MSI4/FVE is required for accumulation of 24-nt siRNAs and DNA methylation at a subset of target regions of RNA-directed DNA methylation.

DNA methylation is an important epigenetic mark. In plants, de novo DNA methylation occurs mainly through the RNA-directed DNA methylation (RdDM) pathway. Researchers have previously inferred that a flowering regulator, MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE, is involved in non-CG methylation at several RdDM targets, suggesting a role of FVE in RdDM. However, whether and how FVE affects RdDM genome-wide is not known. Here, we report that FVE is required for DNA methylation at thousands of RdDM target regions. In addition, dysfunction of FVE significantly reduces 24-nucleotide siRNA accumulation that is dependent on factors downstream in the RdDM pathway. By using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that FVE directly binds to FVE-dependent 24-nucleotide siRNA cluster regions. Our results also indicate that FVE may function in RdDM by physically interacting with RDM15, a downstream factor in the RdDM pathway. Our study has therefore revealed that FVE, by associating with RDM15, directly regulates DNA methylation and siRNA accumulation at a subset of RdDM targets.

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus).

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.

A novel protein complex that regulates active DNA demethylation in Arabidopsis.

Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1 000s of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo. Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.

Roles of DEMETER in regulating DNA methylation in vegetative tissues and pathogen resistance.

DNA methylation is an epigenetic mark important for genome stability and gene expression. In Arabidopsis thaliana, the 5-methylcytosine DNA glycosylase/demethylase DEMETER (DME) controls active DNA demethylation during the reproductive stage; however, the lethality of loss-of-function dme mutations has made it difficult to assess DME function in vegetative tissues. Here, we edited DME using clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein 9 and created three weak dme mutants that produced a few viable seeds. We also performed central cell-specific complementation in a strong dme mutant and combined this line with mutations in the other three Arabidopsis demethylase genes to generate the dme ros1 dml2 dml3 (drdd) quadruple mutant. A DNA methylome analysis showed that DME is required for DNA demethylation at hundreds of genomic regions in vegetative tissues. A transcriptome analysis of the drdd mutant revealed that DME and the other three demethylases are important for plant responses to biotic and abiotic stresses in vegetative tissues. Despite the limited role of DME in regulating DNA methylation in vegetative tissues, the dme mutants showed increased susceptibility to bacterial and fungal pathogens. Our study highlights the important functions of DME in vegetative tissues and provides valuable genetic tools for future investigations of DNA demethylation in plants.

A comparative transcriptomic study on developmental gonads provides novel insights into sex change in the protandrous black porgy (Acanthopagrus schlegelii).

Protandrous black porgy (Acanthopagrus schlegelii) is a popular and valuable commercial marine fish in China and East Asian countries. Controlling and managing its breeding has been an imperative step towards obtaining a sustainable supply of this fish in aquaculture production systems. Therefore, study on the molecular mechanisms of sex change in black porgy has both scientific and commercial importance. Previously, we identified some candidate genes related to sex determination and differentiation from a high-quality genome assembly of the black porgy. In the present study, transcriptome sequencing of developmental gonads (including testis, ovotestis and ovary) of black porgy was performed to further investigate the sex-change mechanisms. Our results showed that the highly expressed male-related genes (dmrt1, piwi1, piwi2, sox9, sox30 and amh) at the male phase were significantly down-regulated to a substantial degree at the intersexual stage, and the female-related genes (jnk1, vasa, wnt4, figla and foxl2) were distinctly up-regulated when the fish grows into a female adult, suggesting the potential roles of these genes in sex change of the black porgy. These data also support a previous hypothesis that the femaleness will be switched on when the testis is entering the degenerated stage through the diminished dmrt1 expression. Our transcriptome data provide a very useful genomic resource for future studies on sex change and practical aquaculture in the black porgy.

Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias.

Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes.

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

The first Conus genome assembly reveals a primary genetic central dogma of conopeptides in C. betulinus.

