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July 7, 2019

Oryza rufipogon Griff.

Oryza rufipogon, the progenitor of present-day cultivated rice, O. sativa, is one of the most studied wild species of rice. It is a perennial plant commonly found in a marsh or aquatic habitats of eastern and southern Asia. It has partial outcrossing behavior and is photoperiod sensitive. The flowering time usually ranges between September and November. It has been and is being exploited as a source of valuable genes and QTLs for yield components as well as resistance against biotic and abiotic stresses. A number of populations like chromosome segment substitution lines, backcross inbred lines, near-isogenic lines, and recombinant inbred lines have been developed from crosses between O. rufipogon and O. sativa as a prebreeding resource. These are being employed for broadening the genetic base of cultivated rice and diversify the breeder’s pool. With the advent of sequencing technologies, a number of phylogenetic studies have been conducted to reveal the evolutionary relationship of O. rufipogon with cultivated rice O. sativa. Further, transcriptomic studies characterizing the effect of various abiotic stresses have been conducted on this wild species. Role of miRNA under stress reaction has also been studied. Though the genetic, genomic, and transcriptomic resources are abundant, the proteomic resources for O. rufipogon are limited.

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July 7, 2019

Oryza meridionalis NQ Ng

Oryza meridionalis is an AA genome species found in Northern Australia. Phylogenetic analysis places this as the most distant of the AA genome species from domesticated rice (Oryza sativa). This makes it a key genetic resource for rice improvement. A draft nuclear genome sequence is available, and also the chloroplast genome has been sequenced from many genotypes. The high amylose starch content in these taxa may be useful for developing new rice grain characteristics. Here we have reviewed the all the research advancements that are made till today on this species.

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July 7, 2019

Oryza glaberrima Steud.

Oryza glaberrima is the African cultivated rice species, domesticated from its wild ancestor by farmers living in Inland Delta of Niger River. Several studies indicated that it has extremely narrow genetic diversity compared to both its wild progenitor, Oryza barthii and the Asian rice, Oryza sativa which can mainly be attributed to a severe domestication bottleneck. Despite its scarcity in farmer’s field due to its low yield potential, high shattering and lodging susceptibility, O. glaberrima is of great value not only to Africa but also globally. Perhaps its greatest contribution to regional and global food security is as a source of genes, as it possesses resistance/tolerance to various biotic and abiotic stresses. It also has unique starch-related traits which give it good cooking and eating properties. Advances in DNA sequencing have provided useful genomic resources for African rice, key among them being whole genome sequences. Genomic tools are enabling greater understanding of the useful functional diversity found in this species. These advances have potential of addressing some of the undesirable attributes found in this species which have led to its continued replacement by Asian rice. Development of new generation of rice varieties for African farmers will therefore require the adoption of advanced molecular breeding tools as these will allow efficient utilization of the wealth and resilience found in African rice in rice improvement.

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July 7, 2019

Paucibacter aquatile sp. nov. isolated from freshwater of the Nakdong River, Republic of Korea.

A Gram-negative, aerobic, motile, and rod-shaped bacterial strain designated CR182T was isolated from freshwater of the Nakdong River, Republic of Korea. Optimal growth conditions for this novel strain were found to be: 25-30 °C, pH 6.5-8.5, and 3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicates that the strain CR182T belongs to type strains of genus Paucibacter. Strain CR182T showed 98.0% 16S rRNA gene sequence similarity with Paucibacter oligotrophus CHU3T and formed a robust phylogenetic clade with this species. The average nucleotide identity value between strain CR182T and P. oligotrophus CHU3T was 78.4% and the genome-to-genome distance was 22.2% on average. The genomic DNA G+C content calculated from the genome sequence was 66.3 mol%. Predominant cellular fatty acids of strain CR182T were summed feature 3 (C16:1 ?7c and/or C16:1 ?6c) (31.2%) and C16:0 (16.0%). Its major respiratory quinine was ubiquinone Q-8. Its polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, and two unidentified phospholipids. Its genomic DNA G+C content was 66.3%. Based on data obtained from this polyphasic taxonomic study, strain CR182T represents a novel species belonging to genus Paucibacter, for which a name of P. aquatile sp. nov. is proposed. The type strain is CR182T (=?KCCM 90284T?=?NBRC 113032T).

