A weighted sequence alignment strategy for gene structure annotation lift over from reference genome to a newly sequenced individual

Genome sequences and gene structure annotation are very important for genomic analysis, while only the reference gene structure annotation is widely used for a wide range of investigations of different natural variation individuals. Herein, we are reporting the software GEAN which could lift over the reference gene structure annotation to other individuals belonging to the same or closely related species whose genome sequence was determined by whole-genome resequencing or de novo assembly. We found that inconsistent sequence alignment makes the coordinate lift over between different individual genomes unreliable, thus obscuring the lift over of gene structure annotations and genomic variants functional prediction. We designed a zebraic dynamic programming (ZDP) algorithm by providing different weights to different genetic features to refine the gene structure lift over. Using the lift over gene structure annotation as anchors, a base-pair resolution whole-genome-wide sequence alignment and variant calling pipeline for de novo assembly have been implemented. Taking Arabidopsis thaliana as example, we show that the natural variation alleles expression level of apoptosis death and defence response related genes might could be better quantified using GEAN. And GEAN could be used to refine the functional annotation of genetic variants, annotate de novo assembly genome sequence, detect syntenic blocks, improve the quantification of gene expression levels using RNA-seq data and genomic variants encoding for population genetic analysis. We expect that GEAN will be a standard gene structure annotation lift over and genome sequence alignment tool for the coming age of de novo assembly population genetics analysis.