Scientists develop high-performance large fragment insertion and deletion variant identification tools

Scientists develop high-performance large fragment insertion and deletion variant identification tools

Scientists develop high-performance large-segment insertion/deletion mutation identification toolsScientists develop high-performance large-segment insertion/deletion mutation identification tools

On October 13, the research group of Qingyong Yang from the bioinformatics team of Huazhong Agricultural University and the research group of Sung Wing-Kin () of the National University of Singapore published an online paper in Nucleic Acids Research , and developed a high-performance large fragment insertion and deletion IndelEnsembler, a variant (InDel) identification tool, improves the identification accuracy of large fragments of InDel from 45% to 84%
.

Nucleic Acids Research

Improved identification accuracy

Improved identification accuracy

Genetic variation refers to the difference in DNA sequence between individuals in a population, mainly including point mutations (SNP/single nucleotide polymorphism), small fragments of InDel and structural variations (including large fragments of InDel, chromosome inversion, translocation and Copy number variation)
.

Genetic variation in the genome is the root cause of human genetic diseases and the genetic basis for the morphological and phenotypic diversity of animals and plants

In plants, a large amount of genetic and molecular biological evidence indicates that large fragments of InDel play a major role in explaining the phenotypic variation that affects a series of important crops
.

For example, the change in the copy number of a large segment of the DNA sequence in the cucumber genome can determine the sex of cucumber, and the yield of cucumbers containing this variation is about 15 times that of ordinary cucumbers

According to Yang Qingyong, the corresponding author of the paper, the study developed a high-performance large-segment InDel identification tool IndelEnsembler by integrating 4 published methods, and applied it to a natural population consisting of 1047 Arabidopsis strains through the whole genome Association analysis (GWAS) identified a new large fragment of InDel related to important traits
.

Compared with GRIDSS and Manta, the two softwares that currently identify the best InDel performance, IndelEnsembler has good performance in different species and different sequencing depths
.

Compared with the developed tool AthCNV ​​in Arabidopsis, IndelEnsembler has doubled and 30% higher accuracy in identifying deletion variants (DEL) and duplicate variants (DUP), respectively

Provide important resources

Provide important resources

The distribution of large fragments of InDel in the Arabidopsis genome is uneven and has a very significant positive correlation with the distribution of transposons.
80%-96% of the chromosome centromere region is covered by InDel
.

Large fragments of InDel tend to be distributed in intergenic regions and non-coding genes

In addition, genes affected by large fragments of InDel are more distributed in the tandem repeat regions of the genome, indicating that the tandem repeat regions on the genome are unstable regions and will accumulate more variation

For example, a 377 bp DEL identified in this study caused a 65 bp deletion in the first exon of the flowering-related gene FRI , and the material containing the deletion had an earlier flowering date
.

In addition, the study also identified a 182 bp deletion in the AT1G11520 gene, and the flowering period of the material containing the deletion was delayed

FRI AT1G11520 AT1G11520

These results indicate that there are still many unknown genomic mutations in Arabidopsis, and the large fragments of InDel identified by IndelEnsembler can be used as a supplement to the phenotypic-related genomic mutation data set in Arabidopsis
.

(Source: Wang Fang, China Science News)

These results indicate that there are still many unknown genomic mutations in Arabidopsis, and the large fragments of InDel identified by IndelEnsembler can be used as a supplement to the phenotypic-related genomic mutation data set in Arabidopsis

https://doi.
org/10.
1093/nar/gkab904