Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Repetitive sequences, primarily transposable elements form an indispensable part of eukaryotic genomes. However, little is known about how these sequences originate, evolve and function in context of a genome. In an attempt to address this question, we performed a comparative analysis of repetitive DNA sequences in the genus Oryza, representing ~15 million years of evolution. Both Class I and Class II transposable elements, through their expansion, loss and movement in the genome, were found to influence genome size variation in this genus. We identified 38 LTRretrotransposon families that are present in 1,500 or more copies throughout Oryza, and many are preferentially amplified in specific lineages. The data presented here, besides furthering our understanding of genome organization in the genus Oryza, will aid in the assembly, annotation and analysis of genomic data, as part of the future genome sequencing projects of O. sativa wild relatives.     

The Future of Rice Genomics: Sequencing the Collective Oryza Genome

The main objectives of the “Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging “comparative phylogenomics” insights into Oryza evolution at two different resolutions—chromosomal and sequence levels. We demonstrate the abundance and impact of structural variations (SV) on genome diversity using African Oryza as a model. The molecular basis of SV was inferred using three genus-wide vertical sequence datasets. Combined, these data demonstrate that a single reference genome sequence for the genus Oryza is insufficient to comprehensively capture the genomic and allelic diversity present within the genus. Towards this end, we present a strategy to generate high-quality and cost-effective de novo reference sequences of collective Oryza. The application and broader scientific impact of the OMAP resources under an international cooperative effort (I-OMAP) are discussed.     

Molecular relationships between Australian annual wild rice,Oryza meridionalis,and two related perennial forms

Background

The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice.

Results

Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets.

Conclusion

Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.     

The Evolutionary History of Ehrhartoideae, Oryzeae, and Oryza

Rice is a member of the genus Oryza, which has a history extending back into the Miocene. Oryza is in turn a member of the tribe Oryzeae, which along with the tribe Ehrharteae is included in the subfamily Ehrhartoideae. This paper reviews current knowledge of the genus, tribe and subfamily, and places rice in the larger evolutionary context of the entire grass family. The morphological characteristics of rice are an amalgam of characters that have originated at different times in its long evolutionary history. Increasingly, genomic characteristics are also being placed in a broad evolutionary context and it is becoming possible see which are characteristic of all grasses and which are more restricted to the genus Oryza or even to rice itself.     

Comparative Analysis of Glycoside Hydrolases Activities from Phylogenetically Diverse Marine Bacteria of the Genus Arenibacter

A total of 16 marine strains belonging to the genus Arenibacter, recovered from diverse microbial communities associated with various marine habitats and collected from different locations, were evaluated in degradation of natural polysaccharides and chromogenic glycosides. Most strains were affiliated with five recognized species, and some presented three new species within the genus Arenibacter. No strains contained enzymes depolymerizing polysaccharides, but synthesized a wide spectrum of glycosidases. Highly active β-N-acetylglucosaminidases and α-N-acetylgalactosaminidases were the main glycosidases for all Arenibacter. The genes, encoding two new members of glycoside hydrolyses (GH) families, 20 and 109, were isolated and characterized from the genomes of Arenibacter latericius. Molecular genetic analysis using glycosidase-specific primers shows the absence of GH27 and GH36 genes. A sequence comparison with functionally-characterized GH20 and GH109 enzymes shows that both sequences are closest to the enzymes of chitinolytic bacteria Vibrio furnissii and Cellulomonas fimi of marine and terrestrial origin, as well as human pathogen Elisabethkingia meningoseptica and simbionts Akkermansia muciniphila, gut and non-gut Bacteroides, respectively. These results revealed that the genus Arenibacter is a highly taxonomic diverse group of microorganisms, which can participate in degradation of natural polymers in marine environments depending on their niche and habitat adaptations. They are new prospective candidates for biotechnological applications due to their production of unique glycosidases.     

Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Heading date determines rice’s adaptation to its area and cropping season. We analyzed the molecular evolution of the Hd6 quantitative trait locus for photoperiod sensitivity in a total of 20 cultivated varieties and wild rice species and found 74 polymorphic sites within its coding region (1,002 bp), of which five were nonsynonymous substitutions. Thus, natural mutations and modifications of the coding region of Hd6 within the genus Oryza have been suppressed during its evolution; this is supported by low Ka (≤0.003) and Ka/Ks (≤0.576) values between species, indicating purifying selection for a protein-coding gene. A nonsynonymous substitution detected in the japonica variety “Nipponbare” (a premature stop codon and nonfunctional allele) was found within only some local Japanese japonica varieties, which suggests that this point mutation happened recently, probably after the introduction of Chinese rice to Japan, and is likely involved in rice adaptation to high latitudes. Phylogenetic analysis and genome divergence using the entire Hd6 genomic region confirmed the current taxonomic sections of Oryza and supported the hypothesis of independent domestication of indica and japonica rice.     

Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.     

Perennial O. sativa × O. rufipogon interspecific hybrids: I. Photosynthetic characteristics and their inheritance

A survey of 24 wild Oryza accessions identified Oryza australiensis and Oryza rufipogon as potential sources of enhanced photosynthetic rate for introgression into cultivated rice. Photosynthetic capacity per unit leaf area (CER) was associated with leaf N content but not with leaf chlorophyll concentration, flag leaf area, or specific leaf area. Eight fertile, perennial F₁ hybrids between O. sativa and O. rufipogon were grown in non-flooded soil, and CER was measured at flowering under saturating light. Two F₁ hybrids had greater CER than the average of 26.1 μmol m² s⁻¹. The F₂ progeny from these hybrids were screened for CER in the field, and segregants with even greater rates of photosynthesis were selected. The basis of high photosynthetic rate in the F₂ populations was not leaf thickness or leaf chlorophyll content. One F₂ line had exceptionally high CER and stomatal conductance. Broad-sense heritability on an individual plant basis for CER in two F₂ populations was 0.44 and 0.37. A highly significant offspring-parent regression of 0.89 for CER was observed in a replicated field evaluation (four blocks, five plants per plot) of 20 vegetatively propagated F₂ selections and their F₃ seedling progeny. Broad-sense heritability for CER on a plot-mean basis was estimated as 0.74 for both selected F_2:3 families and for the selected F₂ clones. Genetic resources in the genus Oryza may represent a source of alleles to increase leaf photosynthetic rate in the cultivated species, which we have demonstrated to be a heritable, though environmentally variable, trait in an O. sativa/O. rufipogon population.     

Comparative Analysis on Genomes from Oryza alta and Oryza latifolia by C0t-1 DNA

In order to reveal the origin and evolutionary relationship between two CCDD genome species, Oryza alta and Oryza latifolia, fluorescence in situ hybridization (FISH) was adopted to analyze the genomes of the two species with C₀t-1 DNA from O. alta as a probe. Karyotype was also comparatively analyzed between O. alta and O. latifolia based on their similar band patterns of the hybridization signals. There were a high homology and close relationship between O. alta and O. latifolia, however, the distinction between the hybridization signals was also clear. C₀t-1 DNA was proved to be species- and genome type-specific. It is suggested that C₀t-1 DNA-FISH could be more efficient to analyze the genomic relationship between different species. According to the comparative analysis of highly and moderately repetitive DNA sequences between the two allotetraploidy species, O. alta and O. latifolia, the possible origin and evolutionary mechanism of allotetraploidy of Oryza were discussed.     

