin B treatment reduced IAA-dependent expression of DR5p:GUS. Overall, our data indicate that specific fungal secondary metabolites can act similarly to protein effectors to subvert plant immune and developmental responses.\n\nHighlightA diterpene secondary metabolite produced by a fungal pathogen suppresses plant jasmonate defense signalling by preventing the proteasomal degradation of JAZ repressor proteins.

plant biology

Root morphology and exudate availability is shaped by particle size and chemistry in Brachypodium distachyon

Root morphology and exudation define a plants sphere of influence in soils, and are in turn shaped by the physiochemical characteristics of soil. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of the model grass Brachypodium distachyon. Root fresh weight and root lengths were correlated with particle size, whereas root number and shoot weight remained constant. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate metabolite profiles detected with liquid chromatography / mass spectrometry were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay. However, when exudates of clay-grown plants were collected by removing the plants from the substrate, their exudate profile was similar to sand- or glass beads-grown plants. Clay particles sorbed 20% of compounds exuded by clay-grown plants, and 70% of compounds of a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides/nucleotides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be de-sorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. We show that root morphology is affected by substrate size, and that root exudation in contrast is not affected by substrate size or chemistry. The availability of exuded compounds, however, depends on the substrate present. These findings further support the critical importance of the physiochemical properties of soils are crucial to consider when investigating plant morphology, exudation, and plant-microbe interactions.

plant biology

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

plant biology

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future.

plant biology

ETHYLENE RESPONSE FACTOR (ERF) genes modulate plant root exudate composition and the attraction of plant parasitic nematodes

Plant root exudates are compositionally diverse, plastic and adaptive. Ethylene signalling influences the attraction of plant parasitic nematodes (PPNs), presumably through the modulation of root exudate composition. Understanding this pathway could lead to new sources of crop parasite resistance. Here we have used Virus-Induced Gene Silencing (VIGS) to knockdown the expression of two ETHYLENE RESPONSE FACTOR (ERF) genes, ERF-E2 and ERF-E3 in tomato. Root exudates are significantly more attractive to the PPNs Meloidogyne incognita, and Globodera pallida following knockdown of ERF-E2, which has no impact on the attraction of Meloidogyne javanica. Knockdown of ERF-E3 has no impact on the attraction of Meloidogyne or Globodera spp. GC-MS analysis revealed major changes in root exudate composition relative to controls. However, these changes do not alter the attraction of rhizosphere microbes Bacillus subtilis or Agrobacterium tumefaciens. This study further supports the potential of engineering plant root exudate for parasite control, through the modulation of plant genes.\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@15fea9dorg.highwire.dtl.DTLVardef@241221org.highwire.dtl.DTLVardef@224609org.highwire.dtl.DTLVardef@24315corg.highwire.dtl.DTLVardef@24953e_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology

Evidence for the involvement of protein lysine methylation in the response of sensitive and tolerant Arabidopsis species to cadmium stress

The mechanisms underlying the response and adaptation of plants to excess of trace elements are not fully described. Here, we analyzed the importance of protein lysine methylation for plants to cope with cadmium. We analyzed the effect of cadmium on lysine-methylated proteins and protein lysine methyltransferases (KMTs) in two cadmium-sensitive species, Arabidopsis thaliana and A. lyrata, and in three populations of A. halleri with contrasting cadmium accumulation and tolerance traits. We showed that some proteins are differentially methylated at lysine residues in response to Cd and that a few genes coding KMTs is regulated by cadmium. Also, we showed that nine out of 23 A. thaliana mutants interrupted in KMT genes have a tolerance to cadmium that is significantly different from that of wild-type seedlings. We further characterized two of these mutants, one was knocked-out in the calmodulin lysine methyltransferase gene and displayed increased tolerance to cadmium, the other was interrupted in a KMT gene of unknown function and showed a decreased capacity to cope with cadmium. Together, our results showed that lysine methylation of non-histone proteins is impacted by cadmium and that several methylation events are important for modulating the response of Arabidopsis plants to cadmium stress.

plant biology

Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci

MotivationRepetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available.\n\nResultsWe examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations, when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent statistically significant association with gene density.\n\nConclusionOur results indicate that repeat content variation in the heterotic populations of maize has not diverged and is uncoupled from population stratification at SNP loci. We also show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.\n\nAuthors contributionsSRB and AB conceived the study, SRB performed the bioinformatic analysis, SRB wrote the paper with input from AB. email contacts: Simon Renny-Byfield: simon.renny-byfield@corteva.com, Andy Baumgarten: andy.baumgarten@corteva.com

plant biology

Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner

Plant root-microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally-adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata (Fisch. ex DC.) G.L. Nesom). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After three months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at the inland site due to an exclusive set of rare taxa associated with each ecotype. Although our results indicate that locally-adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, environmental factors can trump genetic factors in shaping the M. guttatus microbiome. Overall, our findings demonstrate that wild plants strongly impact root-associated microbial communities, but hierarchical drivers interact to shape microbial community assembly outcomes.

