Genome Announcement: The Draft Genomes of Two <i>Radopholus similis</i> populations from Costa Rica

Wram, Catherine; Hesse, Cedar; Wasala, Sulochana K.; Howe, Dana K.; Peetz, Amy B.; Denver, Dee R.; Humphreys-Pereira, Danny A.; Zasada, Inga A.

doi:10.21307/jofnem-2019-052

Cited by 6 publications

(11 citation statements)

References 15 publications

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“…The genome of R . similis previously generated for the Rv population originally collected from Costa Rica was used as input for the following analyses [ 24 ]. The full set of 14,817 protein variants were initially submitted to SignalP 4.0 for prediction of secreted proteins [ 66 ], and transmembrane domains (TMHMM) using the TMHMM server version 2.0 ( http://www.cbs.dtu.dk/services/TMHMM/ ).…”

Section: Methodsmentioning

confidence: 99%

“…Some nematode secreted proteins play key roles for successful invasion and establishment of nematodes within the host plant [17]. Using the genome sequence of R. similis (Rv population [24]) we identified putatively secreted proteins for this nematode. Out of the 14,817 unique transcripts, a total of 2,218 (14.9%) were predicted to encode putatively secreted proteins without transmembrane domains (TMHMM) (S1 Table ).…”

Section: Radopholus Similis Secretome Prediction and Identification Of Known Candidate Effector Genesmentioning

confidence: 99%

“…The sequencing libraries were generated using a minimum of 2 μg of total RNA (per sample) following the manufacturer's instructions (Illumina Inc., San Diego, CA) and 150 base pair paired-ends were sequenced on an Illumina platform. Illumina RNA-seq reads of the nematode were then mapped against the Rv genome of R. similis [24] using the same parameters as described above. Gene expression patterns were deduced from the aligned reads and determined as FPKM values.…”

Section: Plant Inoculation and Effector Gene Expressionmentioning

confidence: 99%

“…The recent release of genome and transcriptome datasets for R. similis provide a general overview of the effector repertoire and evolutionary insights of this migratory nematode [12,[22][23][24]. The majority of the candidate effectors reported so far for R. similis are part of the common panel of effectors often found for other migratory and sedentary nematodes [12,23,25].…”

Section: Introductionmentioning

confidence: 99%

“…The recent release of genome and transcriptome datasets for R . similis provide a general overview of the effector repertoire and evolutionary insights of this migratory nematode [ 12 , 22 – 24 ]. The majority of the candidate effectors reported so far for R .…”

Section: Introductionmentioning

confidence: 99%

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Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

et al. 2021

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The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode.

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Section: Methodsmentioning

confidence: 99%

Section: Radopholus Similis Secretome Prediction and Identification Of Known Candidate Effector Genesmentioning

confidence: 99%

Section: Plant Inoculation and Effector Gene Expressionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The recent release of genome and transcriptome datasets for R . similis provide a general overview of the effector repertoire and evolutionary insights of this migratory nematode [ 12 , 22 – 24 ]. The majority of the candidate effectors reported so far for R .…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

et al. 2021

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Molecular diversity of Radopholus similis (Cobb 1913) Thorne (1949) (Nematoda: Pratylenchidae) affecting banana from Costa Rica

Torres

Segura²,

Sandoval

et al. 2022

Eur J Plant Pathol

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Radopholus similis is one of the most important diseases in banana in tropical/subtropical regions worldwide. The knowledge of its molecular diversity in specific areas could help to understand its distribution, ways of expansion, control methods, differential pathogenicity, and sustainable plant breeding programs. This study explores the molecular diversity of R. similis in an extensive survey in banana plantations in Costa Rica using two molecular markers, one genomic (ITS region) and another mitochondrial (COI). The results showed a low molecular variability, being dominated by a prevalent haplotype in both markers.Three haplotypes have been detected for each molecular marker respectively.The haplotypes present in Costa Rica are similar to others found in other areas of Central America (Colombia, Panama, ) and these haplotypes are also distributed worldwide. These results suggested a unique or limited number of introductions of this pathogen in Central America and a possible expansion within the continent by infected plant material.

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Recent Advances in Population Genomics of Plant-Parasitic Nematodes

et al. 2021

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Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information on genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomic or genome sequencing projects. This review also intends to foster the development of population genomics in plant-parasitic nematodes through the highlighting of recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, the pathogenicity and the evolutionary potential of plant-parasitic nematodes.

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Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica

Abstract: Radopholus similis is an economically important pest of both banana and citrus in tropical regions. Here we present draft genomes from two populations of R. similis from Costa Rica that were created and assembled using short read libraries from Illumina HiSeq technology.

Cited by 6 publications

References 15 publications

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

Molecular diversity of Radopholus similis (Cobb 1913) Thorne (1949) (Nematoda: Pratylenchidae) affecting banana from Costa Rica

Recent Advances in Population Genomics of Plant-Parasitic Nematodes

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