The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.
View / Open Files
Authors
Masonbrink, Rick
Maier, Tom R
Muppirala, Usha
Lord, Etienne
Juvale, Parijat S
Schmutz, Jeremy
Korkin, Dmitry
Mitchum, Melissa G
Mimee, Benjamin
den Akker, Sebastian Eves-van
Hudson, Matthew
Severin, Andrew J
Baum, Thomas J
Publication Date
2019-02-07Journal Title
BMC Genomics
ISSN
1471-2164
Publisher
Springer Science and Business Media LLC
Volume
20
Issue
1
Pages
119
Language
eng
Type
Article
This Version
VoR
Physical Medium
Electronic
Metadata
Show full item recordCitation
Masonbrink, R., Maier, T. R., Muppirala, U., Seetharam, A. S., Lord, E., Juvale, P. S., Schmutz, J., et al. (2019). The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes.. BMC Genomics, 20 (1), 119. https://doi.org/10.1186/s12864-019-5485-8
Abstract
BACKGROUND: Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. RESULTS: Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons. CONCLUSIONS: This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
Keywords
Animals, Tylenchoidea, Soybeans, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Plant Diseases, Gene Duplication, Genotype, Polymorphism, Single Nucleotide, Host-Parasite Interactions, Molecular Sequence Annotation
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/R011311/1)
Identifiers
External DOI: https://doi.org/10.1186/s12864-019-5485-8
This record's URL: https://www.repository.cam.ac.uk/handle/1810/308021
Statistics
Total file downloads (since January 2020). For more information on metrics see the
IRUS guide.