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Angelica dahurica is a common species of medicine and food homology, which is not only a common clinical traditional Chinese medicine, but also a spice, with a wide range of uses. In order to obtain the whole genome sequence information of A. dahurica, we used A. dahurica var. formosana leaf DNA as material, and the Nanopore sequencing technology was used to establish its nucleotide sequences database, then genome assembly, function annotation and evolution analysis were carried out by bioinformatic methods. The results were as follows:(1) A total of 662 Gb of the third-generation data were obtained after fittering the original sequencing data, with the Read N50 about 32 932 bp. The assembled A. dahurica genome size was 5.6 Gb, Contig N50 was about 806 638 bp. (2) The genes were with gene annotations accounted for 66.47% after being compared with functional databases such as NR, KOG and KEGG. The result of KOG gene annotation was that the protein function of A. dahurica concentrated in the general functional prediction, posttranslational modification, protein turnover, chaperones and signal transduction mechanisms. GO functional classification indicated that the genes of A. dahurica concentrated on cell biological processes and components. KEGG analysis found that the A. dahurica genes mostly involved in metabolic pathways. (3) And 45 genes of BGLU family were identified in A. dahurica. In this study, the whole genome of A. dahurica is resolved by the third-generation sequencing technology for the first time, which provides important theoretical references for the systematic biological study and the further study of the function of BGLU in the growth and development of A. dahurica.

Angelica dahurica is a common species of medicine and food homology, which is not only a common clinical traditional Chinese medicine, but also a spice, with a wide range of uses. In order to obtain the whole genome sequence information of A. dahurica, we used A. dahurica var. formosana leaf DNA as material, and the Nanopore sequencing technology was used to establish its nucleotide sequences database, then genome assembly, function annotation and evolution analysis were carried out by bioinformatic methods. The results were as follows: (1) A total of 662 Gb of the third-generation data were obtained after fittering the original sequencing data, with the Read N50 about 32 932 bp. The assembled A. dahurica genome size was 5.6 Gb, Contig N50 was about 806 638 bp. (2) The genes were with gene annotations accounted for 66.47% after being compared with functional databases such as NR, KOG and KEGG. The result of KOG gene annotation was that the protein function of A. dahurica concentrated in the general functional prediction, posttranslational modification, protein turnover, chaperones and signal transduction mechanisms. GO functional classification indicated that the genes of A. dahurica concentrated on cell biological processes and components. KEGG analysis found that the A. dahurica genes mostly involved in metabolic pathways. (3) And 45 genes of BGLU family were identified in A. dahurica. In this study, the whole genome of A. dahurica is resolved by the third-generation sequencing technology for the first time, which provides important theoretical references for the systematic biological study and the further study of the function of BGLU in the growth and development of A. dahurica. [ABSTRACT FROM AUTHOR]

It isolated a Gram positive Paenibacillus sp. strain from the soil at an altitude of 3 000 m in the Kalongla Mountains in Mutuo, Tibet. The entire genome of Paenibacillus sp. strain was sequenced by Illumina Hiseq and was annotated with Prokka software (v1. 14. 6). antiSMASH 7. 0 and BAGEL4 were used to predict the secondary metabolites biosynthesis gene cluster in Paenibacillus sp. In order to validate the metabolic pathway, the total strain proteins were extracted by various extraction methods and performed nanoliter liquid chromatography combining with Mass Spectrometry. We could identify a total of 3 383 proteins by using software. Through homologous comparison, there were the N-terminal region of ATP dependent Cysteine protease B1 and ABC transporter in the lasso peptide biosynthesis gene cluster. It was complete by local blast comparison, and Paenibacillus sp. was likely to have the ability to synthesize lasso peptide. Through the above research, we analyed genomic and proteomic information of Paenibacillus sp. [ABSTRACT FROM AUTHOR]

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Copyright of China Brewing is the property of China Brewing Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: The purpose of this study was to investigate the biological characteristics, whole genome, and antibacterial effect of V. parahaemolyticus phage 474x1 in food. Methods: The phage 474x1 was isolated from shrimp purchased from seafood market with V. parahaemolyticus strain 474 as host strain. The morphology of phage 474x1 was observed by transmission electron microscopy. One-step growth curve was determined, and its sensitivity to temperature and pH was assessed. The whole genome sequence of 474x1 was analyzed, and a phylogenetic tree was constructed based on the sequence of large subunit of phage terminase. The inhibitory effect of the phage on V. parahaemolyticus in shrimp meat was evaluated using the total colony count method. Results: A lytic phage against V. parahaemolyticus was isolated which named 474x1, and it could lyse 19 out of 23 strains of V. parahaemolyticus (82.61%). The phage had typical characteristics of a tailed bacteriophage in Myoviridae. The optimal multiplicity of infection (MOI) was 0.01, and the one-step growth curve showed that the latent period of 474x1 was 10 min, and the burst size was 115 PFU/cell. The phage was active over a wide range of temperature (30~60 ℃) and pH (4~11). The whole genome of 474x1 was 47830 bp long, and 69 open reading frames were predicted and annotated, including 14 genes with specific functions. Comparative genomics analysis showed that 474x1 had high homology with Vibrio phage Vp41s3, and phylogenetic analysis also indicated that 474x1 was most closely related to the phage Vp41s3. In the application experiment, the number of bacteria in the experimental group with MOI=1000 at 4 ℃ decreased by 0.39 lgCFU/mL compared to the control group at 3 h, while the experimental group with MOI=10000 at 4 ℃ decreased by 0.92 lgCFU/mL compared to the control group at 12 h. At 25 ℃, the number of bacteria in the MOI=1000 and MOI=10000 groups decreased by 1.04 lgCFU/mL and 1.82 lgCFU/mL at 6 h, respectively. The results indicated that phage 474x1 could significantly inhibit the growth of host bacteria in shrimp meat. Conclusion: A new V. parahaemolyticus phage was isolated from shrimp, which had large burst size, short latent period, and showed good stability below 60 ℃ and tolerated a wide range of pH. In addition, the phage had good bacteriostatic effect in food, laying a foundation for the prevention and control of pathogenic strains of V. parahaemolyticus.

