The Plant Journal

doi: 10.1111/tpj.14827pmid: N/A

Sweetlove, Lee J.; Cnaai, Alon

doi: 10.1111/tpj.15281pmid: 34003508

Verhage, Leonie

doi: 10.1111/tpj.15288pmid: 34003507

Garcia‐Lozano, Marleny; Natarajan, Purushothaman; Levi, Amnon; Katam, Ramesh; Lopez‐Ortiz, Carlos; Nimmakayala, Padma; Reddy, Umesh K.

doi: 10.1111/tpj.15256pmid: 33788333

Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher‐order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.

Rebaque, Diego; Hierro, Irene; López, Gemma; Bacete, Laura; Vilaplana, Francisco; Dallabernardina, Pietro; Pfrengle, Fabian; Jordá, Lucía; Sánchez‐Vallet, Andrea; Pérez, Rosa; Brunner, Frédéric; Molina, Antonio; Mélida, Hugo

doi: 10.1111/tpj.15185pmid: 33544927

Pattern‐triggered immunity (PTI) is activated in plants upon recognition by pattern recognition receptors (PRRs) of damage‐ and microbe‐associated molecular patterns (DAMPs and MAMPs) derived from plants or microorganisms, respectively. To understand better the plant mechanisms involved in the perception of carbohydrate‐based structures recognized as DAMPs/MAMPs, we have studied the ability of mixed‐linked β‐1,3/1,4‐glucans (MLGs), present in some plant and microbial cell walls, to trigger immune responses and disease resistance in plants. A range of MLG structures were tested for their capacity to induce PTI hallmarks, such as cytoplasmic Ca2+ elevations, reactive oxygen species production, phosphorylation of mitogen‐activated protein kinases and gene transcriptional reprogramming. These analyses revealed that MLG oligosaccharides are perceived by Arabidopsis thaliana and identified a trisaccharide, β‐d‐cellobiosyl‐(1,3)‐β‐d‐glucose (MLG43), as the smallest MLG structure triggering strong PTI responses. These MLG43‐mediated PTI responses are partially dependent on LysM PRRs CERK1, LYK4 and LYK5, as they were weaker in cerk1 and lyk4 lyk5 mutants than in wild‐type plants. Cross‐elicitation experiments between MLG43 and the carbohydrate MAMP chitohexaose [β‐1,4‐d‐(GlcNAc)6], which is also perceived by these LysM PRRs, indicated that the mechanism of MLG43 recognition could differ from that of chitohexaose, which is fully impaired in cerk1 and lyk4 lyk5 plants. MLG43 treatment confers enhanced disease resistance in A. thaliana to the oomycete Hyaloperonospora arabidopsidis and in tomato and pepper to different bacterial and fungal pathogens. Our data support the classification of MLGs as a group of carbohydrate‐based molecular patterns that are perceived by plants and trigger immune responses and disease resistance.

Huang, Yongji; Ding, Wenjie; Zhang, Muqing; Han, Jinlei; Jing, Yanfen; Yao, Wei; Hasterok, Robert; Wang, Zonghua; Wang, Kai

doi: 10.1111/tpj.15186pmid: 33547688

Centromeres in eukaryotes are composed of tandem DNAs and retrotransposons. However, centromeric repeats exhibit considerable diversity, even among closely related species, and their origin and evolution are largely unknown. We conducted a genome‐wide characterization of the centromeric sequences in sugarcane (Saccharum officinarum). Four centromeric tandem repeat sequences, So1, So103, So137 and So119, were isolated. So1 has a monomeric length of 137 bp, typical of a centromeric satellite, and has evolved four variants. However, these So1 variants had distinct centromere distributions and some were unique to an individual centromere. The distributions of the So1 variants were unexpectedly consistent among the Saccharum species that had different basic chromosome numbers or ploidy levels, thus suggesting evolutionary stability for approximately 7 million years in sugarcane. So103, So137 and So119 had unusually longer monomeric lengths that ranged from 327 to 1371 bp and lacked translational phasing on the CENH3 nucleosomes. Moreover, So103, So137 and So119 seemed to be highly similar to retrotransposons, which suggests that they originated from these mobile elements. Notably, all three repeats were flanked by direct repeats, and formed extrachromosomal circular DNAs (eccDNAs). The presence of circular molecules for these retrotransposon‐derived centromeric satellites suggests an eccDNA‐mediated centromeric satellite formation pathway in sugarcane.

