Transcriptome sequencing reveals novel biomarkers and immune cell infiltration in esophageal tumorigenesis

BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.

Evaluation of genetic response of mesenchymal stem cells to nanosecond pulsed electric fields by whole transcriptome sequencing

BACKGROUND Mesenchymal stem cells(MSCs)modulated by various exogenous signals have been applied extensively in regenerative medicine research.Notably,nanosecond pulsed electric fields(nsPEFs),characterized by short duration and high strength,significantly influence cell phenotypes and regulate MSCs differentiation via multiple pathways.Consequently,we used transcriptomics to study changes in messenger RNA(mRNA),long noncoding RNA(lncRNA),microRNA(miRNA),and circular RNA expression during nsPEFs application.AIM To explore gene expression profiles and potential transcriptional regulatory mechanisms in MSCs pretreated with nsPEFs.METHODS The impact of nsPEFs on the MSCs transcriptome was investigated through whole transcriptome sequencing.MSCs were pretreated with 5-pulse nsPEFs(100 ns at 10 kV/cm,1 Hz),followed by total RNA isolation.Each transcript was normalized by fragments per kilobase per million.Fold change and difference significance were applied to screen the differentially expressed genes(DEGs).Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to elucidate gene functions,complemented by quantitative polymerase chain reaction verification.RESULTS In total,263 DEGs were discovered,with 92 upregulated and 171 downregulated.DEGs were predominantly enriched in epithelial cell proliferation,osteoblast differentiation,mesenchymal cell differentiation,nuclear division,and wound healing.Regarding cellular components,DEGs are primarily involved in condensed chromosome,chromosomal region,actin cytoskeleton,and kinetochore.From aspect of molecular functions,DEGs are mainly involved in glycosaminoglycan binding,integrin binding,nuclear steroid receptor activity,cytoskeletal motor activity,and steroid binding.Quantitative real-time polymerase chain reaction confirmed targeted transcript regulation.CONCLUSION Our systematic investigation of the wide-ranging transcriptional pattern modulated by nsPEFs revealed the differential expression of 263 mRNAs,2 miRNAs,and 65 lncRNAs.Our study demonstrates that nsPEFs may affect stem cells through several signaling pathways,which are involved in vesicular transport,calcium ion transport,cytoskeleton,and cell differentiation.

Analyses of Chicken Tenderness Traits Based on Transcriptome Sequencing

The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.

Study on compound Duzhong Jiangu granule in the treatment of knee osteoarthritis based on transcriptome analysis strategy

Duzhong Jiangu Granule in the treatment of primary osteoarthritis(POA)model of postmenopausal kidney deficiency type in Hartley female guinea pigs after ovariectomy,and the correlation between gene expression of bone marrow tissue,cartilage tissue,and knee osteoarthritis.Methods:383-months-old Hartley female guinea pigs after one week of adaptive feeding were weighed about 400 g±20 g,numbered,and sorted by ear tag.Six of them were selected as normal groups by looking up random number tables.The remainder were removed from the bilateral ovaries to construct the postmenopausal kidney deficiency model,and castrated guinea pigs were used to construct the postmenopausal kidney deficiency POA model.After the modeling cycle,a guinea pig from the blank group and a guinea pig from the model group were sacrificed and the right knee was observed.The model was established and the experiments continued.There were five guinea pigs in the blank group,and the remaining model guinea pigs were randomly divided into model control group,high-dose group of compound Duzhong Jiangu granules,middle-dose group of compound Duzhong Jiangu granules,low-dose group of compound Duzhong Jiangu granules and design group,with 5 guinea pigs in each group.Blanks and model groups were given a cellulose sodium solution by gavage.The guinea pigs were sacrificed after 30 days of intragastric administration.The left knee cartilage and bone marrow of the blank group,model group,middle dose group,and high dose group of compound Duzhong Jiangu granule were collected and applied to transcriptome sequencing,and the sequencing data were analyzed,including differential gene expression analysis,functional enrichment analysis of database established by Gene Ontology federation(GO)and Kyoto Encyclopedia of Gene and Genome(KEGG)pathway enrichment analysis.The complete specimens of the right knee joint were collected,and the morphological changes of the cartilage of the right knee joint in each group were observed by saffron rapid green staining,and the subchondral bone was quantitatively analyzed by Micro CT so that the expression of TRAF6,MIP-1βand IL-1βprotein in NF-kappa B signaling pathway was detected by Western Blot technique(WB).Results:The results of Safranin Fast Green staining showed that Compound Duzhong Jiangu Granules could effectively reduce the degree of morphological damage of articular cartilage in guinea pigs with the POA model.According to the analysis results of the subchondral bone structure under Micro CT,Compound Duzhong Jiangu Granules can improve the bone condition of the POA model,thus delaying the process of degenerative changes of the knee joint.From the results of transcriptome analysis,Compound Duzhong Jiangu Granules can inhibit the expression of related genes in POA model guinea pigs.According to the results of Wester Bolt verification,Compound Duzhong Jiangu Granules can effectively improve knee osteoarthritis.Conclusions:The effect of Compound Duzhong Jiangu Granules on OA is obvious,and its mechanism may be related to the expression of genes GZMK,Jchain,igkc,IGHV3-74,IGHV3-11,IGHV4-1,CCL5,and IGKV1–39.