Although there are various Conus species with publicly available transcriptome and proteome data, no genome assembly has been reported yet. Here, using Chinese tubular cone snail (C. betulinus) as a representative, we sequenced and assembled the first Conus genome with original identification of 133 genome-widely distributed conopeptide genes. After integration of our genomics, transcriptomics, and peptidomics data in the same species, we established a primary genetic central dogma of diverse conopeptides, assuming a rough number ratio of ~1:1:1:10s for the total genes: transcripts: proteins: post-translationally modified peptides. This ratio may be special for this worm-hunting Conus species, due to the high diversity of various Conus genomes and the big number ranges of conopeptide genes, transcripts, and peptides in previous reports of diverse Conus species. Only a fraction (45.9%) of the identified conotopeptide genes from our achieved genome assembly are transcribed with transcriptomic evidence, and few genes individually correspond to multiple transcripts possibly due to intraspecies or mutation-based variances. Variable peptide processing at the proteomic level, generating a big diversity of venom conopeptides with alternative cleavage sites, post-translational modifications, and N-/C-terminal truncations, may explain how the 133 genes and ~123 transcripts can generate thousands of conopeptides in the venom of individual C. betulinus. We also predicted many conopeptides with high stereostructural similarities to the putative analgesic ω-MVIIA, addiction therapy AuIB and insecticide ImI, suggesting that our current genome assembly for C. betulinus is a valuable genetic resource for high-throughput prediction and development of potential pharmaceuticals.

A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping.

The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing. In this research, 261,366 single nucleotide polymorphisms (SNPs) were developed, in which 110 SNPs were identified to be correlated with growth and 20 SNPs were further confirmed to be associated with both body weight and total length. From these identified SNPs, we annotated a total of 34 genes, including adgrb2, csnkza1, cers5, col22a1, creb5, dnd1, dzank1, dnai1, npy2r, fat3, lrrk2, lrp5, map3k9, and so on. Among these candidate genes, npy2r (neuropeptide Y receptor Y2) was reported to play a critical role in growth of the orange-spotted grouper. In addition, population structure, principal component analysis, kinship matrix and linkage disequilibrium were examined to verify the accuracy and reliability of our GWAS results. Our data will also provide a valuable genetic resource for further marker-assisted selection program to improve growth quality in groupers.

Effect of Chromium on Corrosion Behavior of P110 Steels in CO2-H2S Environment with High Pressure and High Temperature.

The novel Cr-containing low alloy steels have exhibited good corrosion resistance in CO2 environment, mainly owing to the formation of Cr-enriched corrosion film. In order to evaluate whether it is applicable to the CO2 and H2S coexistence conditions, the corrosion behavior of low-chromium steels in CO2-H2S environment with high pressure and high temperature was investigated using weight loss measurement and surface characterization. The results showed that P110 steel suffered localized corrosion and both 3Cr-P110 and 5Cr-P110 steels exhibited general corrosion. However, the corrosion rate of 5Cr-P110 was the highest among them. The corrosion process of the steels was simultaneously governed by CO2 and H2S. The outer scales on the three steels mainly consisted of FeS1-x crystals, whereas the inner scales on Cr-containing steels comprised of amorphous FeS1-x, Cr(OH)3 and FeCO3, in contrast with the amorphous FeS1-x and FeCO3 mixture film of P110 steel. The more chromium the steel contains, the more chromium compounds the corrosion products contain. The addition of chromium in steels increases the uniformity of the Cr-enriched corrosion scales, eliminates the localized corrosion, but cannot decrease the general corrosion rates. The formation of FeS1-x may interfere with Cr-enriched corrosion scales and lowering the corrosion performance of 3Cr-P110 and 5Cr-P110 steels.

Culturable airborne fungi in outdoor environments in Beijing, China.

