scholarly journals A chromosomal assembly of the soybean cyst nematode genome

2021 ◽  
Author(s):  
Rick Masonbrink ◽  
Tom Maier ◽  
Matthew Hudson ◽  
Andrew Severin ◽  
Thomas Baum
Keyword(s):  
Soybean Cyst Nematode ◽  
Control Strategies ◽  
Cyst Nematode ◽  
Natural Resistance ◽  
Genetic Determinants ◽  
Safe Alternative ◽  
Root Cells ◽  
Long Read ◽  
Soybean Plants ◽  
Root Tissues

The soybean cyst nematode (Heterodera glycines) is a sedentary plant parasite that exceeds a billion dollars in yield losses annually. It has spread across the soybean-producing world, emerging as the primary pathogen of soybeans. This problem is exacerbated by H. glycines populations overcoming the limited sources of natural resistance in soybean and by the lack of effective and safe alternative treatments. 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. Successful H. glycines infection relies on the comprehensive re-engineering of soybean root cells into a syncytium, as well as the long-term suppression of host defenses 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 that control genomic effector acquisition, diversification, and selection are important insights needed for the development of essential novel control strategies. As a foundation to obtain this understanding, we developed a nine scaffold, 158Mb pseudomolecule assembly of the H. glycines genome using PacBio, Chicago, and Hi-C sequencing. An annotation of 22,465 genes was predicted using a Mikado pipeline informed by published short- and long-read expression data. Here we present results from our assembly and annotation of the H. glycines genome.

scholarly journals The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes

2018 ◽  
Author(s):  
Rick Masonbrink ◽  
Tom R. Maier ◽  
Usha Muppiral ◽  
Arun S. Seetharam ◽  
Etienne Lord ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Control Strategies ◽  
Cyst Nematode ◽  
Effective Control ◽  
Evolutionary Mechanisms ◽  
Long Read ◽  
Soybean Plants ◽  
Parasitism Genes ◽  
Nematode Genomes

AbstractHeterodera 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 virulentH. glycinespopulations. The parasitic success ofH. glycinesrelies 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 byH. glycinesinto 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. Here, we use PacBio long-read technology to assemble aH. glycinesgenome of 738 contigs into 123Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7Mb), and horizontal gene transfer events (151 genes). Using previously published effector sequences, the newly generatedH. glycinesgenome, and comparisons to other nematode genomes, we investigate the evolutionary mechanisms responsible for the emergence and diversification of effector genes.

scholarly journals Modulations in Gene Expression and Mapping of Genes Associated with Cyst Nematode Infection of Soybean

2001 ◽  
Vol 14 (1) ◽  
pp. 42-54 ◽  
Author(s):  
Zarir Vaghchhipawala ◽  
Ronald Bassüner ◽  
Kathryn Clayton ◽  
Kimberley Lewers ◽  
Randy Shoemaker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Soybean Cyst Nematode ◽  
Genetic System ◽  
Cyst Nematode ◽  
Infection Process ◽  
Resistance Locus ◽  
Root Cells ◽  
Feeding Site ◽  
Susceptible Line ◽  
Scn Resistance

Infection of the soybean root by the soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) induces a well-documented, yet poorly understood, response by the host plant. The plant response, involving the differentiation of a feeding structure, or “syncytium,” facilitates the feeding and reproduction of the nematode to the detriment of the host. We used a genetic system involving a single dominant soybean gene conferring susceptibility to an inbred nematode strain, VL1, to characterize the nematode-host interaction in susceptible line PI 89008. The restriction fragment length polymorphism marker pB053, shown to map to a major SCN resistance locus, cosegregates with resistance among F2 progeny from the PI 89008 × PI 88287 cross. Cytological examination of the infection process confirmed that syncytium development in this genetic system is similar to that reported by others who used noninbred nematode lines. Our study of infected root tissue in the susceptible line PI 89008 revealed a number of genes enhanced in expression. Among these are catalase, cyclin, elongation factor 1α, β-1,3-endoglucanase, hydroxymethylglutaryl coenzyme A reductase, heat shock protein 70, late embryonic abundant protein 14, and formylglycinamidine ribonucleotide synthase, all of which we have genetically positioned on the public linkage map of soybean. Formylglycinamidine ribonucleotide synthase was found to be tightly linked with a major quantitative trait locus for SCN resistance. Our observations are consistent with the hypothesis proposed by others that feeding site development involves the dramatic modulation of gene expression relative to surrounding root cells.

