Current strategies of polyploid plant genome sequence assembly
Citation
Kyriakidou, M., Tai, H.H., Anglin, N.L., Ellis, D., Strömvik, M.V. (2018). Current strategies of polyploid plant genome sequence assembly, 871 http://dx.doi.org/10.3389/fpls.2018.01660
Plain language summary
All the DNA and genes for an organism is called the genome. Most living organisms carry around DNA inherited from both parents and therefore, carry a two genomes. Some organisms have more than two. These organisms are called polyploids. Many important crops, such as wheat and potato, are polyploids. Knowing what differences in the DNA sequence control beneficial traits in crops is very useful for improving crops. Getting DNA sequence for each of the genomes in polyploids is a challenge since all the genomes are mixed up when the DNA is isolated. Special methods are needed to unravel the DNA sequence data and piece together the puzzle. This article reviews the latest approaches and technologies for polyploidy genome sequencing.
Abstract
© 2018 Kyriakidou, Tai, Anglin, Ellis and Strömvik. Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.