Sequencing Plant Genomes

The field of deciphering the letters of life, i.e. whole or complete genome sequencing not only paves the path for gene discovery and characterization (functional genomics) but also provides raw materials for analyzing the evolutionary history of an organism (molecular phylogeny). The genome sequence provides a bird’s eye view of the information needed for understanding the biology of organisms.  In 1974, two methods of DNA sequencing were independently developed. One team, lead by Maxam and Gilbert, used a “chemical cleavage protocol”, while the other, lead by Sanger, designed a procedure similar to the natural process of DNA replication. Even though both teams shared the 1980 Nobel Prize, Sanger’s method became the standard because of its relatively easier protocol. The first DNA sequence was obtained, of 12 base pair overhang of bacteriophage λ, using laborious methods based on 2-dimensional electrophoresis on cellulose acetate and DEAE cellulose paper. After this sequencing genomes has become easier as automated techniques have been developed from BAC shotgun sequencing to Next-generation sequencing (NGS) methods and technique.

All initial plant genome projects utilized the Sanger sequencing platform of dideoxy sequencing and either large insert clones such as bacterial artificial chromosome (BAC) clones that were subjected to shotgun sequencing or by direct whole genome shotgun sequencing (WGS). Since 2007, methods for sequencing plant genomes have evolved rapidly. This is due entirely to advances in next-generation sequencing (NGS) platforms in terms of throughput, quality, and read lengths. Major sequencing platform include Sanger Chain (termination/dideoxy sequencing), 454 (Pyrosequencing), Illumina (Sequencing by synthesis with reversible terminators), SOLiDTM (Sequencing by ligation in color space), Pacific Biosciences (Real-time single-molecule sequencing), Ion Torrent (pH detection),10X genomics (microfluidics-based platform for generating linked reads) and  nanopore sequencing technologies. The ability to determine the physical organization and expression patterns of genes from many plant species will allow the best leveraging of available resources through comparative genome analysis. For instance, the availability of the Arabidopsis genome sequence has greatly enhanced our knowledge of the entire complement of genes expressed by a typical flowering plant helped in map-based cloning in tomato on the basis of chromosomal synteny between the two species and facilitated functional analysis of tomato genes. Thus, translating the strings of A, G, C and T into an understanding of the various genes that make up the genome, how different genes are related, and how the various parts of the genome are coordinated. and ultimately how the genome works is still an open question and has given rise the various subfields of genomics such as transcriptomics, proteomics, functional genomics, and bioinformatics.