植物科学顶尖文章导读（NG，NP）|4月30日

植物学顶尖杂志 Plant Cell, New Phytol , Mol Plant, Plant Physiol, Plant Biotechnol  J, Plant J, nature Plants及综合期刊Nucleic Acids Res. ， PNAS，NB，NC及NG有关植物学的研究文章导读，每日定时更新，了解行业最前沿进展

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

https://www.nature.com/articles/s41588-018-0110-3

Lignin is a complex and irregular biopolymer of crosslinked phenylpropanoid units in plant secondary cell walls. Its biosynthesis requires three endoplasmic reticulum (ER)-resident cytochrome P450 monooxygenases, C4H, C3ʹH and F5H, to establish the structural characteristics of its monomeric precursors. These P450 enzymes were reported to associate with each other or potentially with other soluble monolignol biosynthetic enzymes to form an enzyme complex or a metabolon. However, the molecular basis governing such enzyme or pathway organization remains elusive. Here, we show that Arabidopsismembrane steroid-binding proteins (MSBPs) serve as a scaffold to physically organize monolignol P450 monooxygenases, thereby regulating the lignin biosynthetic process. We find that although C4H, C3ʹH and F5H are in spatial proximity to each other on the ER membrane in vivo, they do not appear to directly interact with each other. Instead, two MSBP proteins physically interact with all three P450 enzymes and, moreover, MSBPs themselves associate as homomers and heteromers on the ER membrane, thereby organizing P450 clusters. Downregulation of MSBP genes does not affect the transcription levels of monolignol biosynthetic P450 genes but substantially impairs the stability and activity of the MSBP-interacting P450 enzymes and, consequently, lignin deposition, and the accumulation of soluble phenolics in the monolignol branch but not in the flavonoid pathway. Our study suggests that MSBP proteins are essential structural components in the ER membrane that physically organize and stabilize the monolignol biosynthetic P450 enzyme complex, thereby specifically controlling phenylpropanoid–monolignol branch biosynthesis.

https://www.nature.com/articles/s41477-018-0142-9

Wheat is regarded as one of the most important West Asian domesticates that were introduced into Late Neolithic/Early Bronze Age China. Despite a growing body of archaeological data, the timing and routes of its dispersal remain controversial. New radiocarbon (14C) dating evidence from six archaeological sites in the Shandong and Liaoning Peninsulas and Bayesian modelling of available 14C data from China suggest that wheat appeared in the lower Yellow River around 2600 Before Common Era (BCE), followed by Gansu and Xinjiang around 1900 BCE and finally occurred in the middle Yellow River and Tibet regions by 1600 BCE. These results neither support long-standing hypotheses of a progressive spread of wheat agriculture from Xinjiang or Gansu to eastern China nor suggest a nearly synchronous appearance in this vast zone, but corroborate transmission to lower Yellow River elites as an exotic good through cultural interactions with the Eurasian steppe along north–south routes.

https://www.nature.com/articles/s41477-018-0141-x

All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality. Polyploidization has happened repeatedly in plant evolution and, we conclude, is important for crop domestication. Once duplicated, the effect of purifying selection on any one duplicated gene is relaxed, permitting duplicate gene and regulatory element loss (fractionation). We review the general topic of fractionation, and how some gene categories are retained more than others. Several explanations, including neofunctionalization, subfunctionalization and gene product dosage balance, have been shown to influence gene content over time. For allopolyploids, genetic differences between parental lines immediately manifest as subgenome dominance in the wide-hybrid, and persist and propagate for tens of millions of years. While epigenetic modifications are certainly involved in genome dominance, it has been difficult to determine which came first, the chromatin marks being measured or gene expression. Data support the conclusion that genome dominance and heterosis are antagonistic and mechanically entangled; both happen immediately in the synthetic wide-cross hybrid. Also operating in this hybrid are mechanisms of ‘paralogue interference’. We present a foundation model to explain gene expression and vigour in a wide hybrid/new allotetraploid. This Review concludes that some mechanisms operate immediately at the wide-hybrid, and other mechanisms begin their operations later. Direct interaction of new paralogous genes, as measured using high-resolution chromatin conformation capture, should inform future research and single cell transcriptome sequencing should help achieve specificity while studying gene sub- and neo-functionalization.

