A genomic resource for the sedentary semi-endoparasitic reniform nematode, <i>Rotylenchulus reniformis</i> Linford &amp; Oliveira

Showmaker, Kurt C.; Sanders, William S.; Akker, Sebastian Eves‐van den; Martin, Brigitte E.; Platt, Roy Neal; Hsu, Chuan-Yu; Bartlett, Benjamin D.; Peterson, Daniel G.; Wubben, Martin J.

doi:10.21307/jofnem-2019-013

Cited by 8 publications

(7 citation statements)

References 9 publications

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“…Also, more recently, the draft genome of the sedentary semi-endoparasitic nematode species, R . reniformis has also been released in the public domain [14].…”

Section: Introductionmentioning

confidence: 99%

The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes

Mathew

Opperman

2019

PLoS ONE

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Radopholus similis, commonly known as the burrowing nematode, is an important pest of myriad crops and ornamentals including banana (Musa spp.) and Citrus spp. In order to characterize the potential role of putative effectors encoded by R. similis genes we compared predicted proteins from a draft R. similis genome with other plant-parasitic nematodes in order to define the suite of excreted/secreted proteins that enable it to function as a parasite and to ascertain the phylogenetic position of R. similis in the Tylenchida order. Identification and analysis of candidate genes encoding for key plant cell-wall degrading enzymes including GH5 cellulases, PL3 pectate lyases and GH28 polygalactouranase revealed a pattern of occurrence similar to other PPNs, although with closest phylogenetic associations to the sedentary cyst nematodes. We also observed the absence of a suite of effectors essential for feeding site formation in the cyst nematodes. Clustering of various orthologous genes shared by R. similis with other nematodes showed higher overlap with the cyst nematodes than with the root-knot or other migratory endoparasitic nematodes. The data presented here support the hypothesis that R. similis is evolutionarily closer to the cyst nematodes, however, differences in the effector repertoire delineate ancient divergence of parasitism, probably as a consequence of niche specialization. These similarities and differences further underscore distinct evolutionary relationships during the evolution of parasitism in this group of nematodes.

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“…Also, more recently, the draft genome of the sedentary semi-endoparasitic nematode species, R . reniformis has also been released in the public domain [14].…”

Section: Introductionmentioning

confidence: 99%

The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes

Mathew

Opperman

2019

PLoS ONE

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“…However, the rolling circle (RC) mechanism is used by other eukaryotic elements during DNA transposition; this is similar to that occurring in prokaryotes [ 17 ]. In a recent study, DNA transposons or LTR retroelements (20.6 Mb and 11.3 Mb, respectively) were identified in reniform nematode genomic assembly (RREN1.0, GCA_001026735.1) of size 314 Mb [ 8 ].…”

Section: Discussionmentioning

confidence: 99%

“…The prevalence of high low-complexity repeats within the reniform nematode genome suggests high levels of variation in its genome. These low-complexity repeats occupied about 2.2% of the reniform genome [ 8 ].…”

Section: Discussionmentioning

confidence: 99%

“…Whole-genome sequencing has been successfully used in sequencing of two human parasitic nematodes, including Wuchereria bancrofti [ 5 ] and Strongyloides stercoralis [ 6 ]. The usefulness of whole-genome amplification methods has been applied in genome sequencing projects for the reniform nematode [ 7 , 8 ]. Existence of low-complexity regions (LCRs) [ 9 ] and their repeats (2.2%) within the genome of reniform nematode serves as an indication of higher levels of variation [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

“…The usefulness of whole-genome amplification methods has been applied in genome sequencing projects for the reniform nematode [ 7 , 8 ]. Existence of low-complexity regions (LCRs) [ 9 ] and their repeats (2.2%) within the genome of reniform nematode serves as an indication of higher levels of variation [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome

Nyaku

Sripathi

Lawrence

et al. 2021

International Journal of Genomics

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One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.

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Unveiling the draft genome of the seed gall nematode, Anguina tritici: Insights and analysis

Singh,

Das,

Kumar

et al. 2024

Physiological and Molecular Plant Pathology

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A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira

Cited by 8 publications

References 9 publications

The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes

The genome of the migratory nematode, Radopholus similis, reveals signatures of close association to the sedentary cyst nematodes

Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome

Unveiling the draft genome of the seed gall nematode, Anguina tritici: Insights and analysis

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