Legume nodules have two types of hemoglobins: symbiotic or leghemoglobins (Lbs) and nonsymbiotic or phytoglobins (Glbs). The latter are categorized into three phylogenetic classes differing in heme ...coordination and O₂ affinity. This review is focused on the roles of Lbs and Glbs in the symbiosis of rhizobia with crop legumes and the model legumes for indeterminate (Medicago truncatula) and determinate (Lotus japonicus) nodulation. Only two hemoglobin functions are well established in nodules: Lbs deliver O₂ to the bacteroids and act as O₂ buffers, preventing nitrogenase inactivation; and Glb1-1 modulates nitric oxide concentration during symbiosis, from the early stage, avoiding the plant’s defense response, to nodule senescence. Here, we critically examine early and recent results, update and correct the information on Lbs and Glbs with the latest genome versions, provide novel expression data and identify targets for future research. Crucial unresolved questions include the expression of multiple Lbs in nodules, their presence in the nuclei and in uninfected nodule cells, and, intriguingly, their expression in nonsymbiotic tissues. RNA-sequencing data analysis shows that Lbs are expressed as early as a few hours after inoculation and that their mRNAs are also detectable in roots and pods, which clearly suggests that these heme proteins play additional roles unrelated to nitrogen fixation. Likewise, issues awaiting investigation are the functions of other Glbs in nodules, the spatiotemporal expression profiles of Lbs and Glbs at the mRNA and protein levels, and the molecular mechanisms underlying their regulation during nodule development and in response to stress and hormones.
Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ...ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology.
We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm.
We report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.
Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by ...insufficient diagnostic morphological characteristics and frequent natural hybridization. Development of novel DNA markers or barcodes with sufficient resolution to resolve taxonomic issues of Artemisia in East Asia is significant challenge.
To establish a molecular basis for taxonomic identification and comparative phylogenomic analysis of Artemisia, we newly determined 19 chloroplast genome (plastome) sequences of 18 Artemisia taxa in East Asia, de novo-assembled and annotated the plastomes of two taxa using publicly available Illumina reads, and compared them with 11 Artemisia plastomes reported previously. The plastomes of Artemisia were 150,858-151,318 base pairs (bp) in length and harbored 87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNA genes in conserved order and orientation. Evolutionary analyses of whole plastomes and 80 non-redundant protein-coding genes revealed that the noncoding trnH-psbA spacer was highly variable in size and nucleotide sequence both between and within taxa, whereas the coding sequences of accD and ycf1 were under weak positive selection and relaxed selective constraints, respectively. Phylogenetic analysis of the whole plastomes based on maximum likelihood and Bayesian inference analyses yielded five groups of Artemisia plastomes clustered in the monophyletic subgenus Dracunculus and paraphyletic subgenus Artemisia, suggesting that the whole plastomes can be used as molecular markers to infer the chloroplast haplotypes of Artemisia taxa. Additionally, analysis of accD and ycf1 hotspots enabled the development of novel markers potentially applicable across the family Asteraceae with high discriminatory power.
The complete sequences of the Artemisia plastomes are sufficiently polymorphic to be used as super-barcodes for this genus. It will facilitate the development of new molecular markers and study of the phylogenomic relationships of Artemisia species in the family Asteraceae.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Crop breeding programs are reliant on the genetic diversity of varieties and germplasm collections. Raphanus sativus L. is a root crop species of the Brassicaceae family that accounts for ∼2% of ...global vegetable production. We recently reported the assembly of a new radish core collection consisting of 125 accessions obtained from worldwide germplasm banks. To develop a comprehensive plant resource for radish research and breeding, we characterized the agronomic traits of 83 accessions and analyzed their genome‐wide DNA variations along with 17 previously analyzed accessions. A total of 14 agronomically important root, leaf, and flower phenotypic traits were examined according to the guidelines of the International Union for the Protection of New Plant Varieties. Chemical diversity in radish roots was investigated by measuring their sugar, glucosinolate, and anthocyanin contents. Through high‐depth whole‐genome resequencing of 100 accessions and multi‐sample genotyping analysis using the Rs2.0 genome assembly as a reference, we identified a total of 796,294 homozygous high‐quality single‐nucleotide polymorphisms. Genetic structural analysis using a neighbor‐joining algorithm and multi‐dimensional scaling analysis of the variations were applied to classify the accessions into three major groups, including 37 and 55 accessions of European and Asian cultivated radishes, respectively, and eight wild radish accessions. For each accession, the mitochondria‐encoded Ogura cytoplasmic male‐sterility determinant orf138 and nuclear fertility restorer PPR‐B genes were reconstructed by reference‐guided assembly. It is anticipated that these genetic diversity and agronomic properties of the radish core collection will facilitate breeding programs to develop new radish cultivars with desirable profiles.
