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Objective Different library construction methods, combined with high-throughput sequencing methods, were used to understand the genetic characteristics of the virus of the first confirmed imported monkeypox case in mainland China, and to compare the advantages and disadvantages of different library types. Methods The herpetic fluids and nasopharyngeal swabs of the first imported monkeypox case in the Chinese mainland were used as samples. After nucleic acid extraction and quantification, the library was directly constructed or the amplicon library was constructed using the monkeypox virus whole genome capture kit, and the whole genome sequence of the virus was obtained by high-throughput sequencing. Combined with 34 monkeypox virus sequences downloaded from the NCBI and GISAID databases, a phylogenetic evolutionary tree was constructed using vaccinia, variola, and cowpox sequences as out groups. Results The whole genome sequence of the virus was obtained by both library construction methods, named hMpxV/China/CQ-CQCDC-001/2022, which belongs to the monkeypox virus branch lib, located in the same branch as hMpxV/Germany/BE-ChVir28656/2022 belonging to the IIb B.1 branch. Metagenomic libraries have more uniform sequence coverage than amplicon libraries, but the sequencing depth is lower and the effective data volume accounts for less. Conclusion Clade IIb B.1 monkeypox viruses have already been introduced into the mainland China, and the sequencing of subsequently discovered monkeypox viruses should be based on the sample size and sequencing timeframe, sequencing cost-effectiveness ratio, and other factors to choose the appropriate library construction method. [ABSTRACT FROM AUTHOR]

Objective To investigate the application value and significance of low depth genome-wide copy number variation sequencing (CNV-seq) in the diagnosis of genetic etiology of recurrent spontaneous abortion by comparing differences of chromosome abnormalities and copy number variation in recurrent spontaneous abortion (RSA) and sporadic abortion (SA). Methods A total of 402 aborted tissue from 158 RSA patients and 244 SA patients were collected for CNV-seq detection. The chromosome karyotypes in peripheral blood of couples with suspected chromosomal abnormality were detected with high resolution. Results In 402 samples, 2 cases were failed, and the detection success rate was 99.5% (400/402). A total of 238 (59.5%) chromosome abnormalities were detected in 400 samples, including 212 (89.1%) chromosome number abnormalities, 25 (10.5%) pathogenic copy number variation and 1 (0.4%) uniparental disomy. There were no significant differences in the overall incidence rate of chromosome abnormality, aneuploid abnormality and triploid between the two groups. The proportion of pathogenic copy number variation in chromosome abnormalities was significantly higher in the RSA group than that in the SA group (P＜0.05). A total of 4 balanced translocation carriers were detected by high-resolution peripheral blood karyotype analysis. During the age range of 35-39, the rate of chromosomal abnormality was significantly higher in the SA group than that in the RSA group (P＜0.05). In both the RSA group and the SA group, the chromosomal abnormality rate in the first trimester abortion was significantly higher than that in the second trimester abortion, while the rate of POCs chromosomal abnormalities was higher in the SA group than that in the RSA group in the first trimester abortion (P＜0.05). Conclusion CNV-seq can accurately diagnose the numerical chromosomal abnormalities and the duplication/deletion of chromosome fragments in embryos, which is equally important in the genetic etiology diagnosis of RSA and SA, and can provide sufficient evidence for the guidance of reproduction. [ABSTRACT FROM AUTHOR]

Objective To understand the epidemiological characteristics, etiological characteristics, and genome-wide traceability of Bacillus anthracis in Shaanxi Province from 2015 to 2022. Methods The epidemiological characteristics of reported cases of anthrax in Shaanxi Province from 2015 to 2022 were analyzed and described. The case investigation and on-the-spot hygienic investigation on the outbreak of anthrax were carried out, and samples of anthrax cases, diseased animals, and polluted environment were collected. The fluorescent quantitative PCR test, antibody detection, and isolation and identification of Bacillus anthracis were performed. Second-generation sequencing was performed for the isolated strains, and the whole genome data were identified and analyzed for drug resistance gene and virulence gene, core genome multi-locus sequence analysis (cg MLST) and core genome single nucleotide variation analysis (cg SNP). Results A total of 55 cases of skin anthrax were reported in 2015 and 2022 in Shaanxi Province, distributed in 7 cities and 25 counties (districts), mainly in Yan'an city and Weinan city. There was obvious seasonal distribution characteristics, mainly in August, accounting for 52.7% (28/55), and the occupation distribution was dominated by farmers, accounting for 67.3% (37/55), followed by personnel of transporting, breeding, and slaughtering (18.2%, 10/55). A total of 11 strains of Bacillus anthracis were isolated, with sequencing genome sizes ranging from 5.4 to 5.5 MB and GC content ranging from 35.10% to 35.20%. The GC content was 35.10%. All of them carried cap A, cap B, cap C, cap E, cy a, dep/cap D, inh A, lef and pag A virulence genes and β-lactam, carbapenem, Fosfomycin, Streptomyces resistance genes. Cg MLST and cg SNP analysis showed that there were significant differences among isolates from northern Shaanxi, Guanzhong, and southern Shaanxi. There were 30 variation sites between Ganquan county of Yan'an city and Guanzhong area, and 26 variation sites between Nanzheng district of Hanzhong city and Guanzhong area. Anthracnose showed obvious clusters in Weinan city, and there were strains isolated from different regions and years in the same cluster. Conclusion The anthrax epidemic occurred in many places in Shaanxi Province from 2015 to 2022, which decreased at first and then increased. Genome tracing showed that there was no obvious correlation among strains in northern Shaanxi, Guanzhong, and southern Shaanxi, but there was a correlation between different ages and regions in Weinan city. [ABSTRACT FROM AUTHOR]

To reveal the drug-resistance potential of Aeromonas hydrophila, the micro broth dilution method and comparative genomics method were used to analyze its drug-resistance potential in this study. The results showed that enrofloxacin, neomycin sulfate, florfenicol and doxycycline hydrochloride had inhibitory effects on the three strains, while sulfamethoxam had no inhibitory effect on the three strains. The resistance phenotype of the strains was not corresponding to the resistance genes one by one, and some strains could show related resistance phenotype even though the resistance genes were not annotated; The genomes of the three newly sequenced strains differed in size, and their genetic relationships were not close, but the number of drug-resistant genes was basically the same. After calculation of ANI (Average nucleotide identity), comparative analysis of genomes revealed that the genomes of A. hydrophila showed strong variability, and there were still large differences among genomes of even close strains. Phylogenetic analysis showed that the strains from different hosts were scattered in the evolutionary tree, and the related strains were distributed in different countries and regions. A total of 21 drug resistance genes were annotated in all strains in CARD (The Comprehensive Antibiotic Resistance Database ), of which 7 were shared by all strains. The reason for this phenomenon is likely to be due to the strong variability of A. hydrophila genome and the wide distribution of its hosts. Frequent gene exchange between strains promotes the rapid spread of drug-resistance genes throughout the species, so even if the genome changes between strains are large, the changes of drug-resistance genes between strains are small. [ABSTRACT FROM AUTHOR]

