Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars

Joel-E Kuon,Wilhelm Gruissem,Ueli Grossniklaus,Hervé Vanderschuren,Lucy Poveda,Rie Shimizu-Inatsugi,Weihong Qi,Stefan Grob,Andrea Patrignani,Philipp Rogalla Von Bieberstein,Matthias Hirsch-Hoffmann,Miyako Keller,Pascal Schläpfer

doi:10.1186/s12915-019-0697-6

Abstract

BackgroundCassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus, CMD2, for introducing CMD resistance into susceptible cultivars. The CMD2 locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown.ResultsWe report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical Manihot esculenta), which is the origin of CMD2, and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the CMD2 locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars.ConclusionsThe genome maps of the CMD2 locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of CMD2 resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large CMD2 region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.

Highlights

Cassava is an important food crop in tropical and sub-tropical regions worldwide
Using 70× PacBio whole genome shotgun long reads with N50 read length of 12,813 bp (60444) and 12,424 bp (TME3), we assembled the TME3 genome into 12,971 contigs with a N50 of 98 kb (i.e., 50% of the assembly consists of 98 kb or longer contigs)
We evaluated the performance of three different long-read assemblers (CANU-MHAP [34], FALCON v0.5 [35] and PBcR-MHAP [36]) by aligning Illumina paired-end (PE) reads to the corresponding long-read assemblies

Summary

Introduction

Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Genetic gains from breeding in cassava have made little progress over the last century compared to other crops [3]. The whitefly-transmitted virus is spreading and affecting agricultural productivity as a result of substantial yield losses in CMD-susceptible cultivars, in extreme cases up to 100% [5, 6]. An estimated 25 million tons of cassava storage roots are lost to CMD annually, impacting food security for more than 500 million people [7,8,9]

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Results

Conclusion