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Genome Announcement: Further Improved Genome Assembly of Parapristionchus giblindavisi Cover

Genome Announcement: Further Improved Genome Assembly of Parapristionchus giblindavisi

Journal of Nematology
Volume 57 (2025): Issue 1 (February 2025)
By:
Open Access
|Jun 2025

Figures & Tables

Figure 1:

(A) The heatmap shows the Hi-C contact map for the P. giblindavisi genome. The color code for each cell indicates the number of Hi-C read pairs identified for a specific pair of 250-kb windows. (B) The picture shows a sperm cell of P. giblindavisi whereby the chromosomes were stained by Hoechst 33342. The scale bar indicates 2 μm. The bar plots show the proportion of male meiotic cells and sperms with each chromosome number. (C) We defined 1-1 orthologs between P. giblindavisi and P. pacificus proteins using best reciprocal BLAST hits and assigned Nigon elements based on the location of the 1-1 ortholog in the P. pacificus genome. Each bar shows the number of orthologs from different Nigon elements across 500-kb windows of the P. giblindavisi chromosomes.
(A) The heatmap shows the Hi-C contact map for the P. giblindavisi genome. The color code for each cell indicates the number of Hi-C read pairs identified for a specific pair of 250-kb windows. (B) The picture shows a sperm cell of P. giblindavisi whereby the chromosomes were stained by Hoechst 33342. The scale bar indicates 2 μm. The bar plots show the proportion of male meiotic cells and sperms with each chromosome number. (C) We defined 1-1 orthologs between P. giblindavisi and P. pacificus proteins using best reciprocal BLAST hits and assigned Nigon elements based on the location of the 1-1 ortholog in the P. pacificus genome. Each bar shows the number of orthologs from different Nigon elements across 500-kb windows of the P. giblindavisi chromosomes.

Characteristics of different P_ giblindavisi genome assemblies_

P. giblindavisi (Röseler et al., 2022)P. giblindavisi (This study)
Number of contigs/scaffolds735404
Total genome size (Mb)251.6303.1
N50 (Mb)0.843.6
Number of genes22,48822,594
BUSCO (proteins) (%)87.688.4
Median protein length (amino acids)224 [127–389]222 [127–387]
Median exon number7 [4–11]6 [4–11]
Median exon length (nucleotides)93 [71–120]93 [71–120]
Median intron length (nucleotides)132 [54–297]132 [54–297]
DOI: https://doi.org/10.2478/jofnem-2025-0026 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Submitted on: Apr 9, 2025
Published on: Jun 21, 2025
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 times per year
Keywords:
Comparative genomics,
Evolution,
Transposons,
Nigon elements,
Pristionchus pacificus
Related subjects:
Life sciences,
Life sciences, other

© 2025 Waltraud Röseler, Kohta Yoshida, Christian Rödelsperger, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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