Recent Segmental Duplications In The Foxtail Millet Genome

Segmental duplications (also termed "low-copy repeats") are blocks of DNA that range from 1 to 400 kb in length, occur at more than one site within the genome, and typically share a high level of (>90%) sequence identity.Compareing to the transposon,the copy number of SDs is lower and often be referred as low-copy repeat or LCRs.Currently, there are two main methods for detecting SDs, whole genome assembly comparison (WGAC) and wholegenome shotgun sequence detection (WSSD).Inthis paper we improved the pipeline and usedthe improved pipeline and WSSD pipeline to detect SDs in Zhanggu genome. By analysis of SDs’ position in Zhanggu genome, we found that SDs distribution in the genome is not random, not only within the chromosome,but also between chromosomes. There are many new copys of the genes in SDs.These duplicated genes play an important role in the formation of new biological traits. Through GO analysis we found that genes in SDs areassociated with metabolism.