scholarly journals Marker-assisted selection strategies for developing resistant soybean plants to cyst nematode

2014 ◽  
Vol 14 (3) ◽  
pp. 180-186 ◽  
Author(s):  
Fernanda Abreu Santana ◽  
Martha Freire da Silva ◽  
Julierme Kellen Freitas Guimarães ◽  
Marcia Flores da Silva Ferreira ◽  
Waldir Dias Pereira ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Selection Strategies ◽  
Resistant Lines ◽  
Resistance Trait ◽  
Scn Resistance ◽  
Soybean Plants ◽  
Moderate Resistance ◽  
Selection Of

Resistant lines can be identified by marker-assisted selection(MAS), based on alleles of genetic markers linked to the resistance trait. This reduces the number of phenotypically evaluated lines, one of the limitations in the development of cultivars with resistance to soybean cyst nematode (SCN).This study evaluated the efficiency of microsatellites near quantitative traitloci (QTL) for SCN resistance, in the linkage groups (LG) G and A2 of soybean, for the selection of resistant genotypes in populations originated from crosses between the cultivars Vmax and CD201. The QTL of LG A2 was not detected in 'Vmax' (derived from PI 88788). In MAS, the microsatellites of LG G were efficient in selecting F6:7 families with resistance and moderate resistance to SCN race 3. The selection efficiency of the microsatellites Sat_168, Satt309 and Sat_141 was greater than 93%.

Yield components of soybean plants infected with soybean cyst nematode and sprayed with foliar applications of boron and magnesium1

2000 ◽  
Vol 23 (6) ◽  
pp. 827-834 ◽  
Author(s):  
Gordon Smith ◽  
William Wiebold ◽  
T.L. Niblack ◽  
Peter Scharf ◽  
Dale Blevins
Keyword(s):  
Yield Components ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Soybean Plants

scholarly journals Developmental Transcript Profiling of Cyst Nematode Feeding Cells in Soybean Roots

2007 ◽  
Vol 20 (5) ◽  
pp. 510-525 ◽  
Author(s):  
Nagabhushana Ithal ◽  
Justin Recknor ◽  
Dan Nettleton ◽  
Tom Maier ◽  
Thomas J. Baum ◽  
...  
Keyword(s):  
Cell Wall ◽  
Soybean Cyst Nematode ◽  
Molecular Mechanisms ◽  
Cyst Nematode ◽  
Transcript Profiling ◽  
Cyst Nematodes ◽  
Root Cells ◽  
Genes Encoding ◽  
Soybean Roots ◽  
And Function

Cyst nematodes of the genus Heterodera are obligate, sedentary endoparasites that have developed highly evolved relationships with specific host plant species. Successful parasitism involves significant physiological and morphological changes to plant root cells for the formation of specialized feeding cells called syncytia. To better understand the molecular mechanisms that lead to the development of nematode feeding cells, transcript profiling was conducted on developing syncytia induced by the soybean cyst nematode Heterodera glycines in soybean roots by coupling laser capture microdissection with high-density oligonucleotide microarray analysis. This approach has identified pathways that may play intrinsic roles in syncytium induction, formation, and function. Our data suggest interplay among phytohormones that likely regulates synchronized changes in the expression of genes encoding cell-wall-modifying proteins. This process appears to be tightly controlled and coordinately regulated with cell wall rigidification processes that may involve lignification of feeding cell walls. Our data also show local downregulation of jasmonic acid biosynthesis and responses in developing syncytia, which suggest a local suppression of plant defense mechanisms. Moreover, we identified genes encoding putative transcription factors and components of signal transduction pathways that may be important in the regulatory processes governing syncytium formation and function. Our analysis provides a broad mechanistic picture that forms the basis for future hypothesis-driven research to understand cyst nematode parasitism and to develop effective management tools against these pathogens.

scholarly journals First Report of the Soybean Cyst Nematode, Heterodera glycines, on Soybean in Zhejiang, Eastern China