Airborne fungi are being proposed as a cause of adverse health effects. They may adversely affect human health through allergy, infection, and toxicity. Moreover, they have a great influence on urban air quality in Beijing. In this study, a systematical survey on the culturable airborne fungi was carried out for 1 year in Beijing urban area. Fungal samples were collected for 3 min, three times each day, and continued for three consecutive days of each month with FA-1 sampler from three sampling sites. Results showed that the culturable fungal concentrations ranged from 24 CFU (Colony forming units) /m3 to 13960 CFU/m3, and the mean and median was 1165 CFU/m3 and 710 CFU/m3, respectively. Fungal concentrations in the greener area around the Research Center for Eco-Environmental Sciences (RCEES) and Beijing Botanical Garden (BBG) were significantly higher than in the densely urban and highly trafficked area of Xizhimen (XZM) (***P<0.001), but no significant difference was found between RCEES and BBG (P>0.05). The variation of fungal concentrations in different seasons was significant in RCEES and BBG, where the concentrations were higher in Summer and Autumn, and lower in Spring and Winter. However, there were no significant differences in fungal concentrations between the Spring and the Winter for three sampling sites (P>0.05). Fourteen genera, including 40 species of culturable fungi, were identified in this study. Penicillium, with the most abundant species, which comprised more than 50% of the total isolated fungal species. Cladosporium were the most dominant fungal group, and contributed to more than one third of the total fungal concentration, followed by non-sporing isolates, Alternaria, Pencillium and Asperigillus. The concentration percentage of Cladosporium was significantly higher in RCEES than in XZM (*P<0.05), and the concentration percentages of Penicillium (**P<0.01) and Aspergillus (*P<0.05) were higher in XZM than in RCEES and in BBG. For other groups' concentration percentages, no significant differences were observed among the sampling sites. The distribution pattern of airborne fungi presented log-normal distribution. The highest proportion of culturable fungi was detected in stage 4 (2.0-3.5 microm), and the lowest was in stage 6 (<1.0 microm).

[Ecological distributions of airborne fungi in outdoor environments in Beijing, China].

An investigation on fungal types, concentrations, and their dynamic variation in outdoor environments was carried out in three different functional areas around one year in Beijing. Results show that the fungal concentrations varied widely and the average was (1164.8 +/- 73.2) CFU x m(-3), ranging from 23.6CFU x m(-3) to 13 959.5 CFU x m(-3). The most common culturable airborne fungi in all seasons and all functional areas were Cladosporium , nonsporulating fungi, Alternaria, Penicillium and Aspergillus. The most dominant fungus was Cladosporium, which contributed to more than 1/3 of the total. The fungal levels in culture and education region (CER) and garden green region (GGR) were highest in the fall and summer, and lowest in the winter and spring, while the seasonal variation in main traffic line (MTL) was not significant. The fungal concentrations in CER and GGR were significantly higher than in MTL (p <0.05). No statistically significant difference exists between CER and GGR.

[Granularity distribution of airborne microbes in summer in Beijing].

A study on granularity distribution of airborne microbes was conducted in details in summer, and the fluctuation regular was analyzed in Beijing. Results show that the distribution characteristics which are not changed with the different functional regions and periods are very different among airborne bacteria, fungi and actinomycete. Airborne bacteria appear skew distribution, the particles larger than 2.0 microm account for 80.0% of the total while smaller than 1.0 microm contribute 9.0% approximately. Airborne fungi are recorded with normal logarithm distribution, the particles between 1.0 microm and 6.0 microm account for 70.0% while smaller than 1.0 microm contribute 5.0% approximately. The distribution of airborne actinomycete are completely opposite to fungi, the particles larger than 8.2 microm and smaller than 1.0 microm account for 60.0% while between 3.0 microm and 6.0 microm contribute 10.0% approximately. Moreover, the granularity distribution of dominant fungi is consistent in different functional regions. But Cladosporium, Penicillium and Aspergillus are most collected in F3, F4 and F5 grades (1.0-6.0 microm) while Alternaria and nonsporing most in former four grades (>2.0 microm) of FA-I sampler, contributing 85.0%, 85.0%, 85.0%, 90.0% and 75.0% of the total respectively. The granularity of former presents normal logarithm distribution and latter skew distribution. In the past ten years, it is no change on the trend of microbial granularity distribution in Beijing, but the peak value declines from 3.0-6.0 microm to 2.0-3.0 microm.