Copy number variation (CNV) is an important type of genomic structural variation and plays a crucial role in genomic disorders imposed by diseases. Most of the current bioinformatic researches focus on developing algorithms and tools for detecting CNVs from single or paired datasets, but the analysis of such CNVs is not sufficient from a family-based genetic point of view. We performed a trio-sample family based parents-offspring CNV analysis using the 1000G data. We found a number of CNVs that the offsprings inherited from their parents and inferred through hierarchical analysis how they were generated. In addition, we also discovered several de novo CNV candidates.

Copy number variation (CNV) is an important type of genomic structural variation and plays a crucial role in genomic disorders imposed by diseases. Most of the current bioinformatic researches focus on developing algorithms and tools for detecting CNVs from single or paired datasets, but the analysis of such CNVs is not sufficient from a family-based genetic point of view. We performed a trio-sample family based parents-offspring CNV analysis using the 1000G data. We found a number of CNVs that the offsprings inherited from their parents and inferred through hierarchical analysis how they were generated. In addition, we also discovered several de novo CNV candidates.

The unicellular green alga Haematococcus pluvialis accumulates a highly valuable ketocarotenoid, i.e. astaxanthin up to 4%dry weight under stress conditions. Phytoene synthase is considered to be the first rate limiting enzyme in carotenoid biosynthesis pathway in H. pluvialis. The cDNA and genomic genes of phytoene synthase, i.e. psy from H.pluvialis were cloned and characterized.Result showed that psy had one open reading frame of 1 200 bp encoding a putative polypeptide of 400 amino acids which was interrupted by four introns. Phylogenetic analysis revealed that psy from green algae formed a monophyletic clade, and its closer relationship was higher plants. By using genomic walking approach, an approximate 1 kb 5′ flanking region ofpsy gene was cloned and a number of putative cis-regulatory elements were revealed. Fusing a 297 bp internal sequence (-297 to -1 bp from the translation initiation codon ofpsy) with the reporter gene, i.e. lacZ before attemptedintroducing the construct into the green alga via particle bombardment resulted in lacZ transient expression.

Copy number variation (CNV) is an important type of genomic structural variation and plays a crucial role in genomic disorders imposed by diseases. Most of the current bioinformatic researches focus on developing algorithms and tools for detecting CNVs from single or paired datasets, but the analysis of such CNVs is not sufficient from a family-based genetic point of view. We performed a trio-sample family based parents-offspring CNV analysis using the 1000G data. We found a number of CNVs that the offsprings inherited from their parents and inferred through hierarchical analysis how they were generated. In addition, we also discovered several de novo CNV candidates.
Algorithms ; Computational Biology ; DNA Copy Number Variations ; Genomics ; Humans

Quarantine insects are economically important pests that frequently invade new habitats.A rapid and accurate monitoring method to trace the geographical sources of invaders is required for their prevention,detection,and eradication.Current methods based on genetics are typically time-consuming.Here,we developed a novel tracing method based on insect gut microbiota.The source location of the insect gut microbiota can be used to rapidly determine the geographical origin of the insect.We analyzed 179 gut microbiota samples from 591 individuals of 22 quarantine insect species collected from 36 regions in China.The gut microbiota of these insects primarily included Actinobacteria,Bacteroidetes,Cyanobacteria,Firmicutes,Proteobacteria,and Tenericutes.The diversity of the insect gut microbiota was closely associated with geographical and environmental factors.Different insect species could be distinguished based on the composition of gut microbiota at the phylum level.Populations of individual insect species from different regions could be distin-guished based on the composition of gut microbiota at the phylum,class,and order levels.A method for determining the geographical origins of invasive insect species has been established;however,its practical application requires further investigations before implementation.

