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T2T genome =100kb sequence =Super-Long kit
Release time：2022-06-08 08:54 Author：Benagen
T2T genome =100kb sequence =Super-Long kit
Abstract
(1) What is the T2T genome?
(2) The super-long sequence (N 50 > 100Kb) is equal to the T2T genome.
(3) Why is it so difficult to obtain super-long sequences (sequences with N50>100Kb)?
(4) Super-long sequence = Super-long extraction kit of Benagen (+DNA protection solution)
(5) T2T genome =100Kb sequence = Super-long kit
1. What is the T2T genome?
T2T genome refers to a genome with one or more chromosomes at Telomere-to-Telomere level, which is the ultimate goal of genome assembly. ONT super-long sequences (N50>100 Kb) combined with HiFi and short reads can assemble high-quality T2T genomes. The release of T2T genomes in humans and other species marks the arrival of the genome 4.0 era.
2. The super-long sequences (N50>100 Kb) are equivalent to the T2T genome.
(1) Genome assembly and gap
The combination of short reads (PE150) and long reads (10-50 Kb) can assemble the genome well, and the combination of Hi-C technique can obtain genomes at the chromosome level. However, the chromosomes assembled by this method are still incomplete and fragmented, with many gaps in the middle. The more complex the genome (highly repetitive, highly heterozygous, polyploid, etc.), the greater the gaps.
(2) Super-long sequences (N50>100Kb) can span gaps.
Since some species genomes have very long gaps (e.g., human chromosome 8 has a variable number of tandem repeats of 863KB), normal long-read sequencing techniques (10-50 Kb) cannot span these genomes. In theory, reads that are long enough can span all gaps, and gaps are added one by one to reach the level of Contig assembly. That is, Contig is a chromosome.
Super-long sequences (N50>100Kb) can easily bridge these gaps, enabling true T2T assembly.
(3) Centromere region: black hole in genome gaps
DNA in the centromere region is often highly repetitive, with more than 105 repeats or more. In addition, there may also be scattered repeats in the centromeric region. Furthermore, the centromere region is very long. (Human chromosome 8 has a 2.08Mb centromere a satellite array.) The super-long sequence (N50>100Kb) can connect the two arms of chromosome, which is a powerful tool to solve the problem of nail house.
(4) The telomere region: pain of genome assembly
Telomere DNA is mainly composed of highly repetitive sequences. If the telomere sequence is not fully assembled, the chromosome remains incomplete. The best approach for telomere extension and complete assembly is to use super-long sequences (N50>100Kb).
Abstract
(1) What is the T2T genome?
(2) The super-long sequence (N 50 > 100Kb) is equal to the T2T genome.
(3) Why is it so difficult to obtain super-long sequences (sequences with N50>100Kb)?
(4) Super-long sequence = Super-long extraction kit of Benagen (+DNA protection solution)
(5) T2T genome =100Kb sequence = Super-long kit
1. What is the T2T genome?
T2T genome refers to a genome with one or more chromosomes at Telomere-to-Telomere level, which is the ultimate goal of genome assembly. ONT super-long sequences (N50>100 Kb) combined with HiFi and short reads can assemble high-quality T2T genomes. The release of T2T genomes in humans and other species marks the arrival of the genome 4.0 era.
2. The super-long sequences (N50>100 Kb) are equivalent to the T2T genome.
(1) Genome assembly and gap
The combination of short reads (PE150) and long reads (10-50 Kb) can assemble the genome well, and the combination of Hi-C technique can obtain genomes at the chromosome level. However, the chromosomes assembled by this method are still incomplete and fragmented, with many gaps in the middle. The more complex the genome (highly repetitive, highly heterozygous, polyploid, etc.), the greater the gaps.
(2) Super-long sequences (N50>100Kb) can span gaps.
Since some species genomes have very long gaps (e.g., human chromosome 8 has a variable number of tandem repeats of 863KB), normal long-read sequencing techniques (10-50 Kb) cannot span these genomes. In theory, reads that are long enough can span all gaps, and gaps are added one by one to reach the level of Contig assembly. That is, Contig is a chromosome.
Super-long sequences (N50>100Kb) can easily bridge these gaps, enabling true T2T assembly.
(3) Centromere region: black hole in genome gaps
DNA in the centromere region is often highly repetitive, with more than 105 repeats or more. In addition, there may also be scattered repeats in the centromeric region. Furthermore, the centromere region is very long. (Human chromosome 8 has a 2.08Mb centromere a satellite array.) The super-long sequence (N50>100Kb) can connect the two arms of chromosome, which is a powerful tool to solve the problem of nail house.
(4) The telomere region: pain of genome assembly
Telomere DNA is mainly composed of highly repetitive sequences. If the telomere sequence is not fully assembled, the chromosome remains incomplete. The best approach for telomere extension and complete assembly is to use super-long sequences (N50>100Kb).
3.Why is it so difficult to obtain super-long sequences (sequences with N50>100Kb)?
(1) Difficult to extract
DNA extraction is the first step in obtaining super-long sequences. Generally, the complete main band of DNA electrophoresis is above the Marker line of 23Kb, which can be achieved by various extraction kits or CTAB methods. However, conventional extraction methods cannot extract complete sequences above 100 Kb.
(2) Difficult to purify
DNA purification is the second step in obtaining super-long sequences. During the purification process, super-long sequences are easily destroyed and purified, which is the second obstacle in obtaining super-long sequences. Conventional purification methods cannot obtain DNA super-long sequences.
4. Super-long sequence = Super-long extraction kit of Benagen (+DNA protection solution)
(1) Difficult to extract
DNA extraction is the first step in obtaining super-long sequences. Generally, the complete main band of DNA electrophoresis is above the Marker line of 23Kb, which can be achieved by various extraction kits or CTAB methods. However, conventional extraction methods cannot extract complete sequences above 100 Kb.
(2) Difficult to purify
DNA purification is the second step in obtaining super-long sequences. During the purification process, super-long sequences are easily destroyed and purified, which is the second obstacle in obtaining super-long sequences. Conventional purification methods cannot obtain DNA super-long sequences.
4. Super-long sequence = Super-long extraction kit of Benagen (+DNA protection solution)
(1) Extraction process
After years of research and development, Benegen launched the DNA extraction Kit Super-long DNA Isolation Mini Kit (3T) (Cat.No. ZY2203A01) for more complete sequence extraction. There are mainly two models:
Super Long100 (for extraction of DNA sequences above N50 100Kb);
Super Long200 (for extraction of DNA sequences above N50 150 Kb-250 Kb).
(2) DNA library construction
Benagen independently developed and launched special DNA protection solution to ensure that DNA does not break during library construction and operation.
(3) Project experience
Benagene completed library construction and long-read sequencing for 13316 cells (as of March 15, 2022) with extensive experience in 3216-cell library construction and super-long read sequencing, ensuring that super-long sequence are available for all types of samples.
(4) Project examples:
5.T2T genome =100kb sequence =Super-Long kit
Super-long reads cross the gap and complete the assembly of centromere and telomere. Benagen Super-Long DNA Isolation Mini Kit performs well in the acquisition of challenging super-long reads (N50 > 100Kb) .