Core Ideas
This study provides important agronomic phenotypic and phytochemical trait data for a new radish core collection.
Whole‐genome resequencing and multi‐sample genotyping analyses identified 796,294 high‐quality single‐nucleotide polymorphisms.
High‐depth variation data from 100 radish accessions classified the accessions into three main groups.
These resources will enhance research on the trait genetic system, breeding, and diversity conservation of radishes.
Gibberellin (GA) plays a controversial role in the legume-rhizobium symbiosis. Recent studies have shown that the GA level in legumes must be precisely controlled for successful rhizobial infection ...and nodule organogenesis. However, regulation of the GA level via catabolism in legume roots has not been reported to date. Here, we investigate a novel GA inactivating C20-GA2-oxidase gene MtGA2ox10 in Medicago truncatula. RNA sequencing analysis and quantitative polymerase chain reaction revealed that MtGA2ox10 was induced as early as 6 h post-inoculation (hpi) of rhizobia and reached peak transcript abundance at 12 hpi. Promoter::β-glucuronidase fusion showed that the promoter activity was localized in the root infection/differentiation zone during the early stage of rhizobial infection and in the vascular bundle of the mature nodule. The CRISPR/Cas9-mediated deletion mutation of MtGA2ox10 suppressed infection thread formation, which resulted in reduced development and retarded growth of nodules on the Agrobacterium rhizogenes-transformed roots. Over-expression of MtGA2ox10 in the stable transgenic plants caused dwarfism, which was rescued by GA
application, and increased infection thread formation but inhibition of nodule development. We conclude that MtGA2ox10 plays an important role in the rhizobial infection and the development of root nodules through fine catabolic tuning of GA in M. truncatula.
We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on ...mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.
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•Mutation-phosphorylation correlation suggests possible signaling interplays in EOGCs•mRNA-protein correlation suggests genes with high association with patient survival•Integrated analysis of mRNA and protein data identified four subtypes•Phosphorylation data provide cellular signaling pathways underlying the subtypes
Mun et al. perform proteogenomic analysis of diffuse gastric cancers (DGC) in a young population, identifying that correlations of mRNA-protein abundance associate with survival and defining four subtypes of DGC. The associations of some subtypes with related pathways are identified mainly by the proteomic data.
A challenging approach, but one providing a key solution to material growth, remote epitaxy (RE)-a novel concept related to van der Waals epitaxy (vdWE)-requires the stability of a two-dimensional ...(2-D) material. However, when graphene, a representative 2-D material, is present on substrates that have a nitrogen atom, graphene loss occurs. Although this phenomenon has remained a hurdle for over a decade, restricting the advantages of applying graphene in the growth of III-nitride materials, few previous studies have been conducted. Here, we report the stability of graphene on substrates containing oxygen or nitrogen atoms. Graphene has been observed on highly decomposed Al
2
O
3
; however, graphene loss occurred on decomposed AlN at temperatures over 1300 °C. To overcome graphene loss, we investigated 2-D hexagonal boron nitride (h-BN) as an alternative. Unlike graphene on AlN, it was confirmed that h-BN on AlN was intact after the same high-temperature process. Moreover, the overgrown AlN layers on both h-BN/AlN and h-BN/Al
2
O
3
could be successfully exfoliated, which indicates that 2-D h-BN survived after AlN growth and underlines its availability for the vdWE/RE of III-nitrides with further mechanical transfer. By enhancing the stability of the 2-D material on the substrate, our study provides insights into the realization of a novel epitaxy concept.