The genus Alcaligenes shows extensive degradation capacity for aromatic compounds. In the present study, the phenol‑ degrading genes in Alcaligenes faecalis JF101 were analyzed and the potential functions were explored. The whole genome of strain JF101 was sequenced, assembled and annotated for analyzing the genes involved in phenol degradation. Moreover, the comparative genomics with five related strains was carried out. Results showed that the whole genome size of strain JF101 was 4 143 816 bp, and the GC content was 57.44%, with 3 804 protein‑coding genes, 55 tRNAs genes, 9 rRNAs genes and 5 sRNA. There were 3 040, 2 529 and 2 415 annotated genes in COG, GO and KEGG databases, respectively. Eleven genes involving in phenol degradation were identified. Comparative genomics revealed that strain JF101 had no plasmid, and shared 2 008 common homologous gene families and 5 specific gene families with the five related strains. In addition, the putative gene Trk and Kdp involved in compatible solute transport, were found in strain JF101, and the salt‑tolerant ability was confirmed by experiments. The whole‑genome analysis of strain JF101 will benefit the further elucidating mechanism of phenol degradation and developing engineering applications. [ABSTRACT FROM AUTHOR]

Bacillus is an important microbial resource in agricultural production, which can promote plant growth and improve plant disease resistance. Based on morphological, physiological and biochemical characteristics and 16S rRNA phylogenetic relationship, strain A-1 was classified and identified. Brassica napus was used as the experimental object to determine the growth-promoting ability of inoculated strain A-1 under salt stress. The inhibitory effect of strain A-1 on the mycelium of Leptosphaeria biglobosa was determined by antagonistic test. The biological control mechanism of strain A-1 was explored by whole genome sequencing. The results showed that strain A-1 was classified as Bacillus swezeyi. Under salt stress, the root length, plant height and fresh weight of rape inoculated with A-1 strain increased by 42. 35%. 27. 24% and 105. 61%, respectively, compared with the control group. Strain A-1 significantly inhibited the mycelial growth of Leptosphaeria biglobosa and caused mycelial cell lysis. The whole genome size of strain A-1 was 4 591 993 bp, and the G + C content was 44. 39%. A total of 4 948 genes were encoded, including 85 tRNA genes. 24 rRNA genes and 38 sRNA genes. There are genes encoding functional enzymes that hydrolyze the cell wall of pathogenic fungi and genes related to IAA synthesis. as well as seven gene clusters involved in the synthesis of antimicrobial substances in Bacillus. This study will lay the foundation for the development of B. swezeyi bacterial fertilizer and biocontrol agents. [ABSTRACT FROM AUTHOR]

This study is aimed to screen for key genes and loci associated with white leaf formation in kale (Brassica oleracea L. var. acephala DC) and the genetic patterns of heart leaf color traits. The kale red-leaf parent WR, the white-leaf parent WB and their constructed F2 segregating populations were used as test materials. Twenty red-leaf and white-leaf plants were selected from the F2 population, and two DNA mixing pools were constructed. Whole genome sequencing to offspring mixing pool and parents at 50x and 20x cover depth was conducted respectively, and the association interval of white leaf traits was located and candidate genes were predicted according to the gene annotation information. The results showed that re-sequencing 3 987 718 single nucleic acid polymorphism (SNP) markers were obtained via re-sequencing, 8 significant association intervals on chromosomes 2,3, and 9 were obtained, and 8 candidate genes (Bol030253, Bol029431, Bol012077, Bol007709, Bol030318, Bol030235, Bol030286, and Bol005195) were obtained based on gene annotation and functional analysis. Identifying eight genes as candidate genes for white kale leaves may play an important role in the color formation of kale leaves. [ABSTRACT FROM AUTHOR]

The objectives of this study are to explore the mechanism of pathogenic Aeromonas hydrophila XDMG strain infecting fish, and to compare its genome structure, function and evolutionary relationship with the reference strain. The whole genome of A. hydrophila XDMG strain was sequenced, and the original data obtained by sequencing were assembled, spliced and annotated using Newbler, SeqMan, Glimmer and other software. Based on the constructing phylogenetic tree analysis from housekeeping genes and determining evolutionary relationships, the genomes of A. hydrophila were compared with those of four A. hydrophila strains in different regions. The complete genome sequence of A. hydrophila XDMG strain was 4.99 Mb in length and the GC content was 60.84%. A total of 4 935 coding genes were predicted, 4 137 genes with clear function were found, 99 tRNAs and 3 rRNAs were found; 4 061 genes had ortholog family classification, 3 228 genes were related to gene ontology, and 2 663 genes related to metabolic pathways; 101 tandem repeats and 14 gene islands were predicted in the genome of A. hydrophila XDMG strain, with genes related to three QS systems: AI 1, AI 2, and AI 3. Through genome comparative analysis, A. hydrophila XDMG was closely related to domestic A. hydrophila J-1 strain and US-derived A. hydrophila AL0971 strain; it was more conserved with US-derived A. hydrophila AL0971 in the comparison of virulence genes, outer membrane proteins, and O-antigen gene clusters. Comprehensive genome annotation and comparative analysis of the genome of A. hydrophila XDMG strain provide basic data for the study of functional genomics and genetic engineering vaccines of A. hydrophila. [ABSTRACT FROM AUTHOR]

In order to obtain the new cellulose-degrading bacteria at normal temperature, a bacterial strain named as 18B with cellulosedegrading ability was isolated and purified from garden compost in this study. Congo red staining experiment and filter paper degradation experiment were conducted to verify its cellulose-degradation ability. 16S rRNA sequence alignment and whole genome alignment confirmed that it belonged to the genus Olivibacter, and was the closest to Olivibacter jilunii 14-2AT . Further comparative physiological and biochemical characterization revealed differences with O. jilunii 14-2AT in terms of growth temperature, oxidase and glycolysis. The strain 18B grew in the range of 12-48℃, and the optimal growth temperature was 30-37℃ . O. jilunii 14-2AT grew at 4-42℃ . Strain 18B was positive for oxidase and negative for glycolysis, while O. jilunii 14-2AT had no oxidase activity and was positive for glycolysis. Combined with the results of the genomewide covariance alignment, it was known that strain 18B had a certain evolutionary relationship with O. jilunii 14-2AT . The cellulose-degradation ability was found that the cellulase activity of 18B was up to 82.14+0.99 -9.90 U/L at 37℃, 200 r/min until the 5th d. Meanwhile, the enzyme activity could be maintained without degradation under the incubation conditions with sodium carboxymethyl cellulose as the only carbon source and only inorganic nitrogen source added. O. jilunii 14-2AT had no cellulose degrading ability and could not survive in a culture environment where sodium carboxymethylcellulose was the only organic carbon source. The results of whole genome sequencing showed that there were cellulase genes in the genome of strain 18B. The cellulase genes were heterologous expressed in Escherichia coli, and the degradation ability of the expressed products was tested. The results showed that the cellulase genes were active. The above results finally identified strain 18B as a new physiological strain of O. jilunii with cellulase activity. [ABSTRACT FROM AUTHOR]