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July 7, 2019

Supergene evolution triggered by the introgression of a chromosomal inversion.

Supergenes are groups of tightly linked loci whose variation is inherited as a single Mendelian locus and are a common genetic architecture for complex traits under balancing selection [1-8]. Supergene alleles are long-range haplotypes with numerous mutations underlying distinct adaptive strategies, often maintained in linkage disequilibrium through the suppression of recombination by chromosomal rearrangements [1, 5, 7-9]. However, the mechanism governing the formation of supergenes is not well understood and poses the paradox of establishing divergent functional haplotypes in the face of recombination. Here, we show that the formation of the supergene alleles encoding mimicry polymorphism in the butterfly Heliconius numata is associated with the introgression of a divergent, inverted chromosomal segment. Haplotype divergence and linkage disequilibrium indicate that supergene alleles, each allowing precise wing-pattern resemblance to distinct butterfly models, originate from over a million years of independent chromosomal evolution in separate lineages. These “superalleles” have evolved from a chromosomal inversion captured by introgression and maintained in balanced polymorphism, triggering supergene inheritance. This mode of evolution involving the introgression of a chromosomal rearrangement is likely to be a common feature of complex structural polymorphisms associated with the coexistence of distinct adaptive syndromes. This shows that the reticulation of genealogies may have a powerful influence on the evolution of genetic architectures in nature. Copyright © 2018 Elsevier Ltd. All rights reserved.

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July 7, 2019

The complete genome sequence of Colwellia sp. NB097-1 reveals evidence for the potential genetic basis for its adaptation to cold environment

Colwellia sp. NB097-1, isolated from a marine sediment sample from the Bering Sea, is a psychrophilic bacterium whose optimal and maximal growth temperatures were 13 and 25°C, respectively. Here, we present the complete genome of Colwellia sp. NB097-1, which was 4,661,274bp in length with a GC content of 38.5%. The genome provided evidence for the potential genetic basis for its adaptation to a cold environment, such as producing compatible solutes and cold-shock proteins, increasing membrane fluidity and synthesizing glycogen. Some cold-adaptive proteases were also detected in the genome of Colwellia sp. NB097-1. Protease activity analysis further showed that extracellular proteases of Colwellia sp. NB097-1 remained active at low temperatures. The complete genome sequence may be helpful to reveal how this strain survives at low temperature and to find cold-adaptive proteases that may be useful to industry.

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July 7, 2019

Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater

Here we present the complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1T, a flavobacterium isolated from coastal surface seawater. A 3.3Mb genome revealed remarkable specialization of this bacterium particularly in the degradation of sulfated polysaccharides available as detritus or in dissolved phase. Besides utilizing high molecular weight organic biopolymers, this strain appears to accomplish assimilatory sulfate reduction, sulfide oxidation, and acquisition and inter-conversion of inorganic carbon. Genes encoding zeaxanthin and three different kinds of DNA photolyase/cryptochrome (senses blue light) were present, while genes that code for blue light sensing BLUF domain proteins and red/far-red light sensing phytochromes were absent. Furthermore, CC-SAMT-1T lacked the rhodopsin photosystem and all other genes that confer any other known forms of phototrophy. The genomic data revealed that CC-SAMT-1T is highly adapted to sulfur-rich coastal environments, where it most likely contributes to marine carbon and sulfur cycles by metabolizing sulfated polysaccharides as well as inorganic sulfur.

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July 7, 2019

Complete genomes of the marine flavobacterium Nonlabens strains YIK11 and MIC269

Here, we report the complete genome sequences of two strains, which were isolated from sediment samples collected in Korea and Micronesia, and both were classified as members of Nonlabens spp. The complete genome sequence of Nonlabens sp. strain YIK11 consists of 3,260,677bp in two contigs while the one from strain MIC269 consists of 2,884,293bp in one contig, without plasmid. The genomes of YIK11 and MIC269 contain three and two genes encoding rhodopsins of different types, respectively.