A challenging approach, but one providing a key solution to material growth, remote epitaxy (RE)-a novel concept related to van der Waals epitaxy (vdWE)-requires the stability of a two-dimensional (2-D) material.
The legume-rhizobium symbiosis is initiated through the activation of the Nodulation (Nod) factor-signaling cascade, leading to a rapid reprogramming of host cell developmental pathways. In this ...work, we combine transcriptome sequencing with molecular genetics and network analysis to quantify and categorize the transcriptional changes occurring in roots of Medicago truncatula from minutes to days after inoculation with Sinorhizobium medicae. To identify the nature of the inductive and regulatory cues, we employed mutants with absent or decreased Nod factor sensitivities (i.e. Nodulation factor perception and Lysine motif domain-containing receptor-like kinase3, respectively) and an ethylene (ET)-insensitive, Nod factor-hypersensitive mutant (sickle). This unique data set encompasses nine time points, allowing observation of the symbiotic regulation of diverse biological processes with high temporal resolution. Among the many outputs of the study is the early Nod factor-induced, ET-regulated expression of ET signaling and biosynthesis genes. Coupled with the observation of massive transcriptional derepression in the ET-insensitive background, these results suggest that Nod factor signaling activates ET production to attenuate its own signal. Promoter:β-glucuronidase fusions report ET biosynthesis both in root hairs responding to rhizobium as well as in meristematic tissue during nodule organogenesis and growth, indicating that ET signaling functions at multiple developmental stages during symbiosis. In addition, we identified thousands of novel candidate genes undergoing Nod factor-dependent, ET-regulated expression. We leveraged the power of this large data set to model Nod factor- and ET-regulated signaling networks using MERLIN, a regulatory network inference algorithm. These analyses predict key nodes regulating the biological process impacted by Nod factor perception. We have made these results available to the research community through a searchable online resource.
Key message
This study presents an improved genome of
Raphanus sativus
cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison ...of radish and diploid
Brassica
species of U’s triangle reveals that
R. sativus
arose from the
Brassica
B genome lineage and is a sibling species of
B. nigra
.
Radish (
Raphanus sativus
L.) is a key root vegetable crop closely related to the
Brassica
crop species of the family Brassicaceae. We reported a draft genome of
R. sativus
cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where
R. sativus
-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to
B. nigra
centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid
Brassica
species of U’s triangle suggested that the radish genome arose from the
Brassica
B genome lineage through unique rearrangement of the triplicated ancestral
Brassica
genome after splitting of the
Brassica
A/C and B genomes.
Symbiosis between legume plants and soil rhizobia culminates in the formation of a novel root organ, the ‘nodule’, containing bacteria differentiated as facultative nitrogen-fixing organelles. ...MtNF-YA1 is a Medicago truncatula CCAAT box-binding transcription factor (TF), formerly called HAP2-1, highly expressed in mature nodules and required for nodule meristem function and persistence. Here a role for MtNF-YA1 during early nodule development is demonstrated. Detailed expression analysis based on RNA sequencing, quantitiative real-time PCR (qRT-PCR), as well as promoter–β-glucuronidase (GUS) fusions reveal that MtNF-YA1 is first induced at the onset of symbiotic development during preparation for, and initiation and progression of, symbiotic infection. Moreover, using a new knock-out mutant, Mtnf-ya1-1, it is shown that MtNF-YA1 controls infection thread (IT) progression from initial root infection through colonization of nodule tissues. Extensive confocal and electronic microscopic observations suggest that the bulbous and erratic IT growth phenotypes observed in Mtnf-ya1-1 could be a consequence of the fact that walls of ITs in this mutant are thinner and less coherent than in the wild type. It is proposed that MtNF-YA1 controls rhizobial infection progression by regulating the formation and the wall of ITs.
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