[Objective]To clarify the codon usage characteristics and improve expression efficiency of exogenous genes in sugarcane.[Method]Codon usage bias were analyzed by Python and CodonW1.4.2 tools based on their genomes data of three species including Saccharum officinarum (LA-purple), S. sponaneum (NP-X and AP85-441), and Erianthus fulvus (Yunnan2009-3). Neutrality-plot, ENC-plot, and Parity Rule 2(PR2)-plot analysis were also used to explore the possible factors that affect the formation of codon usage bias. Simultaneously, correlation analysis between gene expressions and codon usage bias parameters was carryd out based on transcriptome data. Finally, a comparison analysis of codon usage patterns were performed between sugarcane and the other seven main model organisms, namely, Zea mays, Sorghum bicolor, Oryza sativa, Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli, and Saccharomyces cerevisiae based on the average RSCU value of three species.[Result]S. officinarum, S. sponaneum, and E. fulvus were rich in GC base pairs, the average GC content was 56.3%, and GC3 was the highest, followed by GC1 and GC2, indicating that sugarcane preferred to use synonymous codons ending with a C/G base. The average ENC value was 48.45, suggesting that sugarcane had a lower codon usage bias. According to the results of neutral-plot, ENC-plot, and PR2-plot analysis, the codon usage bias of four genomes was affected by natural selection, mutation pressure, and so on, and the natural selection dominated in them. Correlation analysis showed that codon preference parameters were significantly correlated with the actual transcription expressions of genes, but the correlation was not strong. Based on the RSCU and ∆RSCU values, thirteen identical optimal codons were confirmed, and all of them were ended with C/G base pairs. The codon usage characteristics were not different at genome-wide and chromosome level. In addition, the codon usage bias of sugarcane was similar to that of Z. mays, S. bicolor, and O. sativa, while it had a significant difference with A. thaliana, N. tabacum, E. coli, and S. cerevisiae.[Conclusion]The codon usage bias among S. officinarum, S.sponaneum and E. fulvus was highly similar, and its formation was affected by natural selection and mutation pressure factors. Meanwhile, Z. mays, O. sativa and S. bicolor could be used for elite gene function research on sugarcane as a exogenous expression system on account of their codon usage bias patterns. [ABSTRACT FROM AUTHOR]

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Foxtail millet(Setaria italica(L.) P. Beauv.), a venerable domesticated crop, is widely cultivated in arid and semi-arid regions of northern China. As an important orphan crop, foxtail millet boasts traits such as C4 photosynthesis, a compact diploid genome, robust stress tolerance, and wide adaptability. Its grains are rich in protein, sugar, vitamins, and miscellaneous nutrients. The completion of the foxtail millet genome sequencing project in 2012 marked the dawn of genomics for this ancient crop. The research of the foxtail millet genome has unfolded through three key stages: structural genomics, functional genomics, and comparative genomics. The advent of next-generation high-throughput DNA sequencing technologies has facilitated sequencing-based genotyping and genome-wide association studies(GWAS), propelling genetic research on foxtail millet. In the context of “Healthy China”, foxtail millet has emerged as a pivotal crop for improving dietary patterns and driving the sustainable development of organic dryland farming. While the foxtail millet industry has seen remarkable growth in recent years, the paucity of breakthroughs in breeding has hindered its alignment with the demands of modern organic dryland farming, largely due to the constant reliance on traditional breeding methods. Significant strides in foxtail millet genomics have been witnessed, laying the groundwork for molecular breeding. This review provided a comprehensive overview of the historical and current landscape of whole-genome sequencing in foxtail millet, the advancements in genetic transformation systems, and the achievements on gene discovery stemming from the whole-genome sequence. The effective integration of functional genomics with traditional breeding methods will guarantee to enhance the establishment of an efficient and precise breeding system for foxtail millet, hastening breakthroughs in breeding and aligning with the requirements of related industry and consumers. [ABSTRACT FROM AUTHOR]

Copyright of Science & Technology of Food Industry is the property of Science & Technology of Food Industry Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