Endohyphal bacteria are a special class of bacteria that play an essential role in host fungi and ecosystems. To explore the endohyphal bacteria resources with growth-promoting functions in endophytic fungi of Spiranthes sinensis and explore their biological functions， the endohyphal bacteria were isolated by mycelial tissue grinding and identified by colony morphology, physiological and biochemical properties and molecular characteristics, after detecting the presence of endohyphal bacteria in the mycelium of Epicoccum sorghium by fluorescence in situ hybridization（FISH）. Then the endogeneity of the bacteria was verified by specific primers, and the growth-promoting characteristics were determined by Salkowski colorimetry, CAS colorimetry and Mo-Sb colorimetry. The growth-promoting ability of endohyphal bacteria was preliminarily verified by rice seed growth-promoting experiments, and the whole genome sequencing and growth-promoting functional gene analysis of endohyphal bacteria were performed. The presence of bacteria within the mycelium of the fungus E. sorghinum was observed after hybridization with the fluorescein-labeled single-stranded nucleic acid probe, which might confirm the mycelium contains bacteria. An endohyphal Rhizobium oryzihabitans was isolated from the mycelium and named as 7-2H, which had the ability of producing indole-3-acetic （IAA）and siderophore as well as solublizing phosphate, and significantly increased the shoot length, root length, fresh weight and dry weight of rice seedlings. The average nucleotide identity（ANI）value between the genome of strain 7-2H and the standard strain Rhizobium oryzihabitans M15 was 96.98%. In the genome of strain 7-2H, genes related to IAA production, siderophore and phosphate solubilization were revealed. An endohyphal Rhizobium oryzihabitans is isolated, which has fine plant growth-promoting property and has a potential to be developed to be microbial fertilizer. [ABSTRACT FROM AUTHOR]

In order to explore the molecular genetic characteristics of peste des petits ruminants virus (PPRV) isolated from wild bharal (Pseudois nayaur) in Ningxia, 13 pairs of whole genome amplification primers were designed and synthesized according to the PPRV genome sequence published on GenBank. The whole genome sequence of the virus strain (wild-bharal/ China-NXYH/2021 strain) was obtained through RT-PCR, DNA sequencing and splicing, and its sequence was analyzed with DNASTAR and MEGA 7. 0 software. The results showed that the strain belonged to gene IV strain, with a total genome length of 15, 954 nt. In terms of phylogenetic evolution, it was close to the Chinese epidemic strains since 2013 and the Mongolian epidemic strains from 2016 to 2017, forming a small evolutionary branch. In the genome wide identity analysis, the highest identity (99. 4%) was found with the domestic Xinjiang epidemic strain goat/China-XJYL/2013, and 96. 8%, 98. 8% and 99. 0% with other domestic wild animal PPRV strains wild-bharal/China-Tibet/2008, Ibex/China-XJBZ/2015 and Procapra-przewalskii/China-GS/2018, respectively. In the analysis of amino acid polymorphism of H and F proteins, unique amino acid mutations were found in both H and F proteins of the strain, namely R285Q and S421R of H protein and R/K/T3W and Q305R of F protein. The results showed that the peste des petits ruminants virus had been introduced into the wildlife population of Ningxia, bringing new difficulties and challenges to the eradication of peste des petits ruminants in China. The results suggest that it is necessary to strengthen the tracking and monitoring of PPRV infection of wild animals in Ningxia, so as to timely block the transmission of PPRV from the source of infection and transmission routes. [ABSTRACT FROM AUTHOR]

In order to obtain the optimal conditions for the protoplast preparation of Pleurotus giganteus, two strains, PG46 and PG79, with different temperature types, were selected as materials to study the effects of five factors (mycelial age, osmotic stabilizer type, lywallzyme concentration, enzymatic hydrolysis duration and enzymatic hydrolysis temperature) based on single factor and orthogonal experimental methods. The results were as follows: (1) In the single factor test, the optimal conditions for the protoplast preparation of P. giganteus were mycelial culture for 5 d, using 2.5% lywallzyme with 0.6 mol·L-1 mannitol, incubated for 4 h at 32°C (PG46) or 27-35°C (PG79). (2) Orthogonal experiment verified and optimized the single factor test results. Combination 2 (mycelial age 5 d, lywallzyme concentration 2.5%, 0.6 mol·L-1 mannitol, incubated for 4 h at 32°C) could be used as the optimal condition for the protoplast preparation of PG46 and PG79 at the same time, and the protoplast yields were 11.22 × 106 CFU·mL-1 and 7.28 × 106 CFU·mL-1, respectively. (3) For F-test, the influence degree of various factor on the protoplast preparation were as follows: mycelial age>lywallzyme concentration>enzymatic hydrolysis temperature>enzymatic hydrolysis duration (PG46), and mycelial age>enzymatic hydrolysis duration>enzymatic hydrolysis temperature>lywallzyme concentration (PG79), respectively. In conclusion, the protoplast preparation conditions of the two P. giganteus strains with different temperature types were basically the same, and the effects of mycelial age on the protoplasts yield of the two strains were the most significant. The results can lay a foundation for further cross-breeding, genetic transformation, whole genome sequencing and promote the molecular genetics development of P. giganteus. [ABSTRACT FROM AUTHOR]