Use of transcriptome sequencing to explore the effect of CSRP3 on chicken myoblasts

The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.

Transcriptome-based analysis of key genes and pathways affecting the linoleic acid content in chickens

Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally.The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference.However,the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear.As the molecular mechanisms of linoleic acid deposition are not well understood,to investigate the main effector genes affecting the linoleic acid content,this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing(RNA-Seq)and weighted gene coexpression network analysis(WGCNA).We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers.A total of 399 Tiannong partridge chickens were slaughtered at 126 days of age,fatty acid levels were measured in pectoral muscle,and pectoral muscle tissue was collected for transcriptome sequencing.Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes.KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation.A total of 13310 genes were identified after quality control of transcriptomic data from 399 pectoral muscle tissues.WGCNA was performed,and a total of 26 modules were obtained,eight of which were highly correlated with the linoleic acid content.Four key genes,namely,MDH2,ATP5B,RPL7A and PDGFRA,were screened according to the criteria|GS|>0.2 and|MM|>0.8.The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways.In this study,a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens,and MDH2,ATP5B,RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content.The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle,providing an important reference for the breeding of slow-type yellowfeathered broiler chickens.

The transcriptome analysis of cleft lip/palate-related PTCH1 variants in GMSM-K cells show carcinogenic potential

Cancer progression involves the sonic hedgehog(SHH)pathway,in which the receptor PTCH1 actives the downstream pathways.Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome(NBCCs)including neoplastic disease and congenital disorder.To evaluate the relationship between PTCH1 and cancer,we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells(GMSM-K).Then we screened six PTCH1 variants associated with cleft lip/palate(CL/P),one of the congenital disorders in NBCCs,and generated PTCH1 variant and wild-type recombinant PTCH1^(−/−)GMSM-K cell lines.Transcriptome sequencing was conducted in these cell lines.The results revealed that differentially expressed genes(DEGs)in PTCH1^(−/−)GMSM-K were enriched in extracellular compartments,contributing epithelial diseases by pathway enrichment analysis.RT-PCR confirmed that KRT34,KRT81,KRT86,PDGFB,and WNT10B genes,associated with extracellular compartments were highly expressed in PTCH1^(−/−).The Kyoto Encyclopedia of Genes and Genomes analysis also suggested that DEGs are closely related to focal adhesion,transcriptional misregulation,and proteoglycans in breast and gastric cancers.Comparative analysis of samples revealed that the CL/P-associated PTCH1 variants A443G and V908G are potentially carcinogenic.These findings provide new insights into the carcinogenic potential of PTCH1 dysfunction.

Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

In this study,wild eggplant germplasm No.M239,which is highly susceptible to Verticillium wilt,was used as the experimental material.The physiological and biochemical indices(SOD,PAL,MDA and soluble protein)of M239 roots were measured at different times(0,12,24,36,48,60 and 72 h)post inoculation with Verticillium dahliae,and the key time points for the M239 response to Verticillium wilt infection were screened.Then,RNA-Seq technology was used to screen the differentially expressed genes(DEGs)in M239 roots at 0,12 and 48 h post-inoculation(hpi).The transcriptional results of M239 were also compared with those resistance genes from some reported wild relative Solanum species(S.sisymbriifolium and S.aculeatissimum).Then some DEGs were chosen for validation by qRT–PCR.The results showed that 12 and 48 hpi were the turning points in the changes in all physiological and biochemical indices.A total of 6,783 DEGs were identified by RNA-Seq,including 6,141 DEGs(3,046 upregulated and 3,095 downregulated)at the M_12 h vs.M_0 h,1,903 DEGs(792 upregulated and 1,111 downregulated)at M_48 h vs.M_12 h,and 1,261 DEGs that appeared simultaneously in both stages.KEGG enrichment analysis showed that there were 5 metabolic pathways enriched from DEGs,which were mostly related to primary metabolism,such as glycolysis,amino acid and ribosome biogenesis.Compared with the NCBI non-redundant protein(NR)database,one Ve2 homologous gene and 8 PR protein-related genes were screened.Transcription factor analysis showed that there were a large number of DEGs,such as MYB,AP2-EREBP,bHLH,NAC and Orphans in the two stages.Compared with the reported Verticillium wilt-resistant wild eggplant species,it was found that there were fewer genes and enriched metabolic pathways in the M239 response to Verticillium wilt infection,and it also lacked the response of some known key resistance genes.These results proved that the above resistance genes and metabolic pathways played a key role in the wild eggplant response to V.dahliae infection.

Transcriptome sequencing analysis of ursolic acid-mediated proliferation suppression on cutaneous T-cell lymphoma cells

Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.

The early life immune dynamics and cellular drivers at single-cell resolution in lamb forestomachs and abomasum

Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered stomach is crucial for the health and well-being of young ruminants,especially the immune development.However,the dynamics of immune development are poorly understood.Results We investigated the early gene expression patterns across the four-chambered stomach in Hu sheep,at 5,10,15,and 25 days of age.We found that forestomachs share similar gene expression patterns,all four stomachs underwent widespread activation of both innate and adaptive immune responses from d 5 to 25,whereas the metabolic function were significantly downregulated with age.We constructed a cell landscape of the four-chambered stomach using single-cell sequencing.Integrating transcriptomic and single-cell transcriptomic analyses revealed that the immune-associated module hub genes were highly expressed in T cells,monocytes and macrophages,as well as the defense-associated module hub genes were highly expressed in endothelial cells in the four-stomach tissues.Moreover,the non-immune cells such as epithelial cells play key roles in immune maturation.Cell communication analysis predicted that in addition to immune cells,non-immune cells recruit immune cells through macrophage migration inhibitory factor signaling in the forestomachs.Conclusions Our results demonstrate that the immune and defense responses of four stomachs are quickly developing with age in lamb's early life.We also identified the gene expression patterns and functional cells associated with immune development.Additionally,we identified some key receptors and signaling involved in immune regulation.These results help to understand the early life immune development at single-cell resolution,which has implications to develop nutritional manipulation and health management strategies based on specific targets including key receptors and signaling pathways.

2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-Glucoside modulates CHEK2 and CCND1 alternative splicing to inhibit MCF-7 cells proliferation