Plant Disease ◽  
2009 ◽  
Vol 93 (3) ◽  
pp. 319-319 ◽  
Author(s):  
J. Zheng ◽  
Y. Zhang ◽  
X. Li ◽  
L. Zhao ◽  
S. Chen
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Eastern China ◽  
Mainland China ◽  
Its Region ◽  
Cyst Nematode ◽  
Northeastern China ◽  
First Report ◽  
Soybean Plants ◽  
Two Populations

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a destructive pest of soybean. Damage to soybean by SCN was first reported from northeastern China in 1899 (1). SCN has been documented in Anhui, Beijing, Hebei, Heilongjiang, Henan, Jiangsu, Jilin, Liaoning, Neimenggu, Shaanxi, Shandong, and Shanxi provinces in mainland China (1). These provinces are situated in the Heilongjiang and Songhuajing valleys in northeastern China and the eastern region of the Yangtze and Yellow rivers in northern China and have cold to temperate climates. In June of 2008, cyst-forming nematodes were detected in two soybean-growing areas of Hangzhou and Xiaoshan in Zhejiang Province, in subtropical eastern China. The soybean plants at the Hangzhou site showed symptoms of stunting and chlorosis, whereas no aboveground or root symptoms were observed on soybean plants at the Xiaoshan site, except for the presence of SCN females on the roots. The two populations had the same morphological and molecular characters. The cysts were lemon shaped with posterior protuberance, ambifenestrate, underbridge and bullae strongly developed, and lateral field of second-stage juveniles consisted of four incisures. The key morphometrics of cysts were fenestra length (41 to 52 μm) and width (33 to 48 μm), vulval silt (47 to 55 μm), and underbridge length (79 to 94 μm), all of which were coincident with that of SCN (2). Amplification of rDNA-internal transcribed spacer (ITS) region using primers TW81 (5′-GTT TCC GTA GGT GAA CCT GC-3′) and AB28 (5′-ATA TGC TTA AGT TCA GCG GGT-3′) yielded a PCR fragment of approximately 1,030 bp. The digestion patterns of the PCR fragments of the ITS region with AluI, AvaI, CfoI, MvaI, and RsaI showed identical restriction profiles to H. glycines (3), and the sequences exhibited 100% similarity with those of H. glycines isolates, Accession No. AY667456 from GenBank. Morphological and molecular identification confirmed that the two populations of cyst-forming nematodes from Zhejiang are SCN. To our knowledge, this is the first report of SCN in Zhejiang, now the most southern location in mainland China with confirmed infestation of SCN. References: (1) Z. X. Liu et al. Int. J. Nematol. 7:18, 1997. (2) R. H. Mulvey. Can. J. Zool. 50:1277, 1972. (3) J. Zheng et al. Russ. J. Nematol. 8:109, 2000.

scholarly journals Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum

2019 ◽  
Vol 10 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Charlène Faure ◽  
Marine Veyssière ◽  
Betty Boëlle ◽  
Hélène San Clemente ◽  
Olivier Bouchez ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Dna ◽  
Genetic Determinants ◽  
Pythium Oligandrum ◽  
Free Living ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Rnaseq Data ◽  
Long Read ◽  
Root Tissues

Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defenses. Here we report the first long-read genome sequencing of a P. oligandrum strain sequenced by PacBio technology. Sequencing of genomic DNA loaded onto six SMRT cells permitted the acquisition of 913,728 total reads resulting in 112X genome coverage. The assembly and polishing of the genome sequence yielded180 contigs (N50 = 1.3 Mb; L50 = 12). The size of the genome assembly is 41.9 Mb with a longest contig of 2.7 Mb and 15,007 predicted protein-coding genes among which 95.25% were supported by RNAseq data, thus constituting a new Pythium genome reference. This data will facilitate genomic comparisons of Pythium species that are commensal, beneficial or pathogenic on plant, or parasitic on fungi and oomycete to identify key genetic determinants underpinning their diverse lifestyles. In addition comparison with plant pathogenic or zoopathogenic species will illuminate genomic adaptations for pathogenesis toward widely diverse hosts.

scholarly journals Use of the Glomus etunicatum as biocontrol agent of the soybean cyst nematode

