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

Authors :
Joel-E. Kuon
Weihong Qi
Pascal Schläpfer
Matthias Hirsch-Hoffmann
Philipp Rogalla von Bieberstein
Andrea Patrignani
Lucy Poveda
Stefan Grob
Miyako Keller
Rie Shimizu-Inatsugi
Ueli Grossniklaus
Hervé Vanderschuren
Wilhelm Gruissem
Source :
BMC Biology, Vol 17, Iss 1, Pp 1-15 (2019)
Publication Year :
2019
Publisher :
BMC, 2019.

Abstract

Abstract Background 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. 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. Results We 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. Conclusions The 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.

Details

Language :
English
ISSN :
17417007
Volume :
17
Issue :
1
Database :
Directory of Open Access Journals
Journal :
BMC Biology
Publication Type :
Academic Journal
Accession number :
edsdoj.2c1355fe9154583a04f81644306356c
Document Type :
article
Full Text :
https://doi.org/10.1186/s12915-019-0697-6