ObjectiveThe aim of this study was to detect botulinum toxin and Clostridium botulinum （C.botulinum） in 30 batches of infant formula milk powder obtained from an enterprise and to analyze the whole genome of the strain of C. botulinum type B isolated from the samples.MethodsThe samples were subjected to C. botulinum isolation and botulinum toxin typing experiments according to the “National standard for food safety microbiological examination of C. botulinum and botulinum toxin” （GB 4789.12—2016）. The whole genomes of the isolated strains were sequenced and their genetic characteristics were analyzed.ResultsBotulinum toxin was not detected in any of the 30 batches of samples. After intraperitoneal injection of the enrichment solution into mice， four batches of milk powder samples induced symptoms of botulism， but C. botulinum was isolated from only one batch of milk powder samples. Genome sequencing revealed that the bacterium was C. botulinum group Ⅰ， type B， the toxin gene cluster was type Ha， and the toxin gene was subtype B2.ConclusionThe detection of C. botulinum in infant formula milk powder with a complex background of microorganisms should not be based on the isolation of bacteria as the gold standard but should be confirmed by a mouse toxicity test of the enrichment solution combined with a botulinum toxin antiserum protection test. Whole genome sequencing can accurately identify strains and analyze relevant genetic characteristics， providing reliable technical support for handling poisoning events.

Objective：Based on genomics，this study aims to investigate the distribution of drug-resistant genes，virulence factors， and homology analysis of the hospital isolated carbapenem resistant Klebislla. pneumoniae strains. The molecular mechanisms of nosocomial infections will be elucidated to provide laboratory evidence for the clinical treatment and prevention of multidrug-resistant strains. Methods：A clinical isolate of carbapenem-resistant pan-drug-resistant Klebislla. pneumoniae (KPX) was collected，cultured， and identified. The minimum inhibitory concentrations (MICs) of commonly used antibiotics were determined，and multilocus sequence typing (MLST) was performed for genetic typing，followed by whole-genome sequencing. Based on the results of the genetic sequencing，selected relevant resistance genes for amplification detection in an additional 50 clinical isolates of carbapenem-resistant KPX，verified their carriage status，and further elaborate on the sequencing results. Results：The drug sensitivity test showed that the KPX strain was resistant to all antibiotics except colistin and tigecycline. The sequencing results relevant that the chromosomal gene sequence of this bacterium is 5 468 925 bp in length and contains four plasmids (179 972 bp，141 377 bp，85 181 bp，and 20 247 bp) . It had a total of 5 984 protein-coding genes，85 tRNA genes，and 25 rRNA operons. Additionally，this bacterium carried a large number of resistant genes involved in encoding multiple antibiotics. MLST results indicated that the genetic type of this bacterium is ST11，and most of its sequences are similar to previously reported strains in Sichuan and Hangzhou. The closest match was a strain with the code SCKP020029 (NCBI accession number：CP029384) of Klebislla. pneumoniae. The additional 50 carbapenem-resistant Klebislla. pneumoniae collected were confirmed to produce extended-spectrum beta-lactamases (ESBLs),with 97% being of ST11. Pulsed-field gel electrophoresis (PFGE) results showed that they belonged to three different clones. Among these strains，the detection rates of resistance genes were as follows：KPC-2 (98%),SHV-11 (98%),TEM-1 (76%),CTX -M (76%),Oqxb1 (66%),qnrS (70%),Int1 (42%),sul1 (82%),sul2 (96%),iutA (88%),iucABCD (10%),and rmpA2 (100%) . Conclusion：The experimental results revealed that a high degree of genomic similarity among nosocomial carbapenem resistant Klebislla. Pneumoniae strains，with epidemiological characteristics of both clustering and sporadic cross -infection. Antimicrobial-resistance profiles suggested the presence of significant selective antibiotic pressure. Furthermore，the dissemination of plasmid -mediated resistance genes among bacteria indicates that the spread of these resistant strains within the hospital is primarily through plasmid transfer. Effective monitoring, isolation，and control of these plasmids are essential measures to reduce the spread of bacterial resistance in nosocomial infections. [ABSTRACT FROM AUTHOR]

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[Objectives]The paper aimed to obtain double haploids of the melon (2n=2x=24) inbred line BPC-4 by distant hybridization, and analyse botanical traits and genomic changes. [Methods]The melon inbred line BPC-4 was used as the maternal parent to cross with eight different materials of the genus Cucumis. F1 generation of the obtained cross was selfed to obtain F2 and F3,which were used for chromosome number observation, SSR molecular marker analysis and plant traits consistency in the same generation to identify their double haploid feature; F2 and F3 were genome resequenced and then purified site distribution and stability of double haploid genome SNP were analyzed. [Results]Among the eight hybrid combinations, three seeds were obtained from the combination of (BPC-4×cucumber inbred line YPJ-6) (2n=2x=14),among which one seed was planted and 50 self-crossing progenies were obtained. The chromosome number of the F2 generation were identified to be 2n=2x=24. SSR identification showed that the PCR bands by 27 SSR markers in F2 generation were the same as those of the maternal parent. The PCR bands of F2 was consistent among single plants and F3 was not separated, indicating that the F2 gene loci were homozygous. Statistical analysis of botanical traits showed that the main changes in F2 were compact and dwarf compared with BPC-4. The average values of internode spacing, stem diameter, leaf length and width, and petiole length in F2 were all lower than those of BPC-4,and F2 individual plants were consistent. The above results proved that the progenies obtained from the distant crosses were double haploid, and thus F1,F2 and F3 were named as DH0,DH1 and DH2,respectively. The data of seed number and seed setting rate of dihaploid showed that fertility of DH0 was low, while fertility of DH1 and DH2 had recovered up to that of BPC-4 and could be used for seed propagation and preserved through self-crossing. The genome resequencing revealed that the double haploid SNP loci were further purified by 0.26% compared with BPC-4,and the new purified loci were distributed on all 12 chromosomes. The difference of purified loci between DH1 and DH2 of the double haploid selfing progeny was 1 016,accounting for only 0.05%,which was smaller than the heterozygosity difference of 3.13% from Mendelian theory conventional self-crossing S4 to S5,indicating that the double haploid genome had been stabilized. [Conclusions]Genome resequencing and botanical trait variation demonstrated that it was still necessary to create a double haploid in melon after four generations of self-crossing, and that the double haploids obtained could be saved by seed for further breeding and theoretical studies.  [ABSTRACT FROM AUTHOR]

