Unmapped Reads Analysis Based On BAC Library Sequencing And The Mitochondrial Genome Assembly

The development of high throughput sequencing technology enable us to study species from the perspective of genome.The first step of high throughput sequencing data processing is usually to align sequence reads to the reference genome,extract the matched reads for subsequent analysis,and ignore the unmapped reads.However,these unmapped reads contain some important biological information,such as reference genome deletion sequence,species specific sequence or contamination sequence in samples.In this study,we assembled unmapped reads from the whole genome sequencing data of Broomcorn Millet generated by using BAC library mixed pool sequencing method.A total of 135 deletion sequences,64 specific sequences and some sample contamination sequences were identified.As an indispensable part of plant genetic information,mitochondrial genome plays an important role in phylogenetic evolution and genetic engineering.Broomcorn Millet(Panicum miliaceum L.)is an important ancient crop,assembling and analyzing its mitochondrial genome is of great significance to improve its genomic information.At present,there is no published data on the mitochondrial genome of Broomcorn Millet.In this study,combined with unmapped reads from the second-generation DNA sequencing data and the third-generation DNA sequencing data,the core sequence of the mitochondrial genome of Broomcorn Millet was assembled by iterative assemble method.The length of the core sequence was 484,522 bp and the content of GC was 43.76%.Through gene annotation analysis,it was found that the intergenic region of the mitochondrial genome was in a large proportion,up to 79.22%,the coding region only accounted for 20.78% and contained 71 coding genes.Through the analysis of codon usage bias,it was found that the codon usage bias was weak,the natural selection pressure and mutation affect codon usage bias.By analyzing the codons of protein coding region,10 optimal codons were obtained.