Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed

BACKGROUND

Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood.

RESULTS

We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures. Genome types of rice contributed to compositional variations of both communities, showing a significant phylosymbiosis with microbial composition. Following the domestication, abundance inequality of bacterial and fungal communities also commonly increased. However, composition of bacterial community was relatively conserved, whereas fungal membership was dramatically changed. These domestication effects were further corroborated when analyzed by a random forest model. With these changes, hub taxa of inter-kingdom networks were also shifted from fungi to bacteria by domestication. Furthermore, maternal inheritance of microbiota was revealed as a major path of microbial transmission across generations.

CONCLUSIONS

Our findings show that evolutionary processes stochastically affect overall composition of microbial communities, whereas dramatic changes in environments during domestication contribute to assembly of microbiotas in deterministic ways in rice seed. This study further provides new insights on host evolution and microbiome, the starting point of the holobiome of plants, microbial communities, and surrounding environments.

Transcriptome Profiling of the Rice Blast Fungus Magnaporthe oryzae and Its Host Oryza sativa During Infection

The rice blast (fungal pathogen: Magnaporthe oryzae and host: Oryza sativa) is one of the most important model pathosystems for understanding plant-microbe interactions. Although both genome sequences were published as the first cases of pathogen and host, only a few in planta transcriptome data during infection are available. Due to technical difficulties, previously reported fungal transcriptome data are not highly qualified to comprehensively profile the expression of fungal genes during infection. Here, we report the high-quality transcriptomes of M. oryzae and rice during infection using a sheath infection-based RNA sequencing approach. This comprehensive expression profiling of the fungal pathogen and its host will provide a better platform for understanding the plant-microbe interactions at the genomic level and serve as a valuable resource for the research community.

Evolution of the Genes Encoding Effector Candidates Within Multiple Pathotypes of Magnaporthe oryzae

Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.

Clinical Impact of a Protocolized Kidney Donor Follow-up System

BACKGROUND

Adequate kidney donor management after donation is increasingly emphasized due to concerns of renal function impairment after nephrectomy with increasing life expectancy. In this study, the clinical impact of a protocolized kidney donor follow-up system by nephrologists was evaluated.

METHODS

A total of 427 living kidney donors underwent nephrectomy from January 2010 to December 2014 and were followed for at least 2 years at the Samsung Medical Center. Donors were followed-up by nephrologists after the establishment of a donor clinic with systemized protocols in January 2013. The primary outcomes were incidence of post-donation low estimated glomerular filtration rate (eGFR) and renal function adaptability. Secondary outcomes were changes in compliance and incidence of hyperuricemia and microalbuminuria.

RESULTS

The patients were divided into 2 groups according to the time of nephrectomy: the pre-donor clinic period (n = 182) and the donor clinic period (n = 172). Preoperative eGFR in patients in the pre-donor clinic period was higher than that in patients in the donor clinic period. After donation, poor renal adaptation was less frequent in the donor clinic period compared to the pre-donor clinic period. Low eGFR tended to be less common during the donor clinic period. Shorter mean outpatient clinic visit intervals with more visits within 6 months after donation and earlier detection of de novo hyperuricemia were found during the donor clinic period.

CONCLUSION

A protocolized donor clinic run by nephrologists may improve post-nephrectomy renal outcomes and compliance and facilitate better management of potential risk factors of chronic kidney disease in donors.

Betulinic acid inhibits high-fat diet-induced obesity and improves energy balance by activating AMPK

BACKGROUND AND AIM

Metabolic syndromes are prevalent worldwide and result in various complications including obesity, cardiovascular disease and type II diabetes. Betulinic acid (BA) is a naturally occurring triterpenoid that has anti-inflammatory properties. We hypothesized that treatment with BA may result in decreased body weight gain, adiposity and hepatic steatosis in a diet-induced mouse model of obesity.