In this study, the microsatellite search software MISA was used to search for the perfect microsatellite in the whole genome of three Culterinae species, and its distribution pattern was analyzed. As a result, in the genome of (Culter alburnus, 1. 055 Gb), (Anabarilius grahami, 1. 006 Gb), and (Megalobrama amblycephala, 1. 116 Gb), 772 276, 548 726, and 772 329 perfect microsatellites were screened out, respectively. The relative frequency were 732. 0/Mb, 553. 2/Mb, and 691. 2/Mb, respectively. The total lengths of the microsatellites were 14. 29 Mb, 9. 42 Mb, and 15. 02 Mb, respectively, accounting for 1. 35%, 0. 94%, and 1. 35% of the total length of the genome sequence. Among the complete microsatellites with 1-6 different base repeat types, the orders of 6 base types from the three species of Culterinae were the same. Each had the largest number of mononucleotide repeats, followed by dinucleotide repeats, tetranucleotide repeats, trinucleotide repeats, pentanucleotide repeats, and hexanucleotide repeats. The highest frequency core repeat categories of trinucleotide and tetranucleotide in the three species of fish is AAT and AGAT, respectively. However, the number of AT is more than AC repeat in the dinucleotide of Culter alburnus. The distribution frequency of microsatellites of different base types in the three fish species decreased with the increase of the copy number and length of the repeat units. The length of the microsatellites repeat unit was mainly 10-30 bp, accounting for 90. 54%, 94. 27%, and 89. 17% of the microsatellites, respectively. The results of this study may provide a reference for the further study of Culterinae genome characteristics and contribute basic data for future investigations into molecular marker-assisted breeding and genetic information assessment of 3 Culterinae species. [ABSTRACT FROM AUTHOR]

To explore the molecular mechanism of Stenotrophomonas maltophilia H002 in response to metal uranium impact and the potential of bioremediation of uranium pollution, genome and transcrip- tome analyses were performed in this study. It was shown that the H002 genome consists of 5 099 056 bp to encode 4780 proteins. Compared with the 6 homologous strains, H002 encodes 344 unique proteins, mainly involved in membrane transport, cell motility and secretion. Transcriptome analysis revealed that in the early stage (1 h) of uranium stress, the differentially expressed genes were mainly enriched in KEGG pathways such as cell mobility and secretion, the biosynthesis of protein and peptidogly-can. The downregulation of partial secretion channel-related genes may reduce the absorption of uranium ions, hence decreasing cellular toxicity. In the later stage (2 h and 4 h) of uranium stress, upregulation of the genes encoding phosphatases involved in uranium mineralization and the cytochrome c proteins, which can provide the reducing electronics, may help reduce the toxicity to the cells. [ABSTRACT FROM AUTHOR]

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Streptomyces sp. FXP04 is a gram‑positive actinomycete isolated from the rhizosphere soil of healthy potato in Keshan county, Qiqihar, which has obvious antagonistic effect against Phytophthora infestans. This work aims to analyze the whole genome sequence information of strain FXP04, to explore the mechanism of action as well as the gene resources for the biosynthesis of secondary metabolites. The whole genome of Streptomycessp. FXP04 was sequenced by Illumina and PacBio platform, and gene prediction, functional annotation, comparative genomics analysis and synthesis gene cluster prediction of secondary metabolite were carried out. The genomic size of strain FXP04 was 4 535 201bp, encoding a total of 5 037 genes, with a GC content of 72.95%, including three 5S rRNA, three 16S rRNA, three 23S rRNA, 33 tRNA and 23 sRNA. It contained 1 699 tandem repeats，1 284 microsatellite DNA,188 microsatellite DNA. It was annotated to 2 088, 2 319, 1 530, 73, 139 and 14 genes in GO, COG, KEGG, CAZy, VFDB and ARDB databases, respectively. At the same time, it was predicted that there were 10 secondary metabolite synthesis gene clusters in strain FXP04, which encoded bacteriostatic substances such as piericidin, youssoufene and so on. The internal mechanism of strain FXP04 was analyzed by genome sequencing, which provides further theoretical basis for the development and utilization of strain FXP04. [ABSTRACT FROM AUTHOR]

