Synteny with Allied and Model Genomes

Abstract

Analysis of synteny is an integral part of comparative genomics inasmuch as it helps us to understand the structures and functions of genes in the related genomes in relation to genome evolution and their roles in gene expression. The identification of synteny blocks, the basic unit of genome synteny, may provide insights into the gene structure and regulation that are essential for biological processes. During earlier days, synteny blocks were identified through ad hoc methods that were slow, lacked reproducibility, ignored the conservation of gene order and orientation, and were not suitable for general applications. However, during the last decade, concerted efforts by several researchers have led to the development of a large volume of genomic data as well as computational resources that allow comparative genomic analysis between genomes of interest with high resolution. Comparative analysis of map-based genomic sequences led to the identification of shared intragenomic duplications, which provide important clues on the evolution of crop genomes from common ancestors. Recent studies in synteny analysis involve transcriptomic synteny to understand the functional conservation of orthologous genes and paleogenomic synteny to understand the role of whole-genome duplications on genome evolution. This chapter discusses the role of synteny analysis in comparative genomics; various computational tools employed for synteny analysis; synteny of sorghum with allied and model genomes with reference to molecular maps, markers, and the whole genome; emerging trends in synteny analysis; and future prospects.