The fungal genome assembly based on Nanopore sequencing and used a variety of splicing software and methods to find the optimal assembly strategy and construct high-quality genome contig sequences. After two rounds of Racon error correction, the second-generation data is used for two rounds of Pilon error correction, turns out a high-quality map of the fungal genome which almost at the chromosome level .
Really case
Note: The number of chromosomes assembled of M01 and M02 is consistent with previous reports and karyotype analysis, almost completed genome. The advantages of the high-quality map of fungal genome
can span high-repetition and high-complex regions, and solve the assembly problem of high-repetition and high-heterozygous genomes.
Genome assembly metrics span from Kb to Mb, resulting in a high-quality map at the near-chromosomal level. The methylation modification can be directly detected, which is of great significance for the study of epigenetics. Paper recommend
Recent Asian origin of chytrid fungi causing global amphibian declines[J]. ence, 2018, 360(6389):621.
Suresh P , Hiroshi H , Ishijima S A , et al. Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768[J]. Genome Biology and Evolution, 2018(8):8.
Cui C , Herlihy J H , Bombarely A , et al. Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity[J]. Molecular Plant-Microbe Interactions, 2019, 32(12).
1. What is K-mer and what's the effect?
K-mer refers to a sequence of K bp in length. Iteratively select a sequence of length K bases from a continuous sequence. If the length of the sequence is L and the length of K-mer is K, then L-K+1 K-mers can be obtained.
2. What is the recommended sequencing depth?
Denovo sequencing of fungal genomes is generally more than 100X in depth.
3. What is the best comparison rate for the second generation?
The second-generation alignment rate is generally greater than 90%, and the genome assembly is considered to be better.
4. What is the best rating for BUSCO?
The BUSCO evaluation is generally greater than 90%, and the genome assembly is considered to be better.
5. What is the role of genome-wide collinearity analysis?
Collinearity refers to the linkage relationship of genes in genetics, which is the phenomenon that homologous genes are arranged in the same order on the chromosomes of different species. The degree of collinearity between two species can be used as a measure of the evolutionary distance between them, and the genetic relationship between species can be known.