The cobia, Rachycentron canadum (Linnaeus, 1766), is an important aquaculture species in cage and other intensive systems. This species has many advantages such as fast growth rate, excellent meat quality, and high market value, making cobia an excellent candidate species for commercial aquaculture. However, long-term artificial breeding of cobia has reduced gene exchange and population genetic diversity. To better protect germplasm resources, molecular markers provide a powerful tool in developing the breeding industry of cobia. Microsatellites are widely distributed, large in number with high polymorphism, and have long been considered important molecular markers for genetic diversity and marker-assisted breeding. More polymorphic microsatellite markers need to be developed for cobia because the number of published polymorphic simple sequence repeat (SSR) loci is very limited. In this study, Micro Satellite (MISA) software was used to identify SSR loci based on the genome sequencing data of cobia. We analyzed the distribution, quantity, and composition characteristics of the SSR loci to develop polymorphic microsatellite markers. The identified markers were used to evaluate the genetic diversity in five cultured populations.In this study, a total of 424 827 SSR loci were identified in the genome data of cobia, among which mononucleotides, dinucleotides, and trinucleotides accounted for 50.50%, 30.23%, and 14.02% of the total SSRs, respectively. Among all the repeat units contained in the total SSRs, A/T was the predominant repeat type of the mononucleotide repeats; AT/AT and AC/GT were the dominant repeat types of dinucleotides; AAT/ATT and AGG/CCT were the dominant repeat types of trinucleotides. Repeat numbers of the SSR core sequences in the genome of cobia ranged from 4 to 275 times. The predominant repeat number of the mononucleotide SSR was ten and the predominant number of the dinucleotide and trinucleotide SSR were six and four, respectively. A total of 173 518 SSR loci had a length of ≥20 bp, accounting for 47.98% of the total number of SSRs in the genome. These results indicated that the SSR loci in the genome of cobia were of a high frequency, rich variety, and with high polymorphic potential.Unigenes obtained by the genome sequencing of cobia were used to detect and analyze the SSR loci information using MISA software. The numbers and types of SSR sequences on the single-stranded DNA of the genome were counted. SSR sites in cobia genome mainly contain mononucleotide, dinucleotide, trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats. The screening criteria for the polymorphic SSR loci was set as "mononucleotide repeat units with repeats at least 10 times; dinucleotides with repeats at least six times; trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides with repeats at least four times". Subsequently, based on the information of SSR loci screening, 100 candidate loci were randomly selected to design and synthesize primers for amplification. A total of 16 DNA samples from different cultured populations were used as templates. Multiple PCR amplifications were performed to screen ideal polymorphic SSR loci and suitable PCR primers. PCR products were detected using capillary fluorescence electrophoresis. The GeneMapper 4.1 software was used to analyze the accurate sites of the amplified sequences. Based on the genotyping data of the 100 SSR loci, SSR loci with high polymorphism were selected to analyze the genetic diversity of five cultured populations of cobia.The screening analysis results revealed a total of 344 820 SSR loci were detected in the genome of cobia. Among these SSR (with 1–6 nucleotide as repeat units), the top three repeat types were mononucleotide, dinucleotide, and trinucleotide, accounting for 50.49%, 30.23% and 14.02% of the total detected SSRs, respectively. Among the repeating units included in the detected SSRs, the mononucleotide repeats were dominated by A/T type, accounting for 46.34% of the total detected SSRs; AC/GT was the dominant repeat unit type of dinucleotide, accounting for 21.81% of the total detected SSRs. The number of SSR core sequence repeats in the total detected SSRs fluctuated in the range of 4 to 275 times. The predominant number of repeats of mononucleotide SSR was ten, and the predominant number of repeats of dinucleotide SSR was six. In this study, the length of ≥12 bp was set as the standard for screening high polymorphic SSR loci. A total of 361 684 SSR loci were obtained. However, the SSR loci with fragment lengths of 12–19 bp accounted the largest number, with a total of 188 166; these loci accounted for 52.02% of the total number of SSRs. Among the selected 100 candidate loci for genotyping, a total of ten polymorphic SSR markers were obtained. These markers were used in the genetic diversity analysis of five cultured populations collected in Beihai (RC-BH), Lingshui (RC-LS), Naozhou (RC-NZ), Xuwen (RC-XW), and Sanya (RC-SY). A total of 69 alleles were detected from 145 individuals, the average observed heterozygosity (Ho) was 0.628, and the average expected heterozygosity (He) was 0.706, and the mean polymorphism information content (PIC) was 0.653. The inbreeding coefficient (Fis) of the ten loci in the five cultured populations ranged from –0.317 to 0.270. The genetic distance between the five cultured populations ranged from 0.141 to 0.464, and the genetic similarity was 0.629–0.868. The results were similar to that of previous research using published markers, indicating that the polymorphic markers screened from the genome of cobia were of high accuracy and reliability. These polymorphic SSR markers provide strong support for population genetic diversity evaluation and molecular marker-assisted breeding of cobia, and provide effective technical support for the development of the cobia aquaculture industry.