Background:In our previous study,we observed a synergistic effect of 2,3,5,4’-Tetrahydroxystilbene-2-O-b-D-glucoside combined with adriamycin to induce apoptosis in MCF-7 breast cancer cells.However,the underlying mechanisms of epigenetic modifications,such as alternative splicing,have not been explored.In this study,we aimed to investigate the mechanism by which THSG inhibits MCF-7 cell proliferation using full-length transcriptome sequencing.Methods:First,cell viability was examined using the methyl thiazolyl tetrazolium method and full-length transcriptome sequencing was performed to identify genes and pathways.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used to identify the principal pathways and targets of THSG.Flow cytometry analysis of cell cycle distribution was performed.Meanwhile,the analysis of alternative splicing and domains of the key proteins was conducted.Quantitative polymerase chain reaction and western blotting were performed for verification.Results:THSG showed significant cytotoxic activity in MCF-7 cells.Full-length transcriptome sequencing revealed differential alternative splicing with 173 upregulated and 263 downregulated genes.Further analysis identified distinct differential expression of genes(CHEK2-211 and CCND1-201)involved in the cell cycle in the THSG-treated group.Subsequently,alternative splicing types of CHEK2(mutually exclusive exon)and CCND1(intron retention).We found that THSG downregulated mRNA expression,as confirmed by quantitative polymerase chain reaction analysis.Interestingly,protein structural analysis revealed that THSG treatment led to the generation of CHK2-211,which was the result of a mutation in the amino acid residues(GLU-150,ASN-151)of the CHEK2 domain(VAL-150,GLY-151).and CyclinD1-201 were obtained when an amino acid(ASP-267)in the domain was lost in CyclinD1.Moreover,molecular docking analysis demonstrated that the domains of key proteins could bind THSG more effectively,with no difference in affinity.Western blotting confirmed that THSG inhibited the expression of CHK2 and CyclinD1.Conclusion:THSG modulated the alternative splicing of CHEK2 and CCND1 by inducing G0/G1 cell cycle arrest,consequently suppressing MCF-7 cell proliferation.

Transcriptome analysis of Idesia polycarpa Maxim. var vestita Diels fl owers during sex differentiation

Idesia polycarpa Maxim.var vestita Diels.is a dioecious tree species native to eastern Asia.There are diffi culties associated with distinguishing the sex of the plant at the seedling stage.In order to explore the mechanism of sex diff erentiation in fl ower development,we conducted the transcriptome profi les of male and female fl owers at early,metaphase and late developmental stages.Approximately 123,335 unigenes with a total length of 83,996 Mb and an average length of 168 bp were assembled.The unigenes were blasted into Nr,Nt,Pfam,KOG/COG,Swiss-prot,KEGG,GO databases.Homology analysis demonstrated that I.polycarpa and black cottonwood had the highest homology with the alignment of 92,871 sequences.This study identifi ed 80 groups of transcription factor families with a total of 1475 unigenes,mainly including MYB,WRKY,AP2 and bHLH transcription factor families.KEGG pathway analysis showed that the expression of numerous plant hormones(cytokinin,gibberellin and ethylene)and fl avonoid biosynthesis pathway were diff erent at various stages of female and male fl ower development.In addition,a number of unigenes associated with fl owering were identifi ed which were key genes associated with photoperiodic,vernalization,thermosensory,gibberellin,and autonomic pathways.The results show that I.polycarpa fl oral organ development was in accordance with the ABCDE model,in which the down-regulation of the B gene family might aff ect stamen fertility in late stages of female fl ower development.qRTPCR experiments validated that the expression patterns of 15 unigenes were consistent with those in RNA-seq results.The results highlight a central role for plant sex identifi cation in seedling production and a sex-determining mechanism for dioecious plants.In addition,the transcriptome data provided a theoretical basis for I.polycarpa genetic diversity analysis and molecular-assisted breeding.

Transcriptome-wide evolutionary analysis on essential brown algae(Phaeophyceae)in China

Brown algae （Chromista, Ochrophyta, Phaeophyceae） are a large group of multicellular algae that play im-portant roles in the ocean＇s ecosystem and biodiversity. However, poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field. In this study, we sequenced the de novo transcriptome of 18 major species of brown algae in China, covering six orders and seven families, using the high-throughput sequencing platform Illumina HiSeq 2000. From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum, we identified 108 nuclear-generated orthologous genes and clarified the phy-logenetic relationships among these brown algae based on a multigene method. These brown algae could be separated into two clades：Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmares-tiale-Fucales. The former was at the base of the phylogenetic tree, indicating its early divergence, while the latter was divided into two branches, with Order Fucales diverging from Orders Ectocarpales, Laminariales, and Desmarestiale. In our analysis of taxonomy-contentious species, Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina, respectively, while Petalonia fascia showed possible relation to genus Scytosiphon. The study provided molecular evidence for the phylo-genetic taxonomy of brown algae.

The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome

Phosphomannomutase （PMM;EC 5.4.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project （OneKP） in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.

Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we ana-lyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants （OneKP） Project, by using a next-generation high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST;25 734 scaffolds were clustered into 37 Gene ontology functional groups;6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases （vHPO） in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase （vIPO） and 37 segments of vanadium-de-pendent bromoperoxidase （vBPO）. Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological charac-teristics and economic values of S. japonica species.