METHODS AND RESULTS

Mice fed a high-fat diet and treated with BA showed less weight gain and tissue adiposity without any change in calorie intake. Gene expression profiling of mouse tissues and cell lines revealed that BA treatment increased expression of lipid oxidative genes and decreased that of lipogenesis-related genes. This modulation was mediated by increased AMP-activated protein kinase (AMPK) phosphorylation, which facilitates energy expenditure, lipid oxidation and thermogenic capacity and exerts protective effects against obesity and nonalcoholic fatty liver disease. Overall, BA markedly inhibited the development of obesity and nonalcoholic fatty liver disease in mice fed a high-fat diet, and AMPK activation in various tissues and enhanced thermogenesis are two possible mechanisms underlying the antiobesity and antisteatogenic effects of BA.

CONCLUSIONS

The current findings suggest that treatment with BA is a potential dietary strategy for preventing obesity and nonalcoholic fatty liver disease.

A High-Quality Draft Genome Sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a Causal Agent of Anthracnose on Cunninghamia lanceolata in China

Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts.

Genomic comparisons of the laurel wilt pathogen, Raffaelea lauricola, and related tree pathogens highlight an arsenal of pathogenicity related genes

Raffaelea lauricola is an invasive fungal pathogen and symbiont of the redbay ambrosia beetle (Xyleborus glabratus) that has caused widespread mortality to redbay (Persea borbonia) and other Lauraceae species in the southeastern USA. We compare two genomes of R. lauricola (C2646 and RL570) to seven other related Ophiostomatales species including R. aguacate (nonpathogenic close relative of R. lauricola), R. quercus-mongolicae (associated with mortality of oaks in Korea), R. quercivora (associated with mortality of oaks in Japan), Grosmannia clavigera (cause of blue stain in conifers), Ophiostoma novo-ulmi (extremely virulent causal agent of Dutch elm disease), O. ulmi (moderately virulent pathogen that cause of Dutch elm disease), and O. piceae (blue-stain saprophyte of conifer logs and lumber). Structural and functional annotations were performed to determine genes that are potentially associated with disease development. Raffaelea lauricola and R. aguacate had the largest genomes, along with the largest number of protein-coding genes, genes encoding secreted proteins, small-secreted proteins, ABC transporters, cytochrome P450 enzymes, CAZYmes, and proteases. Our results indicate that this large genome size was not related to pathogenicity but was likely lineage specific, as the other pathogens in Raffaelea (R. quercus-mongolicae and R. quercivora) had similar genome characteristics to the Ophiostoma species. A diverse repertoire of wood-decaying enzymes were identified in each of the genomes, likely used for toxin neutralization rather than wood degradation. Lastly, a larger number of species-specific, secondary metabolite, synthesis clusters were identified in R. lauricola suggesting that it is well equipped as a pathogen, which could explain its success as a pathogen of a wide range of lauraceous hosts.

Role of the Histone Acetyltransferase Rtt109 in Development and Pathogenicity of the Rice Blast Fungus

Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated the implications of Rtt109-mediated response to DNA damage on development and pathogenesis of the rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog of Rtt109 in M. oryzae (MoRtt109) was found via sequence homology and its functionality was confirmed by phenotypic complementation of the Saccharomyces cerevisiae Rtt109 deletion strain. Targeted deletion of MoRtt109 resulted in a significant reduction in acetylation of H3K56 and rendered the fungus defective in hyphal growth and asexual reproduction. Furthermore, the deletion mutant displayed hypersensitivity to genotoxic agents, confirming the conserved importance of Rtt109 in genome integrity maintenance and genotoxic stress tolerance. Elevated expression of DNA repair genes and the results of the comet assay were consistent with constitutive endogenous DNA damage. Although the conidia produced from the mutant were not impaired in germination and appressorium morphogenesis, the mutant was significantly less pathogenic on rice leaves. Transcriptomic analysis provided insight into the factors underlying phenotypic defects that are associated with deficiency of H3K56 acetylation. Overall, our results indicate that MoRtt109 is a conserved histone acetyltransferase that affects proliferation and asexual fecundity of M. oryzae through maintenance of genome integrity and response to DNA damage.