Objective To isolate a strain of lysing carbapenem-resistant Klebsiella pneumoniae phage, and explore its biological characteristics and whole genome information. Methods The phage was isolated and purified from waste water of the General Hospital of Western Theater Command Hospital by the double-layer agar plate method. The morphology of phage was observed by transmission electron microscopy, and its biological properties and in vitro antibacterial activity were determined. Whole-genome sequencing was used to analyze its structural characteristics, and a phylogenetic evolutionary tree and the comparative genomic analysis was conducted to analyze the evolutionary relationships of phage. Results A virulent phage was isolated and named vB_KpnP1, which formed a 2~3 mm transparent circular spot surrounded by a distinct halo; Electron microscopy showed that the head size of the phage was about 68.2 nm×64.3 nm, and the tail length was about 11 nm; The head of the phage was a regular icosahedron with a non-contractile short tail, which was thus identified as a member of the Autographiviridae family and the Caudovirales order; the optimal multiplicity of infection was 0.0 001, the incubation period was 10 min, the lysis period was 30 min, and the amount of lysis was 26 PFU/cell; The adsorption rate was about 80% in 10 min. The phage was insensitive to chloroform and was stable at temperatures of 10~50 ℃ and pH values of 4~12; The lysis rate of carbapenem-resistant Klebsiella pneumoniae was 54.55% (12/22), and the host spectrum was wide; In vitro antibacterial test showed that it could inhibit the growth of host bacteria. Phage vB_KpnP1 was double-stranded DNA (dsDNA) with a 40 352 bp of full genome length, and 53.09% of GC content. It contained 50 CDS. Conclusion A virulent Klebsiella pneumoniae phage, vB_KpnP1, with the potential to treat carbapenem-resistant Klebsiella pneumoniae infections, is successfully isolated.

Copyright of Food Research & Development is the property of Food Research & Development Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Red yeast is a general term for a class of red pigment-producing yeast, and they are widely distributed in various ecological environments such as soil, sea, rivers and lakes. Red yeasts have the ability to produce polysaccharides, oils, carotenoids and other active substances and thus own great potential for applications in agriculture, food, medicine and cosmetics. In recent years, studies on red yeast including their applications, genome sequencing and key metabolic enzymes have expanded the in-depth knowledge of this important group of yeast. In addition, progress has been made in genome editing and metabolic engineering modification of these yeasts, providing basis for developing more efficient red yeast strains for industrial applications. Here, we review the applications of red yeast and related research advances in genomic studies and metabolic engineering. This review would be helpful for better understanding the physiology and metabolic features of red yeast, as well as utilization of renewable biomass for sustainable bioproduction using red yeast. [ABSTRACT FROM AUTHOR]

Copyright of Modern Food Science & Technology is the property of Editorial Office of Modern Food Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The loop-mediated isothermal amplification (LAMP) primers were designed for the conserved region of the selected Nicotiana-specific gene Ntsp151 sequence, and a visual LAMP detection method for tobacco materials based on the SYBR Green I was established. The genomic DNA extraction method and reaction conditions were optimized in the detection process. Furthermore, the specificity and sensitivity of the LAMP reaction system were evaluated. The results showed that the genomic DNA extracted by Chelex-100 could be directly amplified and fluorescently colored by LAMP; the optimal reaction conditions of the LAMP primers were amplification temperature 63 °C, reaction time 60 min, Mg2+ concentration 6 mmol/L; LAMP detection method had good specificity and the results of chromogenic amplification and fluorescence detection of 17 non-tobacco materials and 1 tobacco material were consistent and had good specificity. The sensitivity test showed that the minimum detection limit of the LAMP reaction system was 102 copies/μL. The LAMP detection based on Nicotiana-specific gene Ntsp151 was result-visualized, highly sensitive, and specific, which was suitable for field inspection. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Xinyang Normal University Natural Science Edition is the property of Journal of Xinyang Normal University Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Journal of Hydrobiology is the property of Editorial Department of Journal of Hydrobiology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To investigate the relationship between Fat Mass-and obesity-associated gene (FTO) polymorphisms and the susceptibility of non-alcohol-related fatty liver disease (NAFLD) in a Han population from Qingdao region of China. Methods A total of 119 NAFLD patients were recruited from Qingdao Municipal Hospital and Chengyang District People’s Hospital and 187 control individuals who received annual physical examination were also included. Their clinicopathological information and study questionnaire were collected. Their fasting venous blood was extracted for biochemical analyses and FTO polymorphism genotyping using the polymerase chain reaction combined with DNA sequencing. The data were statistically assessed. Results The data showed statistically significant differences in age, BMI, ALT, GGT, TG and Bil between NAFLD patients and normal controls (all P<0.05). FTO polymorphism genotyping data showed three genotypes of FTO rs1421085 (TT, CT, and CC), rs8050136 (TT, CT, and CC) and rs9939609 (TT, AT, AA). However, there was no statistical difference in both allele frequency and genotype of FTO rs1421085, rs9939609, and rs8050136 between NAFLD and controls (all P>0.05) and there was also no statistical difference in clinical parameters among these genotype carriers (all P>0.05). Conclusion NAFLD patients showed significantly statistical differences in age, BMI, ALT, GGT, TG, and BIL vs. those of normal controls. However, this study did not find any association of FTO rs1421085, rs9939609, and rs8050136 polymorphisms with NAFLD susceptibility in this Qingdao region of Han Chinese population. [ABSTRACT FROM AUTHOR]