Whole transcriptome analysis on blue light-induced eye damage

AIM:To analyze abnormal gene expressions of mice eyes exposed to blue light using RNA-seq and analyze the related signaling pathways.METHODS:Kunming mice were divided into an experimental group that was exposed to blue light and a control group that was exposed to natural light.After 14 d,the mice were euthanized and their eyeballs were collected.Whole transcriptome analysis was attempted to analyze the gene expression of the eyeballs using RNA-seq to reconstruct genetic networks.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis were used to reveal the related signaling pathways.RESULTS:The 737 differentially expressed genes were identified,including 430 up and 307 down regulated genes,by calculating the gene FPKM in each sample and conducting differential gene analysis.GO and KEGG pathway enrichment analysis showed that blue light damage may associated with the visual perception,sensory perception of light stimulus,phototransduction,and JAKSTAT signaling pathways.Differential lnc RNA,circ RNA and mi RNA analysis showed that blue light exposure affected pathways for retinal cone cell development and phototransduction,among others.CONCLUSION:Exposure to blue light can cause a certain degree of abnormal gene expression and modulate signaling pathways in the eye.

Transcriptome based high-throughput SSRs and SNPs discovery in the medicinal plant Lagenaria siceraria

Lagenaria siceraria(Molina)Standley has unique biological characteristics with high nutritional and medicinal values.It is an important pharmaceutical plant with various biologically active ingredients.Genetic improvement and deeper genomic studies require a rich resource of molecular markers.The application of next-generation sequencing technology,especially for transcriptome profiling,has greatly facilitated high throughput single nucleotide polymorphism(SNP)and simple sequence repeat(SSR)discovery.In this study,we sequenced the transcriptome of three major cultivars of L.siceraria and obtained 64.88 GB of clean data.The assembled high-quality reads were clustered into 89,347 unigenes,which were annotated by non-redundant protein database,Swiss-Port,Eukaryotic Ortholog Groups,Kyoto Encyclopedia of Genes and Genomes,and gene ontology databases.A total of 8,891 SSR and 35,873 SNP markers were predicted from unigenes by MISA and SAM tools,respectively.Characterization of the predicted markers in L.siceraria showed that the SSR and SNP densities were 60 and 243 markers per Mb of genome,respectively,and the estimated ratio of transition to transversion of SNP was 2.016.These markers will be very useful for genetic studies in L.siceraria,especially for the high-density linkage map construction and genome-wide association studies.Further genomic studies based on these results will facilitate the identification of novel genes or alleles of pharmaceutical importance.

Identification of key genes and pathways in gastric signet ring cell carcinoma based on transcriptome analysis

BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs have not yet been performed for GSRCC.AIM To identify key mRNAs and signaling pathways in GSRCC.METHODS A transcriptome analysis of two GSRCC and two non-GSRCC samples was performed in this study.Differentially expressed mRNAs and pathways were identified based on the KEGG and PANTHER pathway annotations.The interactive relationships among the differential genes were mapped with the STRING database.Quantitative real-time polymerase chain reaction was used to validate the key gene expression in GSRCC.RESULTS About 1162 differential genes(using a 2-fold cutoff,P<0.05)were identified in GSRCC compared with non-GSRCC.The enriched KEGG and PANTHER pathways for the differential genes included immune response pathways,metabolic pathways,and metastasis-associated pathways.Ten genes(MAGEA2,MAGEA2B,MAGEA3,MAGEA4,MAGEA6,MUC13,GUCA2A,FFAR4,REG1A,and REG1B)were identified as hub genes in the protein-protein interaction network.The expression levels of five genes(MAGEA2,MAGEA3,MAGEA4,MAGEA6,and REG1B)showed potential clinical value.CONCLUSION We have identified the potential key genes and pathways in GSRCC,and these hub genes and pathways could be diagnostic markers and therapeutic targets for GSRCC.

Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.

Comparative analysis on transcriptome sequencings of six Sargassum species in China

Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucle-otides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups （COG）, gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were also performed for further un-derstanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metab-olism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenet-ic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.