scholarly journals Toward 959 nematode genomes

Worm ◽  
2012 ◽  
Vol 1 (1) ◽  
pp. 42-50 ◽  
Author(s):  
Sujai Kumar ◽  
Georgios Koutsovoulos ◽  
Gaganjot Kaur ◽  
Mark Blaxter
Keyword(s):  
Nematode Genomes

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.

Isolation and characterization of tandem repeats in nematode genomes.

2021 ◽  
pp. 240-249
Author(s):  
Philippe Castagnone-Sereno
Keyword(s):  
Case Studies ◽  
Genetic Markers ◽  
Satellite Dna ◽  
Entomopathogenic Nematodes ◽  
Tandem Repeats ◽  
Genomic Resources ◽  
Isolation And Characterization ◽  
Nematode Genomes ◽  
Plant Parasitic

Abstract This chapter provides an overview of the practical methodologies that can be used to identify and characterize the tandem repeats that are most frequently used as genetic markers in nematodes (including plant-parasitic and entomopathogenic nematodes), namely satellite DNA and microsatellites. The objective is not to provide turnkey protocols, but rather to return to the main principles that govern these protocols. Case studies on nematodes will serve to illustrate the point. In that respect, two well-defined situations are to be considered, depending on whether genomic resources for the species under investigation are available or not.

scholarly journals Operons Are a Conserved Feature of Nematode Genomes

Genetics ◽  
2014 ◽  
Vol 197 (4) ◽  
pp. 1201-1211 ◽  
Author(s):  
Jonathan Pettitt ◽  
Lucas Philippe ◽  
Debjani Sarkar ◽  
Christopher Johnston ◽  
Henrike Johanna Gothe ◽  
...  
Keyword(s):  
Nematode Genomes

scholarly journals Comparative Genomics Reveals Novel Target Genes Towards Specific Control of Plant-Parasitic Nematodes

2020 ◽  
Author(s):  
Priscila Grynberg ◽  
Roberto Coiti Togawa ◽  
Leticia Dias de Freitas ◽  
Jose Dijair Antonino ◽  
Corinne Rancurel ◽  
...  
Keyword(s):  
Target Genes ◽  
Cultivated Plants ◽  
Parasitic Nematodes ◽  
Control Methods ◽  
Plant Parasitic Nematodes ◽  
Specific Proteins ◽  
Novel Target ◽  
Nematode Genomes ◽  
Specific Control ◽  
Plant Parasitic

Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

scholarly journals Signatures of adaptation to plant parasitism in nematode genomes

Parasitology ◽  
2014 ◽  
Vol 142 (S1) ◽  
pp. S71-S84 ◽  
Author(s):  
DAVID McK. BIRD ◽  
JOHN T. JONES ◽  
CHARLES H. OPPERMAN ◽  
TAISEI KIKUCHI ◽  
ETIENNE G. J. DANCHIN
Keyword(s):  
Parasitic Nematodes ◽  
Plant Parasitic Nematodes ◽  
Parasitic Species ◽  
Plant Parasitism ◽  
Genomic Signatures ◽  
Global Agriculture ◽  
Parasitism Genes ◽  
Species Specific ◽  
Nematode Genomes ◽  
Plant Parasitic

SUMMARYPlant-parasitic nematodes cause considerable damage to global agriculture. The ability to parasitize plants is a derived character that appears to have independently emerged several times in the phylum Nematoda. Morphological convergence to feeding style has been observed, but whether this is emergent from molecular convergence is less obvious. To address this, we assess whether genomic signatures can be associated with plant parasitism by nematodes. In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species. Candidate horizontal acquisitions of parasitism genes have systematically been found in all plant-parasitic species investigated at the sequence level. Presence of peptides that mimic plant hormones also appears to be a trait of plant-parasitic species. Annotations of the few genomes of plant-parasitic nematodes available to date have revealed a set of apparently species-specific genes on every occasion. Effector genes, important for parasitism are frequently found among those species-specific genes, indicating poor overlap. Overall, nematodes appear to have developed convergent genomic solutions to adapt to plant parasitism.

scholarly journals The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes

2006 ◽  
Vol 23 (12) ◽  
pp. 2303-2315 ◽  
Author(s):  
Asher D. Cutter ◽  
James D. Wasmuth ◽  
Mark L. Blaxter
Keyword(s):  
Amino Acid ◽  
Amino Acid Usage ◽  
Nematode Genomes

scholarly journals Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Werner E Mayer ◽  
Lisa N Schuster ◽  
Gabi Bartelmes ◽  
Christoph Dieterich ◽  
Ralf J Sommer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nematode Genomes

scholarly journals Comparative Genomics Reveals Novel Target Genes towards Specific Control of Plant-Parasitic Nematodes

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1347
Author(s):  
Priscila Grynberg ◽  
Roberto Coiti Togawa ◽  
Leticia Dias de Freitas ◽  
Jose Dijair Antonino ◽  
Corinne Rancurel ◽  
...  
Keyword(s):  
Target Genes ◽  
Cultivated Plants ◽  
Parasitic Nematodes ◽  
Control Methods ◽  
Plant Parasitic Nematodes ◽  
Specific Proteins ◽  
Novel Target ◽  
Nematode Genomes ◽  
Specific Control ◽  
Plant Parasitic

Plant-parasitic nematodes cause extensive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. Chemical methods that have been deployed to control nematodes have largely been banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasite-specific proteins, ca. 1000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of these, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasite-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis constitutes a unique resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.

scholarly journals Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 4 ◽  
Author(s):  
Alan D Winter ◽  
William Weir ◽  
Martin Hunt ◽  
Matthew Berriman ◽  
John S Gilleard ◽  
...  
Keyword(s):  
Haemonchus Contortus ◽  
Parasitic Nematode ◽  
Brugia Pahangi ◽  
Nematode Genomes
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