Current Status of Brown Planthopper (BPH) Resistance and Genetics

Among the planthoppers of rice, the brown planthopper (BPH) is a major threat to rice production and causes significant yield loss annually. Host-plant resistance is an important strategy to reduce the damage caused by BPH and increase rice productivity. Twenty-one major genes for BPH resistance have been identified by using standard evaluation methods developed at the International Rice Research Institute (IRRI) to distinguish resistance or susceptibility of rice genotypes to BPH biotypes/populations. These genes are from diverse genetic resources such as land race cultivars and wild species of Oryza. Of the 21 resistance genes, 18 genes have been localized on specific region of six rice chromosomes using molecular genetic analysis and genomics tools. Some of these resistance genes are clustered together such as Bph1, bph2, Bph9, Bph10, Bph18, and Bph21 on the long arm of chromosome 12; Bph12, Bph15, Bph17 and Bph20 on the short arm of chromosome 4; bph11 and Bph14 on the long arm of chromosome 3 and Bph13(t) and bph19 on the short arm of chromosome 3. Six genes (Bph11, bph11, Bph12, bph12, Bph13 and Bph13) originated from wild Oryza species have either duplicate chromosome locations or wrong nomenclature. The discrepancy should be confirmed by allelism tests. Besides identification of major resistance genes, some quantitative trait loci (QTLs) associated with BPH resistance have also been identified on eight chromosomes. Most of the rice cultivars developed at IRRI possess one or two of the major resistance genes and the variety IR64 has many QTLs and confers strong resistance to BPH. More BPH resistance genes need to be identified from the wealth of gene pool available in the wild species of Oryza. Two BPH resistance genes (Bph14 and Bph18) have been cloned, and a snow drop lectin gene (GNA) has been identified and used in the development of BPH-resistant transgenic plants. Efficient introgression of resistance genes (Bph1, bph2, Bph3, Bph14, Bph15, Bph18, Bph20, and Bph21) into elite rice cultivars by marker-assisted selection together with strategic deployment of these genes can be an important approach to develop stable resistance to BPH and sustain rice production in the tropical and temperate rice growing regions.     

Visualizing Meiotic Chromosome Pairing and Segregation in Interspecific Hybrids of Rice by Genomic in situ Hybridization

Meiotic disturbances in F1 hybrids and their progenies are still major problems in wide hybridization.To investigate the genome affinity reflected in chromosome pairing and segregation,we studied chromosome behaviors during meiosis in two interspecific F1 hybrids[O.minuta×O.australiensis(Om×Oa,BCE genome)and Oa×O.ridleyi(Or,EHJ genome)]by using both traditional staining methods and genomic in situ hybridization(GISH).GISH analysis has been successfully performed on mitotic chromosomes to distinguish different Oryza genomes,but relatively fewer systematic analyses of meiotic chromosomes of interspecific hybrids have been reported.In the hybrids,highly irregular chromosome behaviors through meiosis resulted in producing microspores with unbalanced genome.At diakinesis of these two hybrids,most chromosomes present as univalent,with low frequency as bivalents and occasionally as trivalents.In a pollen mother cell,2 to 8 bivalents and 0 to 4 trivalents were observed in the hybrid Oa×Or,and 1 to 8 bivalents and 0 to 5 trivalents were observed in the hybrid Om×Oa.GISH results indicated that 51.52%bivalents in Oa×Or and 79.65%bivalents in Om×Oa involved allosyndetic association,which indicates that recombination and introgression should be possible if viable backcrosses can be recovered even from triploid hybrids.In this study,we revealed that the meiotic disturbance due to low affinities between parental genomes is the major reason for the sterility of these two triploid interspecific hybrids.The two hybrids showing vigor in reproductive growth are potential genetic resources in future breeding programs.A better understanding of genomic affinities between these distant Oryza species can facilitate planning an effective breeding program by using wide hybridization,and efficient and routine GISH analysis is helpful to monitor alien introgression in the process.     

