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Genome sequence of the coffee root-knot nematode Meloidogyne exigua

Journal of Nematology
Volume 53 (2021): Issue 1 (January 2021)
By:
Open Access
|Jul 2021

Figures & Tables

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.
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:

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.
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.

Statistics of the genome assemblyfor M_ exigua obtained in our study (with Canu; Koren et al_, 2017)_

Assembly features M. exigua genome
Total #scaffolds260
Total length (bp)42,101,073
Largest contig (bp)3,958,915
N50 (bp)1,882,513
N90 (bp1,045,864
L50 (# scaffolds)10
L90 (#scaffolds)18
GC (%)25.55
Mismatches0
Gaps0
CEGMA completenessa (n:248)C:95.97% (C+P: 97.18%)
BUSCO completenessb (n:303)C:89.4% [S: 89.1%, D: 0.3%]
DOI: https://doi.org/10.21307/jofnem-2021-065 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Page range: 1 - 6
Published on: Jul 19, 2021
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 times per year
Keywords:
Genomics,
Illumina,
Mitogenome,
Nanopore sequencing,
Nuclear genome,
Root-knot nematode
Related subjects:
Life sciences,
Life sciences, other

© 2021 Ngan Thi Phan, Guillaume Besnard, Rania Ouazahrou, William Solano Sánchez, Lisa Gil, Sophie Manzi, Stéphane Bellafiore, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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