2021 ◽  
Vol 10 (6) ◽  
pp. e7310615132
Author(s):  
Tatiana Benedetti ◽  
Zaida Inês Antoniolli ◽  
Elisangela Sordi ◽  
Ivan Ricardo Carvalho ◽  
Edson Campanhola Bortoluzzi
Keyword(s):  
Soybean Cyst Nematode ◽  
Mycorrhizal Fungus ◽  
Arbuscular Mycorrhizal ◽  
Cyst Nematode ◽  
Initial Population ◽  
Glomus Etunicatum ◽  
Cyst Nematodes ◽  
Nematode Reproduction ◽  
Soybean Plants ◽  
Disease Pressure

This study investigated the effect of arbuscular mycorrhiza (Glomus etunicatum Becker & Gerd.), on the cyst nematode (Heterodera glycines Ichinohe), in a greenhouse. Mycorrhizal and non-mycorrhizal soybean plants were exposed to the pathogen at different initial population densities (0, 500, 1000, 2000, and 4000 nematodes eggs). Soybean growth, nematode reproduction, and the arbuscular mycorrhizal fungus’s capacity to decrease disease pressure were determined after 60 day-olds. The height of the plants was increased by 26% in the presence of arbuscular mycorrhizal fungus (AMF) despite of a higher initial population of cyst nematodes. The root length was, on average, 32.20% was greater in the presence of AMF. The number of nematodes females found in the root system of mycorrhizal plants was 28.21% lower than in non-mycorrhizal roots. These results suggest that AMF G. etunicatum acts indirectly, promoting an improvement in the nutritional plant status creating tolerance to the presence of the pathogen by soybean.

scholarly journals Esophageal Gland RNA-seq Resource of a Virulent and Avirulent Population of the Soybean Cyst Nematode, Heterodera glycines.

2021 ◽  
Author(s):  
Tom Maier ◽  
Rick E. Masonbrink ◽  
Paramasivan Vijayapalani ◽  
Michael Gardner ◽  
Amanda D. Howland ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Gland Cell ◽  
Heterodera Glycines ◽  
The United States ◽  
Cyst Nematode ◽  
Effector Proteins ◽  
Genomic Research ◽  
Natural Resistance ◽  
Rna Seq ◽  
Management Options

The soybean cyst nematode, Heterodera glycines, is the most economically devastating pathogen of soybean in the United States and threatens to become even more damaging through the selection of virulent nematode populations in the field that can overcome natural resistance mechanisms in soybean cultivars. This pathogen, therefore, demands intense transcriptomic/genomic research inquiries into the biology of its parasitic mechanisms. H. glycines delivers effector proteins that are produced in specialized gland cells into the soybean root to enable infection. The study of effector proteins, thus, is particularly promising when exploring novel management options against this pathogen. Here we announce the availability of a gland cell-specific RNA-seq resource. These data represent an expression snapshot of gland cell activity during early soybean infection of a virulent and an avirulent H. glycines population, which provides a unique and highly valuable resource for scientists examining effector biology and nematode virulence.

scholarly journals Soybean Resistance to the Soybean Cyst Nematode Heterodera glycines: An Update

2016 ◽  
Vol 106 (12) ◽  
pp. 1444-1450 ◽  
Author(s):  
Melissa G. Mitchum
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Cyst Nematode ◽  
Natural Resistance ◽  
Biochemical Basis ◽  
The World ◽  
Scn Resistance ◽  
Soybean Resistance ◽  
Nematode Virulence

The soybean cyst nematode (SCN), Heterodera glycines, remains a serious threat to soybean production throughout the world. A lack of genetic diversity in resistant soybean cultivars has led to a widespread shift toward virulence in SCN populations, leaving farmers with few proven options other than nonhost rotation to manage this nematode. Recent advances in our understanding of the genes controlling resistance to the nematode have led to improved molecular markers, which are, in turn, increasing the efficiency and precision of the breeding pipeline. A better understanding of the molecular and biochemical basis of SCN resistance and nematode virulence will provide information useful for the development of a long-term strategic plan for diversification and the deployment of cultivars that protect current sources of natural resistance while identifying new targets for engineering novel resistance.

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