小麦属植物叶绿体基因组结构的比较分析

为了从叶绿体角度解析小麦属植物的起源进化关系,以14个小麦属植物叶绿体基因组为对象,利用比较基因组分析方法,比较了小麦属植物的叶绿体基因组基因含量、序列变异、结构特性、进化关系和RNA编辑的异同。结果发现,14个小麦属植物叶绿体基因组大小相近,结构特征比较保守,但基因数量存在一定的差异,主要是由于tRNA的数目不一致引起的;IR区的伸缩分析发现硬粒小麦和乌拉尔图小麦在IRb-SSC边界基因存在明显的差异,其他麦类作物间差异很小;基于叶绿体全基因组的系统进化分析发现,有AABB基因型的物种聚在一起,而AAGG型的单独为一支,基本反映了其系统进化关系;对这14个叶绿体基因组的RNA编辑位点进行了预测和比较分析,发现有35个编辑位点在所有小麦属物种中均发生,同时还鉴定到多个物种特异的编辑位点,为从RNA编辑角度解析小麦属植物的系统进化关系提供了重要数据。     

Diversity of Sodium Transporter HKT1;5 in Genus Oryza

Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane (MPM) motifs in OsHKT1;5. HKT1;5 sequences from more recently evolved Oryza species (O. sativa/O. officinalis complex species) contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains, potentially governing transport characteristics, while more ancestral HKT1;5 sequences have shorter intracellular loops. We compared homology models for homoeologous OcHKT1;5-K and OcHKT1;5-L from halophytic O. coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na⁺. Using haplotyping, we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species (O. nivara and O. rufipogon). Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance. Within Asian rice accessions, 10 non-synonymous HKT1;5 haplotypic groups occur. More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica. Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups, corresponding to haplotypes in O. sativa salt-sensitive and salt-tolerant landraces, respectively. This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica, or from different haplotypes selected during domestication. Predominance of specific HKT1;5 haplotypes within the 3 000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.     

Chromosome Segment Substitution Lines: A Powerful Tool for the Introgression of Valuable Genes from Oryza Wild Species into Cultivated Rice (O. sativa)

Wild species of rice (genus Oryza) contain many useful genes but a vast majority of these genes remain untapped to date because it is often difficult to transfer these genes into cultivated rice (Oryza sativa L.). Chromosome segment substitution lines (CSSLs) and backcross inbred lines (BILs) are powerful tools for identifying these naturally occurring, favorable alleles in unadapted germplasm. In this paper, we present an overview of the research involving CSSLs and BILs in the introgression of quantitative trait loci (QTLs) associated with the improved performance of rice including resistance to various biotic and abiotic stresses, and even high yield from wild relatives of rice and other unadapted germplasm into the genetic background of adapted rice cultivars. The CSSLs can be used to dissect quantitative traits into the component genetic factors and evaluate gene action as single factors (monogenic loci). CSSLs have the potential to uncover new alleles from the unadapted, non-productive wild rice accessions, develop genome-wide genetic stocks, and clone genes identified in QTL studies for functional genomics research. Recent development of high-density single-nucleotide polymorphism (SNP) arrays in rice and availability of custom-designed medium- and low-density SNP arrays will enhance the CSSL development process with smaller marker-defined segment introgressions from unadapted germplasm.     

Genetic Variations in Dry Matter Production,Nitrogen Uptake,and Nitrogen Use Efficiency in the AA Genome Oryza Species Grown under Different Nitrogen Conditions

Abstract

To clarify the genotypic variation of nitrogen (N) response in the AA genome Oryza species, we investigated dry matter production, N uptake, N and water use efficiencies (NUE and WUE), bleeding sap rate (BR), and root morphological traits at vegetative stage in 6 cultivars and 4 strains of 6 species (O. sativa, O. glaberrima, O. barthii, O. nivara, O. meridionalis, and O. rufipogon) grown under standard N (SN) and low N (LN) conditions. Some wild Oryza strains and O. glaberrima showed high dry matter production under both N conditions. In most plants, total dry weight decreased and root dry weight increased under the LN condition, resulting in decreased top-root ratio. In japonica cultivars of O. sativa, however, these traits were unaffected by the N condition. There were no significant differences in WUE with plant species or N conditions. In all plants, however, NUE was higher in the LN than SN condition, and was conspicuously high in most wild Oryza species and O. glaberrima. Some of them showed increased capacity of nitrate-N (NO₃-N) uptake under the LN condition. In cultivars and strains with a high NUE, root dry weight, root surface area, and BR were also higher under the LN condition. These results suggest that a high NUE is associated with the development of a root system, increased BR, and probably increased capacity of NO₃-N uptake. This study revealed the presence of superior wild Oryza strains for growth under LN that may be a promising genetic resource for low N-input agriculture.     