OBJECTIVE: To analyze the characteristics of genetic variants in 134 patients diagnosed with Acute myeloid leukemia (AML). METHODS: Clinical data of the 134 patients with AML (non-acute promyelocytic leukemia) initially diagnosed at the 940th Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army from June 2017 to June 2022 were retrospectively analyzed. Potential variants of AML-related genes were detected by next-generation sequencing, and the frequency of variants was analyzed by using SPSS v26.0 software, and likelihood ratio χ² test and Fisher exact test were used for data analysis. RESULTS: The patients had included 72 males and 62 females, with a gender ratio of 1.7 : 1 and a median age of 51 years (9 ~ 86 years old). One hundred twenty patients (76.1%) had harbored at least one genetic variant, including 26 (19.4%) having a single variant, 27 (20.1%) having two variants, and 49 (36.6%) having >= 3 variants. 32 (23.9%) had no detectable variants. Genetic variants detected in over 10% of the 134 patients had included NPM1 (n = 24, 17.91%), FLT3-ITD (n = 21, 15.67%), DNMT3A (n = 20, 14.93%), CEBPA (single variant; n = 14, 10.45%), TET2 (n = 14, 10.45%), and NRAS (n = 14, 10.45%). The patients were also divided into low risk, intermediate risk and high risk groups based on their chromosomal karyotypes. The mutational rates for genes in different groups have varied, with 19 patients from the low risk group harboring variants of NRAS (n = 4, 21.05%), KRAS (n = 4, 21.05%), and KIT (n = 2, 10.53%); and 96 patients from the intermediate risk group harboring variants of NPM1 (n = 24, 25.00%), FLT3-ITD (n = 20, 20.83%), DNMT3A (n = 18, 18.75%), CEBPA (n = 12, 12.50%), and TET2 genes (n = 12, 12.50%). The mutational frequencies for the 19 patients from the high risk group were ASXL1 (n = 7, 21.05%), NRAS (n = 3, 15.97%), TP53 (n = 3, 15.79%), and EZH2 (n = 2, 10.53%). A significant difference was found in the frequencies of KIT, NPM1, FLT3-ITD, DNMT3A, and ASXL1 gene variants among the low-risk, medium-risk, and high-risk groups. CONCLUSION AML patients have a high frequency for genetic variants, with 76.1% harboring at least one variant. The frequency of genetic variants have varied among patients with different chromosomal karyotypes, and there are apparent dominant variants. KIT, NPM1, FLT3-ITD, DNMT3A, and ASXL1 may be used as prognostic factors for evaluating their prognosis.
Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Leukemia, Myeloid, Acute/genetics* ; Leukemia, Promyelocytic, Acute ; Nuclear Proteins ; Retrospective Studies ; Child ; Adolescent ; Young Adult ; Adult ; Aged ; East Asian People

With the development of high throughput sequencing and single-cell genomics technologies, many uncultured bacterial communities have been dissected by combining these two techniques. Especially, by simultaneously leveraging of single-cell genomics and metagenomics, researchers can greatly improve the efficiency and accuracy of obtaining whole genome information from complex microbial communities, which not only allow us to identify microbes but also link function to species, identify subspecies variations, study host-virus interactions and etc. Here, we review recent developments and the challenges need to be addressed in single-cell metagenomics, including potential contamination, uneven sequence coverage, sequence chimera, genome assembly and annotation. With the development of sequencing and computational methods, single-cell metagenomics will undoubtedly broaden its application in various microbiome studies.
Animals ; Bacteria ; genetics ; Computational Biology ; methods ; High-Throughput Nucleotide Sequencing ; methods ; Humans ; Metagenomics ; Single-Cell Analysis ; methods

A comprehensive profiling of the vaginal microbial communities and their variability enables an accurate description of the microbiome in women.However,there is a lack of studies available on Chinese women.In the present study,the composition of the vaginal microbiota during pregnancy and the 6-week postpartum period of 454 Chinese women was characterized by sequenc-ing the V3-V4 region of the 16S ribosomal RNA(rRNA)gene.The vaginal microbiome showed variations during pregnancy and the postpartum period based on the abortion history,hypertensive disorders,delivery mode,and maternal age.Co-variation of 22 bacterial taxa,including the Lacto-bacillus genus and two of its species,may account for the common characteristics of the vaginal microbiome under scenarios of different medical histories and pregnancy outcomes.In contrast,dis-criminant bacterial species were significantly different between women who had preterm birth(PTB)with and without premature rupture of membranes(PROM),and the community state type(CST)Ⅳ-A without any predominant Lactobacillus species in the microbiota was more prevalent during pregnancy in the PROM-PTB cases,suggesting that specific bacterial species could be considered to distinguish between different types of PTB.By providing data on Chinese women,this study will enrich the knowledge of the human microbiome and contribute to a better understanding of the association between the vaginal microbiome and reproductive health.

The characterization of the human T-cell receptor (TCR) repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we analyzed the diversity and complexity of both the TCRα and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene (TRAV42/DV1). Moreover, we uncovered the presence of tandem TRBD (TRB D gene) usage in ~2% of the productive human TCRβ CDR3 sequences.
Complementarity Determining Regions ; genetics ; DNA Primers ; chemistry ; genetics ; Female ; Gene Rearrangement, beta-Chain T-Cell Antigen Receptor ; genetics ; Gene Rearrangement, delta-Chain T-Cell Antigen Receptor ; genetics ; Genes, T-Cell Receptor beta ; genetics ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Joining Region ; genetics ; Immunoglobulin Variable Region ; genetics ; Male ; Receptors, Antigen, T-Cell, alpha-beta ; 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