Compared with metagenome sequencing, GeoChip has significant differences in technical principles, quantitative methods, quantitative performance, and the ability to detect unknown species. Each has its own advantages and disadvantages, and the results can complement each other, but they cannot be directly compared.

The GeoChip is to design specific probes independently according to various functional genes related to microorganisms, which can greatly reduce the influence of animal and plant host genomes in special samples on the detection of microbial community function, and has the characteristics of high reproducibility and high sensitivity between parallel samples, which is suitable for exploring the unknown laws of known genes and species. Metagenomic technology directly targets the total DNA of the microbial community, and the amount of data is huge. Although metagenomic sequencing can reveal new genes, we can obtain sequence fragments and information more only from high-abundance species or multiple copies of genes. At the same time, it is a huge challenge to analyze such a large amount of data in depth. Both GeoChip and metagenome focus on the species composition, functional composition and metabolic pathways in environmental samples, which can be used to mine the functional information of environmental samples.

Species without reference genomes can be analyzed for SNP frequency differences, and candidate segments can be found, but the effect of non-reference positioning is poor, and the lack of annotation files, and the results obtained are few. In general, BSA trait mapping is not recommend for non-ginseng species, and it is recommended to try genetic mapping and other schemes.

The size of the candidate region and the number of candidate genes are related to the size of the population, the size of the difference in parental material, the characteristics of the target trait, the depth of sequencing, the level of the genome of the analyzed species and many other factors, so a unified standard cannot be given, but it can be estimated with reference to the experience of the completed project.

Amplicon sequencing and PhyloChip can reveal the phylogenetic information of the community and is suitable for the detection of 16S rRNA genes, but these techniques rely on PCR amplification and conservative primers. Amplicon sequencing is also suitable for the detection of some functional genes, but most of the functional genes still can not design enough conservative PCR primers, that is to say, in addition to GeoChip, only a few functional genes can be detected by sequencing. Moreover, these sequencing technologies based on traditional PCR amplification are still difficult to achieve accurate quantification due to objective factors of amplification preference, and these technologies are extremely sensitive to systematic random errors. Although these errors can be largely eliminated by obtaining sequence information for most species in the system, there is a significant cost associated with current sequencing technologies. In contrast, the chip-based hybridization technique is not sensitive to random errors, but only focuses on the specific genes in the chip, and the resolution of the GeoChip technique is higher than that of the 16S rRNA gene-based amplicon sequencing. However, sequencing-based detection technology can help us discover new genes and functional information. Therefore, the comprehensive use of a variety of high-throughput detection methods can more comprehensively reveal the phylogeny and functional structure of microbial communities, and ultimately better answer Our scientific questions and hypotheses. Meg Gene, like many companies and institutions, provides amplicon sequencing services. This technique requires a relatively small amount of environmental sample DNA to be amplified by conserved primer-based PCR to either the community's phylogenetic genes (e. g., 16S rRNA genes) or functional genes (amoA genes). Amplicon sequencing can generally be performed after mixing multiple samples.

Regular nucleic acid detection methods include gene clone library, denaturing gradient gel electrophoresis DGGE, temperature gradient gel electrophoresis TGGE, terminal restriction fragment length polymorphism (T-RFLP), quantitative PCR and in situ hybridization, etc. Although these techniques have some value, their disadvantage is that the amount of information is too small to fully reflect the complex environmental microbial diversity and distribution. The workload of gene clone library construction and detection is large, and 99% of the microorganisms in nature have no way to purify and culture in the laboratory. The cloned strains are selected from the culture medium, and the transformation and sequencing of shaking bacteria is inefficient. DGGE method has been widely used to detect the polymorphism of microbial community structure or function, but it needs standard strains, and is limited by gel electrophoresis characteristics, can not detect the species of rare flora, so its repeatability and resolution are not ideal. The GeoChip covers multiple functional categories. At the same time, these related functional genes involve bacteria, archaea, fungi, protists, viruses and other biological groups. Compared with regular research methods, it is more simple, economical and fast, and can be in a short time. Get more and more accurate information.

OTU phylogenetic tree is a phylogenetic tree constructed by selecting representative sequences of OTU with top 50 abundance and genus classification information. The name at the end of each branch consists of the genus name and the corresponding OTU number, with the same color if the genus name is the same. The figure shows which genera are predominantly of higher relative abundance. In addition, the evolutionary taxonomic relationships between species, I .e., different branching structures, are also included. However, because the sequence targeted in the analysis is part of the interval, such as 16S, the information contained in it is not complete, so the information of the system evolution branch in this figure may not be complete or accurate. The numerical value on each branch node is a bootstrap value, that is, a confidence level, and the size of the value represents the accuracy of the corresponding branch node structure, and the greater the value, the higher the accuracy.

For environmental sample recommend, the teacher used the regular CTAB method or SDS method. Among them, human and animal tissue samples used SDS method, and other samples used CTAB method. In addition, for some samples that are difficult to extract or you want to improve the extraction effect of sample DNA, you recommend use Mobio's special environmental sample DNA extraction kit.
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