Trends of Colorectal Cancer Incidence in Thailand by Age, Gender, and Region

Background: Colorectal cancer (CRC) is the third most common cancer in the world. While CRC incidence has decreased in many western countries over the last decades, largely thanks to screening, it is increasing in low and middle-income countries, including Thailand. However, it is unclear if these increases are consistent across different regions, gender and age groups. Aim: To understand the age-, gender- and region-specific temporal variation in CRC incidence in Thailand since the 1990s. Methods: We analyzed CRC incidence data from the Thailand National Cancer Network (TCIN) cancer registries, which include Chiang Mai (1990-2012), Lampang (1993-2014), Lopburi (2000-2014), Khon Kaen (1990-2014) and Songkhla (1990-2014) cancer registries. Trends in age-adjusted incidence (measured by annual percentage change (APC)) were assessed using Joinpoint regression. Trends by birth-year and calendar-year were assessed using age-period-cohort models. All analyses were done by region, gender, and age group (30-49, 50-84, 30-84). Results: CRC incidence has been increasing significantly in all regions, gender, and age groups; Overall, the APC was 3.82 for men and 3.84 for women (Chiang Mai, 4.34 for men & 3.26 for women; Khon Kaen, 2.69 for men & 3.68 for women; Lampang, 2.13 for men & 3.37 for women; Lopburi, 5.31 for men & 4.67 for women; Songkhla, 4.67 for men & 4.32 for women). The increase in incidence was higher for ages 50-84 (APC = 3.99 for men & 4.04 for women) compared with ages 30-49 (APC=2.97 for men & 3.09 for women). Test of parallelism suggests that increases are consistent between gender (P-value=0.97). The age-period-cohort analysis suggests that both calendar-year and birth-year are strongly correlated with CRC incidence trends, with a stronger relationship with birth-year than calendar-year for both genders. Conclusion: In contrast to western countries such as the US, CRC incidence is increasing across all age groups in Thailand, with faster increase in older ages. This highlights the needs for establishing population-wide screening programs to reduce the burden and stop the rise of CRC in Thailand and low-middle income countries.

Nanoconfinement effects of chemically reduced graphene oxide nanoribbons on poly(vinyl chloride)

Polymeric nanocomposites with graphene-based nanocarbons (GNCs) have been extensively studied with emphasis on the percolation of nanofillers toward electrical, rheological, and mechanical reinforcement. In this study, we report an unusual indirect reinforcing phenomenon of highly defective GNCs dispersed in the poly(vinyl chloride) (PVC) matrix via densification of the polymer packing originating from nanoscale confinement. Herein, chemically reduced graphene oxide nanoribbons (C-rGONRs) are employed as a nanofiller. The inclusion of defective and oxygen-functionalized C-rGONRs resulted in a dramatic densification of the PVC host with extremely low C-rGONR loading, largely exceeding the theoretical calculation from a rule of mixture. Along with the densification, the glass transition temperature of PVC also increased by 28.6 °C at 0.1 wt% filler loading. Remarkably, the oxygen barrier property and mechanical toughness under tension for the PVC/C-rGONR nanocomposite were the maximum when the greatest densification occurred. The structure-property relationship of the nanocomposites has been discussed with an emphasis on the nanoscale confinement phenomenon.

Electron beam induced tunneling magnetoresistance in spatially confined manganite bridges

Certain manganites exhibit rich and technologically relevant transport properties which can often be attributed to the existence and changes of the intrinsic electronic phase competition within these materials. Here we demonstrate that a scanning electron beam can be used to artificially create domain configurations within La_0.3Pr_0.4Ca_0.3MnO₃ thin film microbridges that results in novel magneto-transport effects. In particular, the electron beam preferentially produces insulating regions within the narrow film and can be used to create a configuration consisting of ferromagnetic metallic domains separated by a potential barrier. This arrangement enables the spin-dependent tunneling of charge carriers and can produce large switching tunneling magnetoresistance effects which were initially absent. Hence, this work describes a new and potentially powerful method for engineering the electronic phase domains in manganites to generate functional transport properties that are important for spintronic devices.

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Background

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.

Results

We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.

Conclusions

Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

BACKGROUND

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.

RESULTS

We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.

CONCLUSIONS

Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s

The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.