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.; 2021 Feb 18.  doi: 10.1007/s11103-020-01104-w. Online ahead of print.

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.

Cassava researchers have been making genetic maps for over 20 years (Fregene et al. 1997). Since 2012, a series of papers have demonstrated the utility of SNP markers for genetic mapping in cassava, especially when combined with phenotype data to map important traits (Soto et al. 2015; ICGMC 2014; Rabbi et al. 2014a, b; Rabbi et al. 2012). The International Cassava Genetic Map Consortium used GBS data from 10 mapping populations to construct a dense composite reference map, comprising 22,403 genetic markers organized into the expected 18 linkage groups (ICGMC 2014). This composite map has ongoing utility, including for improving or evaluating new genome assemblies (ICGMC 2014; Kuon et al. 2019; Bredeson et al. 2016). From version 5 onward, the chromosomes of the AM560-2 reference assemblies have been numbered according to the composite map, e.g. chromosome 7 corresponds to linkage group VII.

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

Figure 2: Reference genome assembly strategies. a Generating a haploid representation (reference assembly) of a diploid inbred genome is relatively straightforward. Due to homozygosity, sequence reads from the two haplotypes assemble together. b The heterozygosity present in a diploid outbred genome means that sequences from maternal and paternal haplotypes (blue and gold) will tend to assemble separately. In this case, to generate a haploid reference assembly, researchers can either combine maternal and paternal contigs into a haploid representation for each chromosome (haplotype-mosaic reference assembly), or they can try to fully assemble the maternal and paternal chromosomes, choosing one or the other to represent each chromosome in the reference (haplotype-phased reference assembly). Gray, assembly gaps