Shi, Jiewei; Zhang, Qunxia; Yan, Xu; Zhang, Delin; Zhou, Qin; Shen, Yuxiao; Anupol, Nachaisin; Wang, Xiuqing; Bao, Manzhu; Larkin, Robert M.; Luo, Hong; Ning, Guogui

doi: 10.1111/tpj.15187pmid:

Sun, Huwei; Guo, Xiaoli; Qi, Xuejiao; Feng, Fan; Xie, Xiaonan; Zhang, Yali; Zhao, Quanzhi

doi: 10.1111/tpj.15188pmid: 33547682

Nitrogen (N) is an essential major nutrient for food crops. Although ammonium (NH4+) is the primary N source of rice (Oryza sativa), nitrate (NO3−) can also be absorbed and utilized. Rice responds to NO3− application by altering its root morphology, such as root elongation. Strigolactones (SLs) are important modulators of root length. However, the roles of SLs and their downstream genes in NO3−‐induced root elongation remain unclear. Here, the levels of total N and SL (4‐deoxyorobanchol) and the responses of seminal root (SR) lengths to NH4+ and NO3− were investigated in rice plants. NO3− promoted SR elongation, possibly due to short‐term signal perception and long‐term nutrient function. Compared with NH4+ conditions, higher SL signalling/levels and less D53 protein were recorded in roots of NO3−‐treated rice plants. In contrast to wild‐type plants, SR lengths of d mutants were less responsive to NO3− conditions, and application of rac‐GR24 (SL analogue) restored SR length in d10 (SL biosynthesis mutant) but not in d3, d14, and d53 (SL‐responsive mutants), suggesting that higher SL signalling/levels participate in NO3−‐induced root elongation. D53 interacted with SPL17 and inhibited SPL17‐mediated transactivation from the PIN1b promoter. Mutation of SPL14/17 and PIN1b caused insensitivity of the root elongation response to NO3− and rac‐GR24 applications. Therefore, we conclude that perception of SLs by D14 leads to degradation of D53 via the proteasome system, which releases the suppression of SPL14/17‐modulated transcription of PIN1b, resulting in root elongation under NO3− supply.

Lin, Yuan; Zhao, Hainan; Kotlarz, Magdalena; Jiang, Jiming

doi: 10.1111/tpj.15189pmid: 33547831

Gene expression is controlled and regulated by interactions between cis‐regulatory DNA elements (CREs) and regulatory proteins. Enhancers are one of the most important classes of CREs in eukaryotes. Eukaryotic genes, especially those related to development or responses to environmental cues, are often regulated by multiple enhancers in different tissues and/or at different developmental stages. Remarkably, little is known about the molecular mechanisms by which enhancers regulate gene expression in plants. We identified a distal enhancer, CREβ, which regulates the expression of AtDGK7, which encodes a diacylglycerol kinase in Arabidopsis. We developed a transgenic line containing the luciferase reporter gene (LUC) driven by CREβ fused with a minimal cauliflower mosaic virus (CaMV) 35S promoter. The CREβ enhancer was shown to play a role in the response to osmotic pressure of the LUC reporter gene. A forward genetic screen pipeline based on the transgenic line was established to generate mutations associated with altered expression of the LUC reporter gene. We identified a suite of mutants with variable LUC expression levels as well as different segregation patterns of the mutations in populations. We demonstrate that this pipeline will allow us to identify trans‐regulatory factors associated with CREβ function as well as those acting in the regulation of the endogenous AtDGK7 gene.

Schiavinato, Matteo; Bodrug‐Schepers, Alexandrina; Dohm, Juliane C.; Himmelbauer, Heinz

doi: 10.1111/tpj.15190pmid: 33547826

Polyploidization is a well‐known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.