plant biology

Partial-resistance against aphids in wild barley reduces the oviposition success of the generalist parasitoid, Aphidius colemani

Aphids are significant agricultural pests of cereal crops with a worldwide distribution. The control of aphids in agricultural systems is currently heavily reliant on insecticidal compounds, but it is becoming increasingly apparent that chemical-based control of agricultural pests has far-reaching unintended consequences on agro-ecosystems. As a result, more sustainable means of aphid control are becoming increasingly desirable. Potential options include increasing plant resistance against aphids, promoting biocontrol, and the combined use of both strategies. When used together it is important to understand how, and to what extent, increased plant resistance against aphids affects the success of biocontrol agents. In this current study, we examine how partial-resistance against cereal aphids in a wild relative of barley, Hordeum spontaneum 5 (Hsp5), affects the success of the common parasitoid of cereal aphids, Aphidius colemani. We show that the parasitism success of A. colemani attacking nymphs of the bird cherry-oat aphid, Rhopalosiphum padi, contained on Hsp5 is reduced compared with the parasitism success of wasps attacking R. padi nymphs feeding on a susceptible modern cultivar of barley, H. vulgare cv. Concerto. Explanta parasitism assays showed that the in parasitoid success is a direct effect of the plant environment (such as differential architectural traits), rather than an indirect effect dur to a decrease in aphid suitability resulting from increased resistance against aphids in Hsp5. Our study highlights the importance of understanding the direct and indirect effects of plant resistance against aphids on biocontrol strategies.

plant biology

The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene

Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a (\"Peking-type\", low copy number, 3 or fewer Rhg1 repeats) and rhg1-b (\"PI 88788-type\", high copy number, 4 or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode -SNAP (alpha-Soluble NSF Attachment Protein) variants -SNAPRhg1LC and -SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (-SNAP-encoding) gene. We termed this retrotransposon \"RAC\", for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a -SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic -SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated -SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for -SNAPRhg1HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just [~]42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded -SNAPRhg1LC, and thus they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.

plant biology

Comparative analyses of 3654 chloroplast genomes unraveled new insights into the evolutionary mechanism of green plants

BackgroundChloroplast are believed to arise from a cyanobacterium through endosymbiosis and they played vital roles in photosynthesis, oxygen release and metabolites synthesis for the plant. With the advent of next-generation sequencing technologies, until December 2018, about 3,654 complete chloroplast genome sequences have been made available. It is possible to compare the chloroplast genome structure to elucidate the evolutionary history of the green plants.\n\nResultsWe compared the 3654 chloroplast genomes of the green plants and found extreme conservation of gene orders and gene blocks in the green plant such as ATP synthase cluster, Phytosystem, Cytochrome cluster, and Ribosomal cluster. For the chloroplast-based phylogenomics, we used three different data sets to recover the relationships within green plants which accounted for biased GC content and could mitigate the bias in molecular data sets by increasing taxon sampling. The main topology results include: I) Chlorokybales + Mesostigmatales as the earliest-branching lineage and a clade comprising Zygnematales+ Desmidiales formed a grade as the sister group to the land plants, II) Based on matrix AA data, Bryophytes was strongly supported as monophyletic but for matrix nt123 data, hornworts, mosses and liverworts were placed as successive sister lineages of Tracheophytes with strong support, III) Magnoliids were placed in the outside of Monocots using the matrix nt123 data and the matrix AA data, IV) Ceratophyllales + Chloranthales as sister to the Eudicots using matrix nt123 data, but when using matrix nt12 data and AA data, only Ceratophyllales sister to the Eudicots.\n\nConclusionWe present the first of its kind large scale comparative analyses of the chloroplast coding gene constitution for 3654 green plants. Some important genes likely showed co-occurrence and formed gene cluster and gene blocks in Streptophyta. We found a clear expansion of IRs (Inverted Repeats) among seed plants. The comprehensive taxon sampling and different data sets recovered a strong relationship for green plants.

plant biology

Marine cyanobacteria tune energy transfer efficiency in their light-harvesting antennae by modifying pigment coupling

Photosynthetic organisms regulate energy transfer to fit to changes in environmental conditions. The biophysical principles underlying the flexibility and efficiency of energy transfer in the light-harvesting process are still not fully understood. Here we examine how energy transfer is regulated in-vivo. We compare different acclimation states of the photosynthetic apparatus in a marine cyanobacterial species that is well adapted to vertical mixing of the ocean water column and identify a novel acclimation strategy for photosynthetic life under low light intensities. Antennae rods extend, as expected, increasing light absorption. Surprisingly, in contrast to what was known for plants and predicted by classic calculations, these longer rods transfer energy faster i.e. more efficiently. The fluorescence lifetime and emission spectra dependence on temperature, at the range of 4-300K, suggests that energy transfer efficiency is tuned by modifying the energetic coupling strength between antennae pigments.

plant biology