Using molecular technique to explore the mechanism of hedgehog hide and other tissues applied as traditional Chinese medicine, and promote molecular evolution of Erinaceus amurensis in the Far East, taking the complete mitochondrial genome sequence of Erinaceus amurensis as the material, 12 non- repeating coding sequences (CDS) with a length greater than 300 bp were selected as the research objects in this study, and their codon preference was analyzed by using CodonW1.4.2, SPSS 25.0, Excel 2007 and other software. The average GC content of the third codon was 24.30%; the number of effective codons (ENC) ranged from 31.83 to 50.67, with an average value of 43.37; and the relative synonymous codon usage (RSCU) value of 32 codons was greater than 1.00, and the preference ends with either A or U (T). According to neutral plot analysis, the correlation coefficient between the average value (GC12) of GC1, and GC2 and GC3 was 0.443. In addition, ENC-plot analysis also revealed that most genes cluster near the standard curve; besides, the corresponding analysis showed that the contribution rates of the 1-4 vector axes were 35.64%, 16.22%, 10.26% and 9.13%, respectively; and the GC content of the third synonymous codon (GC3s) and ENC were significantly positively correlated with the first vector axis (Axis1). In addition, the codon adaptation index (CAI) was negatively correlated with Axis1. Hence, it could finally be determined that CUA, AUA, GUU, UCU, CCC, ACA, GCU, CAU, AAA, GAA, UGA, CGC, GGC and GGA were optimal codons. Studying the optimization of the mitochondrial genome codon of Erinaceus amurensis using the molecular technique, the mechanism of drug action of its tissue could be explored further. [ABSTRACT FROM AUTHOR]

In order to understand the genomic characteristic and evolutionary relationship of Listeria monocytogenes LMXJ15 from Xinjiang, PacBio and Illumina HiSeq platforms were used to have the whole genome sequencing of LMXJ15, then the relevant software were applied to predict and annotate the sequenced data. Multilocus sequence typing (MLST) and collinearity analysis were conducted to analyze the homologies among the LM strains. The results showed that the length of LMXJ15 genome was 3 017 732 bp with a GC value of 37.81%. It was predicted to contain 3154 protein-coding genes with a total length of 2 734 315bp. The genome of LMXJ15 contained 6 rRNA operons and 57 tRNA, 88 virulence genes being predicted from the genome. Through the CRT prediction, a CRISPR sequence was found in the LMXJ15 genome sequence. A total 2 241 genes of 3 GO contents were obtained by comparing GO database. Total 88 possible virulence genes were predicted. MLST analysis showed that LMXJ15 was sequence type (ST) 8 and belonged to CC8 (clonal complex 8). Evolutionary analysis showed that the LMXJ15 had a close evolutionary relationship with two clinical IZSAM_Lm_15_17439_A144 isolates from Italy, LmN1546 isolates from Switzerland, R479a isolates from smoked salmon, and had the same ST type and serotype (1/2a), and comparative genomics among 4 LM strains showed scant collinearity. In summary, we preliminarily analyzed the genomic characteristics and virulence genes situation of LMXJ15 isolate, which may provide basic data for analysis of the evolution relationship and the virulence of L. monocytogenes in Xinjiang province. [ABSTRACT FROM AUTHOR]

[Objective] The candidate GPCR proteins of three trophic pathogenic fungi of wheat were searched and their properties were ana- lyzed, which laid a theoretical foundation for further searching of new pesticide targets. [Method] The study selected three trophic pathogenic fungi, whose whole genome sequence had been published. Based on the typical structure characteristics of GPCR proteins, three online pro- tein transmembrane prediction programs (TOPCONS, TMHMM, Philius) were used to search for candidate GPCR proteins in the pathogenic fungi. The sequence length, theoretical isoelectric point, instability coefficient and the strongest hydrophilic (hydrophobic) residues of can- didate GPCR proteins of different trophic fungi were compared and analyzed. [Result】 There were 11, 32 and 69 candidate GPCR proteins in Blumeria graminis f. sp. tritici, Zymoseptoria tritici and Parastagonospora nodorum, respectively, and the average protein sequence length of GPCR was 396 aa. The average theoretical isoelectric point, instability coefficient, hydrophilicity and hydrophobicity of the above candidate proteins were about 8.78, 40, -2.70 and 3. 20, respectively, while the distribution of the strongest hydrophilic (hydrophobic) residues were inconsistent. The genetic relationships of the 112 candidate GPCR proteins were clustered into three categories with 71, 36 and 5 pro- teins, respectively. [Conclusion] The number of candidate GPCR proteins of viable fungi was the least among the three trophic wheat patho- genic fungi, whereas the number of dead fungi was the most, and the number of semi-viable fungi was in between. Different candidate GPCR proteins had certain homogeneity in theoretical isoelectric point, instability coefficient and other physicochemical properties and genetic rela- tionships, but the strongest hydrophilic and hydrophobic amino acid residues were relatively different. [ABSTRACT FROM AUTHOR]

Cucurbitaceae family includes many common vegetables and fruits, and plays an important role in agricultural production. High quality genome is essential for gene mining of agronomically important traits, evaluation of germplasm resources and construction of molecular breeding system. With the rapid development of sequencing technology, Sanger, Roche 454, Illumina and PacBio sequencing platform had been established, which resulted in the continuous reduction of sequencing costs and many genomes of different species have been reported. Cucumber is a model crop for Cucurbitaceae crop research, and is the first vegetable crop to complete the genome sequencing. Subsequently, more and more Cucurbitaceae crops including watermelon, melon, pumpkin and winter gourd have completed the whole genome De Novo sequencing, which significantly improved research level of genomics, systematic evolution and molecular biology of Cucurbitaceae family. In this review, we summarized the progresses made on the De Novo sequencing of main Cucurbitaceae crops, and their application in understanding the origin and evolution of the family and mining genes controlling agronomically important traits. Moreover, we also prospected the construction of Telomerase-to-Telomere (T2T) genome and pan-genome of Cucurbitaceae family. [ABSTRACT FROM AUTHOR]

Gelidibacter sp. PG-2 is a carotenoid-producing strain, and genome-wide sequencing was conducted in order to further study its carotenoid-producing mechanisms. After the carotenoids were extracted from PG-2, qualitative analysis was performed by LC-MS/MS, the content was calculated by liquid UV full wavelength scanning, and the metabolic pathways of carotenoid-producing in this strain were predicted based on the results of whole genome sequencing. The results showed that the carotenoids produced by PG-2 were zeaxanthin with a content of 185.81 μg/g of dry weight, the whole genome size of PG-2 was 3 850 413 bp, the GC content was 37.91%, the total rRNA was 5, the total tRNA was 37, and the sRNA was 19, which were annotated in COG, GO and KEGG databases to genes 3 401, 1 797 and 1 495, respectively. The strain PG-2 contained three core genes associated with carotenoid production, crtI, crtZ, and lcyB, and their metabolic pathways were predicted. GenBank accession number JAMJTV000000000 was obtained after Genome Framework Sequencing Data submitted to NCBI. The above results demonstrate that the strain PG-2 has the ability to produce carotenoids, and it is speculated that its carotenoid production is related to the genes crtI, crtZ and lcyB. [ABSTRACT FROM AUTHOR]

