A list of SMRT gene sequencing applications

In the field of gene sequencing, PacBio has outstanding position. Since last year, Illumina acquired PacBio for the highest price in history of 1.2 billion U.S. dollars, which has consolidated its position in cutting-edge genetic research, especially its Single-molecule real-time sequencing (SMRT).

SMRT sequencing has abroad application in different research fields. In this article, we collected some SMRT related researches, such as basic science, agriculture, environment and medical research.

1. Mosquito genome recombination

Scientists at the Sanger Institute used a new approach to create a high-quality de novo genome sequence assembly from Anopheles coluzzii. Researchers have adopted an improved library construction method that avoids DNA splicing and size selection. The initial sample size required only 100 ng of genomic DNA to generate the SMRTbell library. The newly assembled Anopheles genome highlights the power of the SMRT sequencing platform: a new low sample volume DNA sequencing.

1. The medicinal value of elm mushroom

Elm mushroom is a precious edible mushroom widely cultivated in Asia. Researchers use the SMRT sequencing platform to provide high-quality elm mushroom genomes. This is the first complete genome sequenced in the wallbell family. In addition, researchers have identified gene clusters related to terpene and polysaccharide biosynthesis. Another research team at Jilin Agricultural University and Shenyang Agricultural University also studied edible mushrooms and a fungus that threatened them through the SMRT sequencing platform.

1. Differences in detecting bone marrow subpopulations

The researchers used the SMRT sequencing platform to analyze the transcriptome of newly harvested human bone marrow progenitor cells and differentiated cells. Analysis showed that the number of transcript isomers increased by about 5-fold compared to previously detected data. Studies have also revealed the unique composition of single transcript isomers that represent a subset of bone marrow cells.

1. Expand human genetic diversity data

Swedish scientists use SMRT sequencing to expand the diversity of the human genome data set. The current reference sequence (GRCh38) is the basis for large-scale sequencing projects. However, research suggests that GRCh38 may be incomplete. The researchers performed de novo sequencing and sequence assembly on the genomes of two Swedes, and found that each person had more than 10Mb of deletion in the GRCh38 gene, but they had about 6Mb of new sequence (NS) being the same as a Chinese. The researchers said: "Our results highlight that the references to GRCh38 are incomplete. De novo genomic sequence assembly of individual genomes from populations in different regions can help improve the analysis of short-sequence whole-genome sequencing data."

1. Challenges of Diploid Methylation

The so-called DNA methylation means that under the action of DNA methylation transferase, a methyl group is covalently bonded to the 5 'carbon position of the cytosine of a genomic CpG dinucleotide. DNA methylation can cause changes in chromatin structure, DNA conformation, DNA stability, and the way DNA interacts with proteins. Bioinformatics scientists use the SMRT sequencing platform to solve the problem of differentiating the homologous chromosome methylation of individual genomes. The SMRT sequencing platform can output long sequence information containing CpG methylation, but the segmented output of CpG sites may still bring errors. Researchers have proposed a statistical method to observe individual diploid methylation and transcriptome. This method can reduce the error rate to 1%, thereby detecting each haplotype CpG hypomethylation and accuracy and sensitivity of> 90%.

1. Improve the resolution of rare and Mendelian diseases

At present, although the detection of DNA mutations by DNA sequencing has played a great role in exploring the causes of human diseases, the causes of many diseases have not yet been revealed. The scientists used the SMRT sequencing platform to work on previously unsolved diseases. Many high-impact research publications, such as Nature Communications, have reported expanded detection of human genome mutations, which has led to the discovery of genetic mutations that cause rare and Mendelian diseases. For example, a Japanese research team used PacBio whole-genome sequencing data to detect more than 17,000 DNA structural variants associated with familial hereditary epilepsy and quickly identified a 12.4 kb DNA deletion.