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July 7, 2019

Complete genome sequence of Granulosicoccus antarcticus type strain IMCC3135T, a marine gammaproteobacterium with a putative dimethylsulfoniopropionate demethylase gene

Granulosicoccus, the only genus of the family Granulosicoccaceae, occupies a distinct phylogenetic position within the order Chromatiales of the Gammaproteobacteria. The genus has been found in various marine regions, especially associated with diverse marine macroalgae. No genomes have been reported for the genus Granulosicoccus thus far, hampering studies on physiology and lifestyles of this genus. Here we report the complete genome sequence of strain IMCC3135T, the type strain of Granulosicoccus antarcticus isolated from Antarctic coastal seawater. The genome was 7.78Mbp long and harbored many genes involved in sulfur metabolism. In particular, a gene for dimethylsulfoniopropionate (DMSP) demethylase was found in the genome, rendering strain IMCC3135T one of the few marine gammaproteobacteria equipped with the potential for DMSP demethylation.

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July 7, 2019

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19?Mbp with a 62.45% G?+?C content. The chromosome harbours several metabolic pathways providing a wide catabolic potential, where the upper biphenyl route is described. Also, Rhodococcus sp. H-CA8f bears one linear mega-plasmid of 301?Kbp and 62.34% of G?+?C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. These genetic characteristics provide relevant insights regarding Chilean marine actinobacterial strains.

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July 7, 2019

Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS-derived antibiotics: a perspective.

Combinatorial biosynthesis of novel secondary metabolites derived from nonribosomal peptide synthetases (NRPSs) has been in slow development for about a quarter of a century. Progress has been hampered by the complexity of the giant multimodular multienzymes. More recently, advances have been made on understanding the chemical and structural biology of these complex megaenzymes, and on learning the design rules for engineering functional hybrid enzymes. In this perspective, I address what has been learned about successful engineering of complex lipopeptides related to daptomycin, and discuss how synthetic biology and microbial genome mining can converge to broaden the scope and enhance the speed and robustness of combinatorial biosynthesis of NRPS-derived natural products for drug discovery.

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July 7, 2019

Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases.

Contents Summary 45 I. Introduction 45 II. Targeted chromosome-based cloning via long-range assembly (TACCA) 46 III. Resistance gene cloning through mutational mapping (MutMap) 47 IV. Cloning through mutant chromosome sequencing (MutChromSeq) 47 V. Rapid cloning through resistance gene enrichment and sequencing (RenSeq) 49 VI. Cloning resistance genes through transcriptome profiling (RNAseq) 49 VII. Resistance gene deployment strategies 49 VIII. Conclusions 50 Acknowledgements 50 References 50 SUMMARY: Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.© 2017 Commonwealth of Australia. New Phytologist © 2017 New Phytologist Trust.

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July 7, 2019

Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05.

Ralstonia solanacearum is a soil-borne phytopathogen associated with bacterial wilt disease of sesame. R. solanacearum is the predominant agent causing damping-off from tropical to temperate regions. Because bacterial wilt has decreased the sesame industry yield, we sequenced the SEPPX05 genome using PacBio and Illumina HiSeq 2500 systems and revealed that R. solanacearum strain SEPPX05 carries a bipartite genome consisting of a 3,930,849 bp chromosome and a 2,066,085 bp megaplasmid with 66.84% G+C content that harbors 5,427 coding sequences. Based on the whole genome, phylogenetic analysis showed that strain SEPPX05 is grouped with two phylotype I strains (EP1 and GMI1000). Pan-genomic analysis shows that R. solanacearum is a complex species with high biological diversity and was able to colonize various environments during evolution. Despite deletions, insertions, and inversions, most genes of strain SEPPX05 have relatively high levels of synteny compared with strain GMI1000. We identified 104 genes involved in virulence-related factors in the SEPPX05 genome and eight absent genes encoding T3Es of GMI1000. Comparing SEPPX05 with other species, we found highly conserved secretion systems central to modulating interactions of host bacteria. These data may provide important clues for understanding underlying pathogenic mechanisms of R. solanacearum and help in the control of sesame bacterial wilt.

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July 7, 2019

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies.

Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a saprotrophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on host-microbiome interactions.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

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July 7, 2019

Complete genome sequence of multiple-antibiotic-resistant Streptococcus parauberis strain SPOF3K, isolated from diseased olive flounder (Paralichthys olivaceus).

Here, we report the complete genome sequence of multiple-antibiotic-resistant Streptococcus parauberis strain SPOF3K, isolated from the kidney of a diseased olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded a circular chromosome of 2,128,740?bp and a plasmid of 23,538?bp, harboring 2,123 and 24 protein-coding genes, respectively. Copyright © 2018 Lee et al.

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