In order to clarify codon usage bias in chloroplast genome of Elaeagnus mollis, in this study, the whole chloroplast genome sequence of E. mollis was downloaded from GenBank database, the gene sequence of appropriate length was screened, and codon usage bias and its influencing factors were analyzed. Then CodonW software was used to analyze the sequence and obtain the important parameters including A3, T3, C3, G3, GC3, effective number of codon(ENC), relative synonymous codon usage(RSCU). Correlation index analysis, neutral plot analysis, ENc-plot analysis, PR2-plot analysis, and determination of optimal codons were carried out. The results showed that GC content at different locations of codons in the chloroplast genome of E. mollis was different: GC1(41.08%) >GC2(38.17%) >GC3(36.55%). The average ENC value was 50.95, indicating the codon usage bias was weak. Adenine and Uracil were used more frequently in the ends of codons and the finally selected 20 optimal codons had the ends with A or U. Neutral plot analysis and ENc-plot analysis showed that there was no significant correlation within the composition of codons in the chloroplast genome of E. mollis, and the selection pressure was much higher than the mutation pressure. Analysis of PR2-plot revealed that the codon usage in the chloroplast genome of E. mollis was also strongly affected by external stress in addition to mutation pressure. It was concluded that natural selection was the most important factor influencing codon usage pattern in the chloroplast genome of E. mollis. [ABSTRACT FROM AUTHOR]

WA4-43 from the intestinal tract of cockroaches was the first Gordonia that was resistant to gram-positive bacteria. Wholegenome sequencing and comparative genome analysis of WA4-43 revealed the commonness and difference between WA4-43 and other Gordonia, providing a basis for subsequent research. Strain WA4-43 had inhibitory activity only against gram-positive bacteria. The strain WA4-43 was identified as G. terrae by morphological characteristics and molecular biological identification. Genome-wide bioinformatics analysis showed that the strain had a genome size of 5.44 Mb, GC content of 67.76%, and 4 963 protein coding genes, including 3 563, 4 178 and 1 870 genes annotated in GO, COG and KEGG databases, respectively. AntiSMASH predicted 13 secondary metabolite gene clusters in 8 types with an average homology of（22.67±24.72）%. PRISM 4 was used to predict compounds in gene clusters. Comparative genome analysis showed that the G. terrae gene cluster was conserved, but its homology was significantly lower than that of the known gene cluster, and it had the potential to synthesize new compounds. [ABSTRACT FROM AUTHOR]

The phosphate-solubilizing bacterium PSB-R was identified as Serratia marcescens by physiological and biochemical indicators combined with molecular biology technology. Second-generation sequencing platform Illumina NovaSeq PE150 was used to have the whole genome of PSB-R sequenced, and to analyze and predict the composition of genes related to phosphate-solubilizing ability and other plant growth-promoting genes. The response surface optimization test showed that the maximum phosphorus dissolving capacity of PSB-R was 805.199 mg/L.After 10 generations of continuous culture, the phosphorus dissolving capacity was stable and had the ability to dissolve a variety of insoluble phosphates. This study provides a genomic data basis for the further study of the mechanism of phosphate solubilization by phosphate solubilizing bacteria, and confirms that there is a potential for PSB-R to be applied to bacterial fertilizer, which provides a research basis for the subsequent development of phosphate-solubilizing bacterial fertilizer. [ABSTRACT FROM AUTHOR]

Objective: To analyze the influence of three common schemes of endometrial preparation on the pregnancy outcome and related influencing factors during the frozen-thawed embryo transfer (FET) cycle after preimplantation genetic testing (PGT), so as to provide a reference for the assisted reproduction treatment of PGT patients. Methods: The clinical data and pregnancy outcomes of 195 patients with 219 cycles of FET assisted by PGT from January 2017 to January 2022 at the First Clinical Medical College of Lanzhou University were analyzed retrospectively, including the cycles of PGT for aneuploidies (PGT-A), PGT for monogenetic (PGT-M), and PGT for structural rearrangements (PGT-SR). According to the endometrial preparation schemes, these cycles were divided into three groups: the natural cycle group (NC group, 56), the gonadotropin releasing hormone agonist (GnRHa) combined with hormone replacement therapy (HRT) cycle group (GnRHa+HRT group, 102) and the simple HRT cycle group (61). The general clinical data and pregnancy outcomes of the three groups were compared, and the influencing factors of live birth were analyzed by logistic regression. Results: The NC group, GnRHa+HRT group and HRT group all achieved higher clinical pregnancy rate (64.29%, 80.39%, 73.77%, P＞0.05) and live birth rate (83.33%, 85.37%, 84.44%, P＞0.05). The difference of PGT methods used in the three groups was statistically significant (P=0.002). The ratio of patients receiving PGT-SR in the NC group was higher than that in GnRHa+HRT group (P＜0.05). The ectopic pregnancy rate in the NC group was higher than that in the other two groups (P＜0.05). There were significant differences in the BMI, number of oocytes retrieved, number of transferable embryos and number of high-quality blastocysts between the live birth group and the non live birth group (P＜0.05). In addition to the above four factors, the adverse pregnancy history and total number of blastocysts (P＜0.2) of the two groups were included in the logistic regression analysis. It was found that only the number of high-quality blastocysts had an impact on the pregnancy outcomes, and that the number of high-quality blastocysts ＞2 was a protective factor for the outcome of live birth of PGT patients (OR=0.480, P＜0.05). Conclusions: The clinical pregnancy rate and live birth rate of three FET endometrial preparation protocols are similar, but the ectopic pregnancy rate in the NC group is higher. It should be noted that the BMI, number of oocytes retrieved, number of transferable embryos and number of high-quality blastocysts may jointly affect the outcome of live birth of PGT patients, especially the number of high-quality blastocysts, so as to improve the live birth rate of PGT patients. [ABSTRACT FROM AUTHOR]