Biodiversity of the genus Cladophialophora

Cladophialophora is a genus of black yeast-like fungi comprising a number of clinically highly significant species in addition to environmental taxa. The genus has previously been characterized by branched chains of ellipsoidal to fusiform conidia. However, this character was shown to have evolved several times independently in the order Chaetothyriales. On the basis of a multigene phylogeny (nucLSU, nucSSU, RPB1), most of the species of Cladophialophora (including its generic type C. carrionii) belong to a monophyletic group comprising two main clades (carrionii- and bantiana-clades). The genus includes species causing chromoblastomycosis and other skin infections, as well as disseminated and cerebral infections, often in immunocompetent individuals. In the present study, multilocus phylogenetic analyses were combined to a morphological study to characterize phenetically similar Cladophialophora strains. Sequences of the ITS region, partial Translation Elongation Factor 1-α and β-Tubulin genes were analysed for a set of 48 strains. Four novel species were discovered, originating from soft drinks, alkylbenzene-polluted soil, and infected patients. Membership of the both carrionii and bantiana clades might be indicative of potential virulence to humans.Taxonomic novelties: Cladophialophora samoënsis Badali, de Hoog & Padhye, sp. nov., Cladophialophora subtilis Badali & de Hoog, sp. nov., Cladophialophora mycetomatis Badali, de Hoog & Bonifaz, sp. nov., Cladophialophora immunda Badali, Satow, Prenafeta-Boldú, Padhye & de Hoog, sp. nov.     

An in planta, Agrobacterium-mediated transient gene expression method for inducing gene silencing in rice (Oryza sativa L.) leaves

Background

Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.

Results

From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.

Conclusions

Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.     

The Endosperm Morphology of Rice and its Wild Relatives as Observed by Scanning Electron Microscopy

While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspecies japonica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remaining Oryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.     

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.     

Global distribution of rice weeds – A review

This review provides an overview on the most common rice weed species of the world. It shows that a few generalists have established in rice independent from sites, crop management systems, and local climatic conditions. Cosmopolitan weeds are even constant elements where rice cultivation started just a century ago. Local differences may be explained by cultivation methods, growing seasons, or special weed management. Some general changes in weed spectra have been observed globally in recent years. Weedy rice (Oryza sativa L.) and herbicide resistance have become general global problems within the last decades. Some global key weed genera such as Echinochloa, Cyperus, Scirpus, or Fimbristylis species are, however, still dominating rice fields despite the decade long use of well performing herbicides. On the other side, general species shifts as a result of resistance have not been observed yet. Leptochloa species started to become major problems in Asia in the end of the last century and now in Europe also. Several modern herbicides allow the control of perennial weeds, such as Cyperus rotundus L. or Eleocharis kuroguwai Ohwi which makes them no longer serious threats. Some genera in rice such as Echinochloa and Oryza (weedy rice) are characterized by an enormous germplasm variability which makes species definitions difficult. The fact that weeds in rice have to adapt to wet or aquatic conditions reduces the biodiversity range in comparison to other arable crops. Water management has a considerable impact on weed spectra. The increase of rice acreages with reduced irrigation may end up in higher weed infestations. Long term results of weed surveys in rice as they exist for other crops are, however, not available. This makes predictions on biodiversity changes in this crop quite difficult.