Jessica B Lyons, Jessen V Bredeson, Ben N Mansfeld, Guillaume Jean Bauchet, Jeffrey Berry, Adam Boyher, Lukas A Mueller, Daniel S Rokhsar, Rebecca S Bart.

Plant Mol Biol.; 2022 Jun; 109(3):177-191. doi: 10.1007/s11103-020-01104-w. 

Abstract

We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

See https://pubmed.ncbi.nlm.nih.gov/33604743/

Fig. 3

Repeats, genes, and recombination frequency in the AM560-2 v7 cassava genome. Repeat density (light blue lines), gene count (blue lines), and recombination rate (gold lines) are plotted. Genic regions are anticorrelated with repetitive regions (Y-axis). Regions with low recombination frequency tend to co-occur with areas of high repeat density, thus, these hard-to-assemble regions also tend not to benefit from scaffolding information provided by a genetic map. Repeat density is measured as the fraction of bases that are annotated as repetitive in 1 Mb sliding windows sampled every 100 kb along the AM560-2 v7 chromosomes. The gene count was also taken with 1 Mb sliding windows every 100 kb. Recombination rate is measured as the number of recombinations per 1 Mb sliding window (100 kb step) using the first derivative of a natural cubic spline-smoothed fit line to the ICGMC 2014 framework map anchored to the v7 genome sequence. The marker positions of the framework map are plotted with vertical black ticks below the X-axis.