https://www.nature.com/articles/s41477-018-0136-7

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of ‘core microbiomes’, which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

https://www.nature.com/articles/s41477-018-0139-4

The colonization of land by vascular plants is an extremely important phase in Earth’s life history. This key evolutionary process is thought to have begun during the Middle Cambrian1 period and culminated in the Silurian/Early Devonian period (interval about 509–393 million years ago (Ma)), and is documented primarily by microfossils (that is, by dispersed spores, phytodebris including fragments of algae, tissues, sporangia and cuticles), tubes and rare megafossils2. A newly recognized fossil cooksonioid plant with in situ spores from the Barrandian area, Czech Republic, is of the highest importance because it represents extremely ancient megafossil evidence of land plant diploid generation: sporophytes (~432 Ma). The robust size of this plant places it among the largest known early polysporangiate land plants and it is probable that it attained adequate size for both aeration and effective photosynthetic competence. This would mean not only that sporophytes were photosynthetically autonomous but also that the they might have been able to sustain a relatively gametophyte-independent existence.

https://www.nature.com/articles/s41477-018-0140-y

Xylan is one of the main compounds determining wood properties in hardwood species. The xylan backbone is thought to be synthesized by a synthase complex comprising two members of the GT43 family. We downregulated all GT43 genes in hybrid aspen (Populus tremula × tremuloides) to understand their involvement in xylan biosynthesis.All three clades of the GT43 family were targeted for downregulation using RNA interference individually or in different combinations, either constitutively or specifically in developing wood.Simultaneous downregulation in developing wood of the B (IRX9) and C (IRX14) clades resulted in reduced xylan Xyl content relative to reducing end sequence, supporting their role in xylan backbone biosynthesis. This was accompanied by a higher lignocellulose saccharification efficiency. Unexpectedly, GT43 suppression in developing wood led to an overall growth stimulation, xylem cell wall thinning and a shift in cellulose orientation. Transcriptome profiling of these transgenic lines indicated that cell cycling was stimulated and secondary wall biosynthesis was repressed. We suggest that the reduced xylan elongation is sensed by the cell wall integrity surveying mechanism in developing wood.Our results show that wood‐specific suppression of xylan‐biosynthetic GT43 genes activates signaling responses, leading to increased growth and improved lignocellulose saccharification.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15160

Post‐transcriptional gene silencing in plants results from independent activities of diverse small RNA types. In anthers of grasses, hundreds of loci yield noncoding RNAs that are processed into 21‐ and 24‐nucleotide (nt) phased small interfering RNAs (phasiRNAs); these are triggered by miR2118 and miR2275.We characterized these ‘reproductive phasiRNAs’ from rice (Oryza sativa) panicles and anthers across seven developmental stages. Our computational analysis identified characteristics of the 21‐nt reproductive phasiRNAs that impact their biogenesis, stability, and potential functions.We demonstrate that 21‐nt reproductive phasiRNAs can function in cis to target their own precursors. We observed evidence of this cis regulatory activity in both rice and maize (Zea mays). We validated this activity with evidence of cleavage and a resulting shift in the pattern of phasiRNA production.We characterize biases in phasiRNA biogenesis, demonstrating that the Pol II‐derived ‘top’ strand phasiRNAs are consistently higher in abundance than the bottom strand. The first phasiRNA from each precursor overlaps the miR2118 target site, and this impacts phasiRNA accumulation or stability, evident in the weak accumulation of this phasiRNA position. Additional influences on this first phasiRNA duplex include the sequence composition and length, and we show that these factors impact Argonaute loading.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15181

There is growing evidence for the convergent evolution of physically linked gene clusters encoding chemical defense pathways. Metabolic clusters are proposed to evolve because they ensure co‐inheritance of all required genes where the defense is favored, and prevent inheritance of toxic partial pathways where it is not. This hypothesis rests on the assumption that clusters evolve in species where selection favors intraspecific polymorphism for the defense; however, they have not been examined in polymorphic species.We examined metabolic cluster evolution in relation to an adaptive polymorphism for cyanogenic glucoside (CNglc) production in clover. Using 163 accessions, we performed CNglc assays, BAC sequencing, Southern hybridizations and molecular evolutionary analyses.We find that the CNglc pathway forms a 138‐kb cluster in white clover, and that the adaptive polymorphism occurs through presence/absence of the complete cluster. Component genes are orthologous to those in the distantly related legume Lotus japonicus.These findings provide empirical support for the co‐inheritance hypothesis, and they indicate that adaptive CNglc variation in white clover evolves through recurrent deletions of the entire pathway. They further indicate that the shared ancestor of many important legume crops was likely cyanogenic and that this defense was lost repeatedly over the last 50 Myr.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15184