Hibiscus mutabilis is native to China with a long cultivation history, and is an ancient garden tree species and medicinal plant. In this study, we selected three cultivars of H. mutabilis in a hybrid combination(H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen)to investigate evolutionary characteristics between the cultivars of H. mutabilis and its related species, and clarify the phylogenetic relationship between the cultivars of H. mutabilis and its related species, as well as explore the genetic model of chloroplast genome(cpDNA)of H. mutaibilis at the same time. We first sequenced the three cultivars of H. mutaibilis using Illumina NovaSeq. After assembly and annotation, three complete chloroplast genome sequences were obtained. The cpDNAs of the related species H. taiwanensis from our group, and H. syricus and H. rosa-sinensis from the gene bank. Then we carried out comparative analysis on composition and structure of cpDNAs of four species of Hibiscus and three cultivars of H. mutabilis, and completed its phylogenetic tree reconstruction. The results were as follows: (1)Total sizes of cpDNAs of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 160 880, 160 879, 160 920 bp, respectively, and the total gene number was 130, including 85 protein-coding genes, eight ribosomal RNAs, and 37 transfer RNAs. (2) The comparative analyses showed that the cpDNAs of three cultivars of H. mutabilis and the related species H. taiwanensis were highly conserved, and the inverted repeat regions(IR)were all 26 300 bp; H. rosa-sinensis and H. syriacus shrank to at 25 745 and 25 598 bp, respectively.(3)The phylogenetic analysis revealed that the three cultivars were planted into a monophyletic branch, and then together with H. taiwanensis into a high support branch, indicating that H. mutabilis and H. taiwanensis had the closest relationship; Compared with H. syriacus and H. rosa-sinensis, H. mutabilis and H. taiwanensis were more closely related to H. hamabo, H. tiliaceum and H. canabinus.(4)Three cultivars of H. mutabilis could be distinguished by cpDNA sequence, the length of LSC/SSC of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 89 355 bp/18 925 bp, 89 353 bp/18 926 bp, 89 400 bp/18 920 bp, respectively. And candidate molecular markers and DNA barcodes had been developed from repeat sequence and nucleotide diversity analyses, which could be used as a tool for cultivars identification.(5)The cpDNAs of H. mutabilis cv. Danbanbai and H. mutabilis cv. Jinqiusong showed a minimum difference and had the closest phylogenetic relationship. According to the relationship between their female and offspring, the maternal genetic characteristics of the cpDNAs of Hibiscus were proved. This study will help us to understand the evolutionary characteristics and phylogenetic relationship of cpDNAs of three cultivars of H. mutabilis and H. taiwanensis, and provide basic data on cpDNA for accurate identification of the cultivars of H. mutabilis and breeding of excellent cultivars. [ABSTRACT FROM AUTHOR]

[Objectives]The paper aimed to identify the grape homeobox(HB)gene family using bioinformatics methods, systematically analyze their sequence and structural characteristics, evolutionary features and expression characteristics, and screen candidate grape HB genes in response to bud dormancy and various stresses. [Methods]Using the local BLAST program, the HB gene in Arabidopsis thaliana was used as the target sequence for comparison with the grape whole genome protein sequence. ExPASy was used to predict the physical and chemical properties of grape HB gene family proteins, and MapGene2Chro was used to locate chromosomes. Based on Neighbour-joining method, the MEGA X software was used to perform phylogenetic tree of these HB genes in grape and A.thaliana. Meanwhile, TBtools software was used to analyze the gene structure, conserved domain and promoter cis-elements characteristics of HB family members. Genomic collinearity of HB gene family members between grape and A.thaliana was analyzed by MCScanX. Based on known transcriptomic data, the expression of HB genes was analyzed under bud dormancy, fruit development and different abiotic stresses. [Results]Eighty HB genes were identified in the grape genome, distributed on 18 chromosomes, which were divided into 9 subfamilies based on evolutionary analysis. The amino acid quantity was 66-1 772, molecular weight was(8.28-198.55)×103 and isoelectric point was 4.60-10.03. The prediction of subcellular localization indicated that the family members were mainly located in chloroplasts. Gene structure analysis revealed that all grape HB members contain exons ranging from 1 to 20 in number. There were 2 pairs of tandem duplicated genes and 23 co-linear pairs in the grape HB gene family, and 82 co-linear pairs between A.thaliana and grape. Promoter cis-elements analysis showed that the HB family contained cis-elements related to light response, plant hormones and stress, and tissue-specific expression. Among grape HB family proteins, KNOX and BEL subfamily members had the closest interaction. Through the analysis of the expression profile of grape HB gene family, it was found that most HB family members were significantly differentially expressed under bud dormancy and drought stress. In addition, seven HB family members were found to be involved in bud dormancy regulation, and VvHB9 and VvHB34 were involved in various abiotic stresses. [Conclusions]In this study, basic information was identified and analyzed on the members of the grape HB family, and several key genes were screened which were involved in the regulation of bud dormancy and response to multiple abiotic stresses based on transcriptomic data. [ABSTRACT FROM AUTHOR]

canthocalyx alba is a common medicinal plant in Tibetan of China, and there are few reports on its whole chloroplast genome now. In order to reveal basic characteristics of the whole chloroplast genome of A. alba and explore its phylogeographic structure, ten individuals from five wild populations were sequenced by Illumina sequencing platform. After assembly and annotation, ten complete chloroplast genome sequences were obtained. Moreover, genome characteristics and phylogenetic relationships were explored. The results were as follows:(1)The complete chloroplast genomes of A. alba were 155 335-156 266 bp. A total of 113 genes were annotated, including 72 protein-coding genes, 30 tRNA genes and four rRNA genes. The chloroplast genome was highly conserved in species in terms of size, structure, GC content and gene composition.(2)Genomic comparative analysis showed that the fragments with large variation were located in the single copy region, and there was no obvious expansion and contraction at the IR boundaries.(3)Analysis of population genetics revealed rich genetic diversity in the wild populations and significant geographic structure, and there were certain relationships between genetic distances and geographic distances. This study lays the foundation for studies on population genetics and phylogenomics of species in Acanthocalyx. [ABSTRACT FROM AUTHOR]

Carpinus tientaiensis is an endangered plant species with sparse population densities and is endemic to China. The distribution of this species is restricted to the territory of Zhejiang Province and its survival rate is very low. Based on data of chloroplast genome(cpDNA)single nucleotide polymorphism(SNP)in six natural populations(including the mother plants of all populations), we investigated genealogical structure and systematic development, assessed how endangered C. tientaiensis is and put forward relevant conservation strategies. The genomic DNA of C. tientaiensis was extracted using TIANGEN kit method and a library was constructed for high-throughput sequencing with Illumina NovaSeq 6000. To obtain the sequence of chloroplast complete genome, cpDNA maps were constructed using the online program OGDRAW. Nucleotide diversity was analyzed by DnaSP software while PopART was used for haploid network construction and RAxML was adopted for maximum likelihood(ML)tree construction. Finally, MrBayes software was used for construction of Bayes tree. The results were as follows:(1)According to chloroplast complete genome sequence analysis of C. tientaiensis, most of the protein-coding genes and amino acid sequences showed obvious codon preference. Moreover, chloroplast long-term relationship(cpLTR)revealed 32 forward repeats, 25 palindromic repeats and 22 reverse repeats. We detected 87 simple sequence repeats(SSR)in different types, most of which were A/T rich and the number of single nucleotides was the largest.(2)A total of 314 SNPs was identified in the cpDNA of C. tientaiensis. Single-nucleotide substitution indicated that C. tientaiensis was monophyletic and could be categorized into Tiantai County(THS)and Jingning County(JST)populations. The evolution of the haplotypes of the population manifested stellar radiation.(3)The variation of nucleotide diversity was low in all populations(Pi<0.005)and the haplotype diversity of THS and JST populations was also low(Hd 0.5-0.6). This indicated that C. tientaiensis had undergone historically local expansions after experiencing bottlenecks across its evolution history, with lower genetic variation within populations and higher level of diversity among populations. The results of SNP of the cpDNA reveal the genetic diversity and lineage differentiation of C. tientaiensis, and provide theoretical basis for conservation of the genetic resources as well as rescue of this endangered plant species. [ABSTRACT FROM AUTHOR]

