Expert consensus on microbiome sequencing and analysis / 生物工程学报

In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.

Single-cell metagenomics: challenges and applications

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.

Detection and analysis of copy number variation from 1000 Genomes trio data / 南方医科大学学报

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.

Phylogenomics of non-model ciliates based on transcriptomic analyses

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.

Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains

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.

Molecular Cloning and Characterization of Phytoene Synthase Gene From a Unicellular Green Alga Haematococcus pluvialis / 生物化学与生物物理进展

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.