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. 2021 Jul 19:53:e2021-65.
doi: 10.21307/jofnem-2021-065. eCollection 2021.

Genome sequence of the coffee root-knot nematode Meloidogyne exigua

Ngan Thi Phan  1 , Guillaume Besnard  2 , Rania Ouazahrou  3 , William Solano Sánchez  4 , Lisa Gil  5 , Sophie Manzi  2 , Stéphane Bellafiore  1
Affiliations

Genome sequence of the coffee root-knot nematode Meloidogyne exigua

Ngan Thi Phan et al. J Nematol. .

Abstract

Root-knot nematodes (Meloidogyne spp.) cause serious damages on most crops. Here, we report a high-quality genome sequence of Meloidogyne exigua (population Mex1, Costa Rica), a major pathogen of coffee. Its mitogenome (20,974 bp) was first assembled and annotated. The nuclear genome was then constructed consisting of 206 contigs, with an N50 length of 1.89 Mb and a total assembly length of 42.1 Mb.

Keywords: Genomics; Illumina; Mitogenome; Nanopore sequencing; Nuclear genome; Root-knot nematode.

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Figures

Figure 1:
Figure 1:
Circular gene map of the complete mitochondrial genome of M. exigua. Protein-coding genes, rRNA genes, and repeated regions are represented as boxes. Position of tRNAs are indicated by black lines. The direction of transcription of all genes is the same and indicated by the arrow. Abbreviations of protein coding and rRNA genes are: nadi = subunit i of NADH dehydrogenase; coxi = subunit i of cytochrome c oxydase; cob = cytochrome b; atp6 = subunit 6 of ATP-synthase; rrnS = small subunit ribosomal RNA (12S); rrnL = large subunit ribosomal RNA (16S). tRNA genes (trnX) are named with a single-letter amino acid abbreviation (X) except for those coding for leucine, which are named as L1 (anticodon uag) and L2 (uaa). Two minisatellite regions, namely 102R and 313R, are composed of 102-bp and 313-bp repeats.
Figure 2:
Figure 2:
Haploid genome length, genome ploidy estimation and contaminant analysis of the M. exigua genome assembly. (A) GenomeScope profile showing estimated genome length of 43.26 Mb and heterozygosity of 0.028% at k-mer = 21. (B) Smudge plots showing the coverage and distribution of k-mer pairs that fit to diploid genome model. (C) Blobplot showing the lack of contamination in the final assembly by foreign (non-Nematoda) genetic material.
See this image and copyright information in PMC

References

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