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Bioinformatics is widely used in the studies of reproductive system at various technical levels, including genome, transcriptome, proteome and metabolome. Through systematic data collection and visual processing, the mechanisms of key molecules in the reproductive process have been gradually discovered and elucidated. The application of bioinformatics technology in reproductive system not only has effectively promoted the development and innovation of reproductive system research on the basis of ensuring preciseness and scientificity, such as analyses of the normal functions, abnormal and pathological phenomena of different reproduction organs at the different levels of genome, transcriptome, proteome and metabolome, but also has enhanced the progress of clinical diagnosis and treatment of the related diseases in reproductive system, such as the discoveries of new disease markers and drug targets for the diagnosis and treatment. In this review, we mainly introduced the latest bioinformatics technologies in the reproductive medicine in recent years. Meanwhile, we also summarized the current research progress in reproductive system using bioinformatics, which may provide some key guidance and ideas for future research. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Xinjiang Agricultural Sciences is the property of Xinjiang Agricultural Sciences Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Chinese Journal of Applied Entomology is the property of Chinese Journal of Applied Entomology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Acta Agriculturae Zhejiangensis is the property of Acta Agriculturae Zhejiangensis Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Chinese Journal of Applied Entomology is the property of Chinese Journal of Applied Entomology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The MYB(v-myb avian myeloblastosis viral oncogene homolog) family of transcription factors is the largest class of genes among higher plant transcription factors, which can be divided into four subfamilies, with the R2R3-MYB being the most common subfamily type. R2R3-MYB transcription factors are widely involved in the regulation of organ development and secondary metabolite biosynthesis in plants. To investigate the role of R2R3-MYB family transcription factors in the synthesis of flavonoids and glandular trichome development in Artemisia argyi, this study screened and identified 92 R2R3-MYB transcription factors based on the whole genome data of A. argyi, and predicted their potential functions based on bioinformatics. The results showed that the amino acid lengths of the 92 transcription factors ranged from 168 to 547 aa, with relative molecular weights ranging from 19. 6 to 60. 5 kDa, all of which were hydrophilic proteins. Subcellular localization analysis showed that 89 AaMYB proteins were located in the nucleus, while three proteins were simultaneously located in the nucleus and cytoplasm. According to the classification of Arabidopsis R2R3-MYB family, the 92 A. argyi R2R3-MYB proteins were divided into 26 subfamilies, with similar gene structures within the same subfamily.Cis-acting element prediction results showed that light-responsive elements, methyl jasmonate elements, and abscisic acid elements were widely distributed in the promoter regions of R2R3-MYB genes. Transcriptome expression analysis results showed that the expression of AaMYB60, AaMYB63, and AaMYB86 in leaves was higher than that in stems and roots, indicating that these three transcription factors mainly function in leaves. Additionally, five candidate R2R3-MYB transcription factors involved in A. argyi flavonoid biosynthesis or glandular trichome development were selected through phylogenetic analysis. This study provides important genetic resources for the breeding of superior varieties and germplasm innovation of A. argyi in the future.

ObjectiveTo investigate the genomic and virulence characteristics of seven invasive non-typhoidal Salmonella (iNTS) isolates.MethodsBased on the collection of seven iNTS strains, whole genome sequencing were performed. The serotypes, genomes and virulence factors were identified, annotated and analyzed according to the comparison of genome data and relevant databases.ResultsAmong the seven tested iNTS isolates, six were monophasic, including one Salmonella Typhimurium and two Salmonella I 4, [5], 12∶i∶-(ST34 type), two Salmonella Enteritidis, one Salmonella Corvallis and one unknown serotype with the antigenic formulae of I 4, [5], 12∶d∶- (ST279 type). No consistent rule was found in genomic components and relevant parameter differences varies much between different serotypes than those of the same serotype from different sources. The distribution of virulence factors (VF) was significantly different among different Salmonella serotypes, but the common VF characteristics in iNTS strains were not found, though Capsule/Immune evasion, toxin, peritrichous_flagella and Salmochelin may be associated with high invasiveness. All tested isolates contained type III and type VI secretion systems. The number of secretion protein, type III for S. Corvallis and type VI for Salmonella I 4, [5], 12∶d∶-was the highest among the seven isolates. Pseudogenization of the secreted effector SseI may exist among some Salmonella serotypes which may contribute to the enhancement of Salmonella invasiveness.ConclusionThe common characteristic differences of virulence factor between iNTS and gastroenteritis NTS were not observed at the moment, and highly invasive pathogenic mechanisms still require further analysis and research at the functional transcriptome and proteomic levels to determine the genetic basis of iNTS occurrence and transmission.

In order to enrich the data on genome sizes of Polygonatum species, flow cytometry was used for ploidy detection and estimation of genome sizes of four Polygonatum species recorded in the Chinese Pharmacopoeia, including P. kingianum, P. sibiricum, P. cyrtonema, and P. odoratum from different habitats. The results show that Phyllostachys pubescens can be used as a suitable reference standard for the estimation of genome sizes of Polygonatum species. Regarding the four diploid Polygonatum species, the present study found that the genome size of P. odoratum（13 829-14 083 Mb） is similar to that of P. kingianum（13 780 Mb); the genome size of P. sibiricum（12 792-13 516 Mb） is slightly smaller than that of P. odoratum and P. kingianum; and the genome size of P. cyrtonema（9 311 Mb） is the smallest. The genome size of triploid P. cyrtonema is 11 032-11 267 Mb, which is 1.2 times larger than that of diploid P. cyrtonema. The genome size of tetraploid P. kingianum is 12 088-12 411 Mb, which is 89% of the size of diploid P. kingianum. The results append the data on the genome sizes of Polygonatum species, which will provide a reference for a follow-up study on genomics, species classification, and population evolution. [ABSTRACT FROM AUTHOR]