Estimating the time scale of species evolution is an important part of life evolution study. It is found that there are significant differences in the evolution rates of different genes and species in recent years, which challenges the molecular clock hypothesis to a great extent. Therefore, new methods are needed to re-estimate the evolutionary event time. The whole genome sequence of angiosperms makes it possible to estimate the evolutionary time from the whole genome perspective. In order to re-estimate the evolution time of angiosperms, an evolution rate correction model based on genomic data is established according to the idea that shared polyploidy events or shared divergence events should have the same Ks peak. The results were as follows:(1)Three common ways to obtain Ks distribution were compared and analyzed, which showed that the best way was to extract the median of Ks values on collinear blocks.(2)The change process of Ks distribution was simulated with time accumulation coefficient(v)of Ks values. When v was assumed to obey the normal distribution, the Ks distribution had a long tail phenomenon.(3)The correction process was described in detail, which was conducive to the understanding and wide spread of this method. From the application of correction method in angiosperms, it was found that the Ks peak before correction was not linear with time, while the Ks peak after correction was directly proportional to time, indicating that it is very necessary to estimate the time of species evolution events after correcting the Ks peak. It was also found that although the evolution rate of angiosperms was significantly different, the evolution rate between different branches was still partially consistent. For example, Magnoliids had the slowest evolutionary rate, followed by Eudicots and Monocots. When the environment changed greatly, most species of different lineages of angiosperms had synchronous radial evolution and adaptive evolution. Finally, a relatively reliable angiosperm evolution time axis was establish, which helps to understand the evolution process and model, especially to understand the phylogenetic relationship and the causes of diversity and provides phylogenetic and evolutionary support for plant research. [ABSTRACT FROM AUTHOR]

Acinetobacter junii WCO-9 is a high-yield lipase-producing strain isolated from oil-contaminated soil. The lipase produced by this strain has significantly better hydrolysis activity than that of the control strain ATCC 17908. In order to explore the efficient enzyme production mechanism of WCO-9 strain and to discover specific lipase functional genes，ONT（Oxford Nanopore Technologies）was used to complete the whole genome sequencing of WCO-9 strain，and the comparative genomic analysis of the same strain was carried out. The results showed that the genome size of lipase-producing WCO-9 strain was 3.19 Mb，GC content was 38.62%，and there were 2 929 coding genes， including 11 lipase-coding genes（1 specific gene）and 3 lipase molecular chaperones. The collinearity analysis also revealed that the WCO9 strain was significantly different from the control strain ATCC 17908. The whole genome sequence analysis of WCO-9 strain will be of great significance for the study of high-efficiency enzyme production mechanism and the discovery of new lipase-specific genes，which provides a theoretical basis for the creation and industrial application of high-yield lipase engineering bacteria in the future. [ABSTRACT FROM AUTHOR]

Opisthopappus taihangensis and O. longilobus, being perennial cliff herbs and endemic to Taihang Mountains, are important wild germplasm resources of Compositae, and have high economic and ecological values. To determine the appropriate sequencing strategy for the whole genome of O. taihangensis and O. longilobus, in this study, the genome sizes, heterozygosity, GC content, and repeatability were analyzed through the flow cytometry and high-throughput sequencing methods. The results were as follows:(1) Using maize of known genome size as controls, the genome size of O. taihangensis was approximately 2.1 Gb, while that of O. longilobus was approximately 2.4 Gb.(2) For O. taihangensis, the revised genome size was 3.13 Gb, and the repetitive sequences proportion, heterozygosity and GC content in the whole genome were estimated to be 84.35%, 0.99% and 36.56% respectively. Within O. longilobus, the revised genome size, the repetitive sequences proportion, heterozygosity and GC content were 3.18 Gb, 83.83%, 1.17% and 36.62% respectively.(3) The initial depth and content distribution of GC appeared abnormal after initial assembly, which might be related to the relatively high heterozygous rate of the two species. Above all, the whole genomes of O. taihangensis and O. longilobus were both large and complex genomes with high heterozygosity and repetitiveness. Therefore, it suggests that the use of Illumina + PacBio sequencing assembly strategy for the whole genome sequencing analysis of two Opisthopappus species in the future. [ABSTRACT FROM AUTHOR]

The pan-genome can represent all of the genetic diversities in a species or population, which is a limitation for obtaining only one single reference genome. The pan-genomics is becoming a new hot research area and being widely applicated in researches of many species in plants, animals and microorganisms, as the development of the whole genome sequencing and analysis technology. It provides powerful tools for resolving the genetic variation and polymorphism at levels of species or taxa, researches of functional genomics and reconstruction of phylogenetics, obtaining abundant of significant research achievements. However, present researches on pan-genomics still need to improve due to several problems, e.g., extensive cost of whole genome sequencing and data analysis, inconsistent analysis standards, lack of deeper and comprehensive explanation of the obtained data, and difficulty of application of the research achievements. We summarized the research progresses of pan-genomes on exploitation of genetic diversity and functional genomics, including construction of a pan-genome map, identification of genome variations and favorable genes, polymorphism of functional genes, population genetic diversity and systematic evolution, and discussed its potential in application of different research fields. Furthermore, we discussed the limitations existed in the present studies and possible solutions, and presented the prospect in the future on pan-genomics. [ABSTRACT FROM AUTHOR]

[Objective] The present study aimed to reveal the relationship between the amino acid sequence, secondary structure, tertiary structure and their functions of the three keratinases produced by the Streptomyces sp. DJ strain. [Method] Based on whole genome sequencing results of DJ strain, the sequence and structure of its three keratinases were analyzed and predicted by using software, such as Bio-edit, DNAMAN, Discovery Studio2.5 et al, and website like https://swissmodel.expasy.org/,and so on. [Result] DJ strains secreted three kinds of keratinases（K1,K2 and K3）,and the keratinases belonged to serine proteases of the S8 family, and their signal peptides, leading peptides and mature peptides were more consistent in the composition, polarity and length of amino acid residues. Three keratinases were modeled using 5 WSL.1.A as template by the homology modeling technique. The 3-D structure of each keratinase contained six α-helix, two 310-helix and fifteen β-folded secondary structures.K1 contained two disulfide bonds, 1 Ca and 2 Ca sites, while K2 and K3 had only one disulfide bond and 1 Ca site. The Pro270 residues of all three keratinases were respectively located in the loop ring, while only Pro242 residue of K2 was also located in the loop ring. The substrates binding regions of the three keratinases were mainly composed of hydrophobic residues, so these keratinases preferred substrate with strong hydrophobicity. For the substrate binding regions of the keratinases, the S1 and S2 played a key role in substrate specificity. And the substrate specificity was different due to the non-conservative nature of the residues at important sites in the S1 and S2 of the three keratinases. [Conclusion] The differences in amino acid, disulfide bond, proline and calcium binding sites leaded to the different stability of the three keratinases, besides the surface charge distribution and substrate binding regions resulted the complementarity to the feather hydrolysis sites. This might be an important reason for the efficient degradation of feathers by DJ strains. [ABSTRACT FROM AUTHOR]

