Emerging Knowledge from Genome Sequencing of Crop Species

Abstract

Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population's viability.

Characterization of Transposable Elements in the Ectomycorrhizal Fungus Laccaria bicolor

“…A large proportion of class II elements also were found, mainly TIRs, Helitron and MITEs . In L. bicolor the single Helitron and its related copies account for about 0.13% of the genome and are mainly found in comparatively gene-rich regions, as has been reported in maize [31], while conversely they appear to be preferentially localized in the gene-poor region in Arabidopsis and rice genomes [35], [36]. In either case, the characteristics of Helitrons make them one of the primary sources of DNA variation [35].…”

Next generation breeding

“…With the advent of NGS technologies a different dimension to the exploration of plant diversity arose. Extensive insights into plant genome composition and organization have been gained from the genome sequencing and new findings on plant origin and evolution (genome duplication, ancestral re-arrangements and polyploidization events) have been revealed [2]. An in silico paleogenomic study based on a deep comparison of monocot and eudicot genomes, allowed the reconstruction of ancestral protochromosome segments and a description of the evolutionary dynamics leading to the present-day genomes, their genome organization and regulation [25].…”

Computational Pan-Genomics: Status, Promises and Challenges

“…Large-scale genomics projects to characterize the genetic diversity in plants are already ongoing, not only for the model plant Arabidopsis thaliana [5], but also for crops [50]. Examples include the resequencing of hundreds to thousands of varieties of rice [51], maize [52], sorghum [53], and tomato [6].…”