[Objectives]This article aimed to identify the homologous proteins of major transcription factor families in Ganoderma lucidum,analyze their sequence characteristics and changes in transcription level under acetic acid treatment, and provide a theoretical basis for further studies of G.lucidum gene expression and product metabolism regulation. [Methods]Using bioinformatics methods, the G.lucidum protein database was analyzed. Compared with 19 common fungal transcription factor families in public database, the homologous proteins of G.lucidum transcription factor families were identified. Homologous proteins of bZIP were chosen to analyze their bioinformatics characteristics. The transcriptome data was used to analyze transcription level changes of these homologous proteins under the condition of acetic acid treatment. [Results]Compared with the database, 261 G.lucidum homologous proteins of 19 transcription factor families were identified. The number of homologous proteins containing OB-fold, Zn2 Cys6 or C2H2 conserved domain was the largest, with 61,55 and 40,respectively. Evolutionary tree showed that the homologous proteins of bZIP in G.lucidum could be divided into four subgroups. Chromosome location analysis showed that Chr 3 had the most transcription factors and Chr 13 had the least. The prediction of subcellular localization indicated that the number of transcription factors located in the nucleolus and cytoplasm was relatively large, which was 108 and 78,respectively. The transcriptome data of acetic acid treatment showed that transcription level of GL22568＿R1 containing TEA domain was significantly down-regulated after acetic acid treatment; GL16029＿R1 containing C2H2 domain, GL17627＿R1,GL16724＿R1 and GL21326＿R1 containing Zn2 Cys6 domain were significantly up-regulated after acetic acid treatment. [Conclusions]There were many classifications of transcription factor families in G.lucidum,which were widely distributed. Among them, five homologous proteins containing TEA domain, C2H2 and Zn2Cys6 could respond to acetic acid treatment. [ABSTRACT FROM AUTHOR]

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective To investigate the gene mutations of Chinese patients with pancreatic cancer in the coastal regions of Eastern China, and to provide a basis for individualized treatment. Methods A total of 40 patients who were admitted and diagnosed with malignant pancreatic tumor after surgical treatment in The Affiliated Hospital of Qingdao University, Qingdao Municipal Hospital, Yantaishan Hospital, and Yantai Sino-France Friendship Hospital from January 2017 to June 2019 were enrolled. Next-generation sequencing（NGS） was used to detect gene mutations in tumor tissue and somatic cells, and the map of gene mutations was plotted to analyze genomic alterations. The chi-square test or the Fisher’s exact test was used for comparison of categorical data between groups. The Kaplan-Meier method was used to plot survival curves, and the log-rank test was used for comparison between groups. Results Among the 40 patients, 34（85.0%） had pancreatic ductal adenocarcinoma, 3（7.5%） had solid pseudopapillary neoplasm of the pancreas, 1（2.5%） had pancreatic neuroendocrine tumor, and 2（5.0%） had unclear typing. KRAS（80.0%, 32/40）, TP53（70.0%, 28/40）, CDKN2 A（32.5%, 13/40）, SMAD4（17.5%, 7/40）, and AKT2（17.5%, 7/40） were the most common mutations, and there was no significant difference in survival time between the patients with these five common gene mutations（all P>0.05）. Conclusion NGS technology can provide comprehensive and accurate information of genomic alterations and may provide novel potential biomarkers for the diagnosis and precise treatment of pancreatic cancer. The analysis of mutant genes also lays a foundation for the individualized treatment of pancreatic cancer.  [ABSTRACT FROM AUTHOR]

Copyright of South China Fisheries Science is the property of South China Fisheries Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Chinese Journal of Preventive Veterinary Medicine / Zhongguo Yufang Shouyi Xuebao is the property of Chinese Journal of Preventive Veterinary Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Mycosystema is the property of Mycosystema Editorial Board and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The tea plant has the characteristics of high heterozygosity, large genome and high duplication, which has led to the slow progress of the preliminary research on the tea plant genomes. The rapid development of genome sequencing technologies has strongly promoted the deciphering and improvement of the tea plant genomes. This article reviewed the development of genome sequencing technologies, and classified the assembly and research progress of tea plant genomes in recent years according to the draft level, chromosome level and haplotype level. By discussing the future application and development direction of tea plant genomes, it provided a reference for the functional genomics research and precision molecular breeding in tea plants. [ABSTRACT FROM AUTHOR]

With the rapid development of high-throughput sequencing technology represented by the second generation sequencing technology, whole-genome detection technology has been able to detect data from multiple levels, such as genome, transcriptome and epigenome. Biomass is a complicated regulatory system, involving many levels of complicated regulatory mechanism. Considering the limitation of single omics data analysis in exploring pathogenic factors, integrative multi-omics analysis with linear or nonlinear relationship can provide a new method for the study of the disease. Integrative analysis of multiple omics has widely used in various diseases, including lung cancer, and DNA or gene molecular level is particularly important as a basis for intermolecular correlations and complex networks. Hence, this paper briefly describes integrative analysis of genome, transcriptome and epigenome in lung cancer.

Single-cell sequencing is a technique that analyzes DNA and RNA sequences on the cellular level with next generation sequencing. The ultra high resolution of single-cell sequencing provides new perspectives and opens new frontiers for our understanding of many areas of life sciences, including forensic genome. This paper summarizes the recent advancements in single-cell sequencing and the prospect of its forensic application.