High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O

Sato, Kenzo; Kadota, Yasuhiro; Gan, Pamela; Bino, Takahiro; Uehara, Taketo; Yamaguchi, Katsushi; Ichihashi, Yasunori; Maki, Noriko; Iwahori, Hideaki; Suzuki, Takamasa; Shigenobu, Shuji; Shirasu, Ken

doi:10.1128/genomea.00519-18

Cited by 32 publications

(23 citation statements)

References 13 publications

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“…To further assess genome completeness, we used CEGMA and BUSCO and this allowed to retrieve 94.76 and 87.5 % of the CEGMA and eukaryotic BUSCO genes in complete length, respectively ( Table 1). The CEGMA score is the highest obtained for a Meloidogyne to date and is only paralleled by the 2017 versions of M. incognita and M. arenaria (Blanc-Mathieu et al 2017) as well as the 2018 version of M. arenaria (Sato et al 2018) . Similarly, the BUSCO scores obtained are only surpassed by those of M. incognita and M. javanica produced in 2017 (Blanc-Mathieu et al 2017) .…”

Section: Resultsmentioning

confidence: 93%

The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

Koutsovoulos

Poullet

Ashry³

et al. 2019

Preprint

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Root-knot nematodes (genus Meloidogyne ) are plant parasitic species that cause huge economic loss in the agricultural industry and affect the prosperity of communities in developing countries. Control methods against these plant pests are sparse and the current preferred method is deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, some species such as M. enterolobii are not controlled by the resistance genes deployed in the most important crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Like the other most damaging Meloidogyne species (e.g. M. incognita , M. arenaria and M. javanica ), M. enterolobii reproduces by obligatory mitotic parthenogenesis. Genomic singularities such as a duplicated genome structure and a relatively high proportion of transposable elements have previously been described in the above mentioned mitotic parthenogenetic Meloidogyne. To gain a better understanding of the genomic and evolutionary background we sequenced the genome of M. enterolobii using high coverage short and long read technologies. The information contained in the long reads helped produce a highly contiguous genome assembly of M. enterolobii , thus enabling us to perform high quality annotations of coding and non-coding genes, and transposable elements.The genome assembly and annotation reveals a genome structure similar to the ones described in the other mitotic parthenogenetic Meloidogyne, described as recent hybrids. Most of the genome is present in 3 different copies that show high divergence. Because most of the genes belong to these duplicated regions only few gene losses took place, which suggest a recent polyploidization. The most likely hypothesis to reconcile high divergence between genome copies despite few gene losses and translocations is also a recent hybrid origin. Consistent with this hypothesis, we found an abundance of transposable elements at least as high as the one observed in the mitotic parthenogenetic nematodes M. incognita and M. javanica .

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Section: Resultsmentioning

confidence: 93%

The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

Koutsovoulos

Poullet

Ashry³

et al. 2019

Preprint

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“…Repetitive sequence statistics and classification results are shown in Tables S10 and S11 and Figure S4. The genome of H. glycines is diploid and consists of repeated sequences with higher nucleotide divergence (19.21%) than the genomes of Meloidogyne species, which are polyploid and consist of duplicated regions with low nucleotide divergence (~8%) (Abad et al, ; Blanc‐Mathieu et al, ; Sato et al, ; Szitenberg et al, ).…”

Section: Resultsmentioning

confidence: 99%

“…Results of repeat prediction showed that the X12 genome contains 51.10% repeat sequences. Repetitive sequence statistics and classification results are shown in Tables S10 and S11 and Figure TA Blanc-Mathieu et al, 2017;Sato et al, 2018;Szitenberg et al, 2017).…”

Section: Genome Summarymentioning

confidence: 99%

Chromosome‐level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Lian

Wang

et al. 2019

Molecular Ecology Resources

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Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome‐level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole‐genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired‐end sequencing, 10X Genomics linked reads and high‐throughput chromatin conformation capture (Hi‐C) genome scaffolding techniques, a 141.01‐megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single‐Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second‐stage juveniles (J2), third‐stage juveniles (J3) and fourth‐stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high‐quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN–plant interactions and co‐evolution, and also contribute to the development of technology for overall SCN management.

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“…For these reasons and also the lack of detailed and clearly defined sequences of paralogous genes of PPNs, we did not focus on whether the genes we studied had paralogs or not. Recent advances in genome sequencing technologies have made it possible to study the detailed biology of several species of rootknot nematodes including M. incognita, Meloidogyne hapla, Meloidogyne arenaria, Meloidogyne floridensis, Meloidogyne javanica, Meloidogyne enterolobii, and Meloidogyne graminicola (Abad et al, 2008;Opperman et al, 2008;Lunt et al, 2014;Szitenberg et al, 2017;Sato et al, 2018;Somvanshi et al, 2018). However, the presence of paralogs and their possible functions in the nematodes' genomes are only recently becoming available (Blanc-Mathieu et al, 2017;Pratx et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode, Meloidogyne incognita Results in Diverse Responses Including Increase and No Change in Expression of Some Genes

2020

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Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative.

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High-Quality Genome Sequence of the Root-Knot Nematode Meloidogyne arenaria Genotype A2-O

Abstract: Root-knot nematodes (Meloidogyne spp.) cause serious damage to many crops globally. We report the high-quality genome sequence of Meloidogyne arenaria genotype A2-O.

Cited by 32 publications

References 13 publications

The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

The polyploid genome of the mitotic parthenogenetic root-knot nematodeMeloidogyne enterolobii

Chromosome‐level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines

Attempt to Silence Genes of the RNAi Pathways of the Root-Knot Nematode, Meloidogyne incognita Results in Diverse Responses Including Increase and No Change in Expression of Some Genes

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