由于真核生物基因组通常包括大的基因间区域,真核生物的泛基因组通常被定义为物种中所有DNA序列的集合,包括存在于所有个体中的核心基因组和存在于某些个体中的可有可无的基因组部分。 目前构建泛基因组,通常采用homolog-based,map-to-pan或graph databse方法将一个物种的所有DNA序列组合成一个简单的序列集合。然而,...
a, TheSetariapan-genome. The detrended growth curve of the pan-genome indicates a closed pan-genome ofSetaria. The pie chart shows the proportion of gene family marked by composition.b, Stacked bar graph of SV number and type from the 110 accessions.c, Distribution of SVs of 112 genomes a...
Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativusL.) have been hindered by the lack of a high-quality pan-genome. He...
section. Subsequently, a graph-based pangenome was constructed by using DM8.1 as the backbone integrated 194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 ...
With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are...
Tognon M, Bonnici V, Garrison E, Giugno R, Pinello L (2021) GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs. PLOS Computational Biology 17(9): e1009444.https://doi.org/10.1371/journal.pcbi.1009444 License
For KEGG, we selected 93 KEGG PATHWAY (http://www.kegg.jp/ or http://www.genome.jp/kegg/) belonging to human diseases and then mapped them to a PubMed ID. For MeSH, we employed the NCBI database (https://www.ncbi.nlm.nih.gov/) using Medical Subject Heading (MeSH) terms and ...
Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framewor
Furthermore, compared to alternate linear reference-based methods, the sequence graph approach minimizes the reference allele bias and enables the representation of pan-genome reference structures (e.g., small variants in the vicinity of an SV) so that variants can be accurate even when variants ...
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes Article Open access 11 April 2022 Introduction Haplotyping is the process of distinguishing the alleles that are inherited together on a chromosome from a parent in a diploid or polyploi...