[Objective] The Unigene produced by leaf transcriptome of Nymphaea colorata and N.micrantha and the whole genome sequence of N.colorata were analyzed according to SSR loci characteristics. It provided basic data for the germplasm resource identification, genetic diversity analysis and genetic linkage map construction of water lily plants.[Method] Based on the leaf transcriptome data of N.colorata and N.micrantha which were acquired previously in the laboratory and the published genome of N.colorata,MISA software was used to search SSR loci and analyze the frequency, length and primitive types of SSR.[Result] 38 998 SSR loci were found among the 114 762 Unigenes sequences obtained from the transcriptome of N.colorata and N.micrantha.The SSR site frequency was 33.98%.Among them, 30 124 SSR loci belong to complete types. The total length of the SSR motif sequence was 465 550 bp, and had a total average of 21.65 bp.249 029 SSR sites were searched in the N.colorata genome, with an average distribution frequency of 609.0/Mb, including 163 265 intact SSR sites; the total length of SSR motif sequence was 2 775 181 bp, and 27.25 bp, accounted for 0.68% of N.colorata genome size. In the transcriptome and genome, the SSR loci were mainly dinucleotide and single nucleotide repeats, which respectively accounted for 48.87%,41.03% and 51.70%,43.37% of the total SSR. Among dinucleotide repeat motifs, AG/TC and AT/TA types were higher and both much higher than other types of repeat motifs. The number of repetitions of each type in the SSR primitive was mainly 5 to 11 times, of which 10 times were the most. Twelve pairs of SSR primers with good amplification and high polymorphism were selected based on fluorescence capillary electrophoresis from synthetic 144 pairs of SSR primers.[Conclusion] Low-level primitive types are abundant in the SSR of N.colorata and N.micrantha transcriptome and genome, which has great potential for developing and screening SSR primers with high polymorphism. The selected 12 pairs with good amplifications and high polymorphism of SSR primers can be used to study the identification of germplasm resources, genetic diversity analysis and genetic construction of plant chain map. [ABSTRACT FROM AUTHOR]

Aeromonas veronii JY01 is a strain of dominant gram-negative bacterium isolated from the lesions of goldfish, such as rotten tails, rot, and ulcers in a farm in Fuzhou. In this study, the whole genome of the strain of Aeromonas veronii JY01 was sequenced based on the Illumina PE150 sequencing platform and Pacbio sequencing platform. The sequencing data was assembled and analyzed, the gene prediction and functional annotation were performed by bioinformatics methods, meanwhile the prediction of pathogenic genes and drug resistance genes were carried out. The results showed that the genomic sequence length of the strain of Aeromonas veronii JY01 was 4. 97 Mb, and the GC content was 58. 17%. A total of 4 601 encoding genes, 31 rRNA, 16 gene islands and 124 tRNA were predicted, among which, 3 461 genes were annotated in COG, 3 082 genes were aggregated in GO cluster analysis, and 4 345 genes were enriched in KEGG metabolic pathway. It was predicted that the strain of Aeromonas veronii JY01 carried 13 virulence factors including 240 related virulence genes, and 9 types of antibiotics resistance including 175 antibiotic resistance genes. [ABSTRACT FROM AUTHOR]

[Objectives] The objectives of this study were to identify the defensin-like(DEFL) gene family of pear(Pyrus bretschneideri) genome, and analyze their sequence characteristics, evolutionary relationship, gene structure, conservatively functional domains of amino acid sequences, chromosomal locations and expression characteristics, and provide a reference to the functional research and application of PbrDEFL.[Methods] Based on the whole genome sequencing of P. bretschneideri, the sequences of PbrDEFL were identified and analyzed by bioinformatics. Quantitative real-time PCR(RT-qPCR) and transcriptome data were used to analyze the expression patterns of PbrDEFL from various tissues and different stages of pollen tube development. Subcellular localization was used to analyze the distributions of PbrDEFL38 and PbrDEFL15 in cells. Optimum conditions were established for the production and purification of recombinant PbrDEFL38 and PbrDEFL15 from Escherichia coli.[Results] The results showed that PbrDEFL family were divided into 2 groups, which included 39 DEFL genes(PbrDEFL1-PbrDEFL39) containing the stable cysteine αβ model(CS αβ motif). Members of PbrDEFL gene family were unevenly distributed among 9 chromosomes and purification selection was the driving force of PbrDEFL gene family. RT-qPCR analysis showed that the expression of PbrDEFL presented tissue-specificity, mainly expressed in pollen or leaves; and over 60% of PbrDEFL genes showed a single peak expression trend during the pollen tube development in two pear cultivars('Dangshansuli' and 'Huanghua'). The prediction of PbrDEFL subcellular localization indicated that all proteins were located outside the cell, which was further confirmed by transient expression of PbrDEFL38-GFP and PbrDEFL15-GFP in tobacco. Additionally, the expression and purification conditions of PbrDEFL38 and PbrDEFL15 from E.coli were further analyzed. And the most suitable induction was 15℃ and 0.5 mmol·L-1 IPTG.[Conclusions] This study showed that the members of PbrDEFL gene family were highly conserved, and function was mainly outside the cell. It played an important role in the process of plant immune defense as well as in the pear pollen tube growth and self-incompatibility. [ABSTRACT FROM AUTHOR]

There are a number of structural variations of different lengths in the human genome, which has a significant impact on the occurrence of cancer. With the development of new generation high -throughput sequencing technology and the falling cost of sequencing make it possible to study structural variation at whole genome level. This paper analyzed the samples from three different regions of the 1000 genomes and colorectal cancer samples from the CGHub database based on the clustering algorithm. It analyzed the mechanisms of the structural variation according to the sequence homology at the breakpoints. And it analyzed the relationship between structural variation and cancer，as well as the relationship between structural variation and regional factors by variance analysis and non-parameter tests. In the end，it pointed out the future development in this research area. [ABSTRACT FROM AUTHOR]