Hemoglobin A2 ; genetics ; Humans ; Thalassemia ; genetics ; Transcriptome

Objective Circular RNAs (circRNAs) are non-coding RNAs (ncRNA) circularized without a 3' polyadenylation [poly-(A)] tail or a 5' cap, resulting in a covalently closed loop structure. circRNAs were first discovered in RNA viruses in the 1970s, but only a small number of circRNAs were discovered at that time due to limitations in traditional polyadenylated transcriptome analyses. With the development of specific biochemical and computational methods, recent studies have shown the presence of abundant circRNAs in eukaryotic transcriptomes. circRNAs play vital roles in many physiological and pathological processes, such as acting as miRNA sponges, binding to RNA-binding proteins (RBPs), acting as transcriptional regulatory factors, and even serving as translation templates. Current evidence has shown that circRNAs can be potentially used as excellent biomarkers for diagnosis, therapeutic effect evaluation, and prognostic assessment of a variety of diseases, and they may also provide effective therapeutic targets due to their stability and tissue and development-stage specificity. This review focuses on the properties of circRNAs and their immune relationship to disease, and explores the role of circRNAs in immune-related diseases and the directions of future research.
Biomarkers ; MicroRNAs/genetics* ; RNA, Circular ; Transcriptome

Since synthetic pigments are potentially harmful to human health, natural ones such as bixin, one of the carotenoids, are favored. As the second widely used natural pigment in the world, there is significant interest in the biosynthetic pathway of bixin which has not been fully elucidated. This review summarizes the chemical properties, extraction methods, biosynthetic pathway and application of bixin. In addition, we compared the difference between traditional extraction methods and new extraction techniques. Moreover, we described the genes involved in the biosynthetic pathway of bixin and the effects of abiotic stress on the biosynthesis of bixin, and discussed the application of bixin in food, pharmaceutical and chemical industries. However, the researches on bixin biosynthesis pathway are mostly carried out at the transcriptome level and most of the gene functions have not been elucidated. Therefore, we propose to characterize the entire bixin biosynthetic pathway using techniques of genomics, bioinformatics, and phytochemistry. This will help facilitate the synthetic biology research of bixin and development of bixin into new drugs.
Bixaceae/genetics* ; Carotenoids ; Humans ; Pigmentation ; Transcriptome

Schizophrenia is a severe psychiatric disorder with an unclear etiology and various clinical manifestations. The diagnosis and consequent treatment of schizophrenia mainly rely on clinical symptoms. Multiple risk sites associated with schizophrenia have been identified, yet objective indicators have not been found to facilitate clinical diagnosis and treatment of schizophrenia. The development of omics technology provides different perspectives on the etiology of schizophrenia and make the early identification, diagnosis and treatment of the disorder possible. This article summarizes the prevalence of schizophrenia, reviews the research results and shortcomings of transcriptomics and proteomics, as well as the latest achievements and prospects of multi-omics, aiming to reveal the use of omics in SZ, provide more comprehensive biological evidence to reveal the complex pathogenesis of schizophrenia and provide a theoretical basis for the early identification, accurate diagnosis, disease progression control, and prognosis improvement of schizophrenia.
Humans ; Proteomics/methods* ; Transcriptome ; Schizophrenia/genetics*

Schizophrenia is a severe psychiatric disorder with an unclear etiology and various clinical manifestations. The diagnosis and consequent treatment of schizophrenia mainly rely on clinical symptoms. Multiple risk sites associated with schizophrenia have been identified, yet objective indicators have not been found to facilitate clinical diagnosis and treatment of schizophrenia. The development of omics technology provides different perspectives on the etiology of schizophrenia and make the early identification, diagnosis and treatment of the disorder possible. This article summarizes the prevalence of schizophrenia, reviews the research results and shortcomings of transcriptomics and proteomics, as well as the latest achievements and prospects of multi-omics, aiming to reveal the use of omics in SZ, provide more comprehensive biological evidence to reveal the complex pathogenesis of schizophrenia and provide a theoretical basis for the early identification, accurate diagnosis, disease progression control, and prognosis improvement of schizophrenia.
Humans ; Proteomics/methods* ; Transcriptome ; Schizophrenia/genetics*

Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep sequencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phylogenomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epiplasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.
Ciliophora ; genetics ; metabolism ; Phylogeny ; RNA, Protozoan ; genetics ; metabolism ; Transcriptome ; physiology

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.
Humans ; Genetic Variation ; Asarum ; Transcriptome/genetics* ; Microsatellite Repeats/genetics* ; Phylogeny

Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain.
Codon ; Escherichia coli ; Genome, Fungal ; Reishi ; genetics ; Saccharomyces cerevisiae ; Transcriptome

Pear is one of the main fruits with thousands of years of cultivation history in China. There are more than 2000 varieties of pear cultivars around the world, including more than 1200 varieties or cultivars in China (Legrand et al., 2016). Xinjiang Uygur Autonomous Region is an important pear production region in China with 30 of varieties or cultivars. Pyrus sinkiangensis is the most popular variety, which is mainly distributed in Xinjiang (Zhou et al., 2018). Chlorogenic acid (CGA), p-coumaric acid, and arbutin are the main polyphenols in pear fruit, and their levels show great differences among different varieties (Li et al., 2014). CGA is a potential chemo-preventive agent, which possesses many important bioactivities including antioxidant, diabetes attenuating, and anti-obesity (Wang et al., 2021). Therefore, the specific CGA content of a variety is considered the embodiment of the functional nutritional value of pears.
Chlorogenic Acid ; Fruit ; Gene Expression Profiling ; Pyrus/genetics* ; Transcriptome

Platycodon grandiflorum is a medicinal and edible medicinal material. Our study is aimed to explore the differences in the gene expression of P. grandiflorum in different growth years, and the expression rules of key genes in the biosynthesis of the main active substances of P. grandiflorum. Illumina Hiseq 4000 sequencing platform was used to sequence the transcriptome of P. grandiflorum in different years. Then, 59 654 unigenes were obtained through filtering, assembly, splicing and bioinformatics analysis of the sequencing data, of which 1 671 unigenes were differentially expressed between at least two samples. The results of cluster analysis showed that there was a great difference in the gene expression of P. grandiflorum from one-year-old to two/three-year-old. There were 1 128 different genes between one-and three-year old P. grandiflorum, and only 57 different genes between two-and three-year-old P. grandiflorum. KEGG enrichment results showed that the differential genes of P. grandiflorum in different years were mainly concentra-ted in the biosynthesis of sesquiterpenes and triterpenes, and the biosynthesis of terpenoid skeletons. In the triterpenoid biosynthesis-related pathways, a total of 15 unigenes were identified, involving 5 enzymes. The expression levels of ACAT, HMGR, FDFT1, SQLE decreased with the increase of the growth year of P. grandiflorum. The expression of HMGS was the highest in the one-year-old P. grandiflorum, followed by the three-year-old sample. This study provides useful data for the development of P. grandiflorum, and also provides a basis for the study of related genes in the biosynthetic pathway of platycodin.
Gene Expression Profiling ; Plant Roots ; Platycodon/genetics* ; Saponins ; Transcriptome ; Triterpenes