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Genome Announcement: Further Improved Genome Assembly of Parapristionchus giblindavisi

Waltraud Röseler

Waltraud Röseler

Department for Integrative Evolutionary Biology, Max Planck Institute for BiologyTübingen, Germany
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Röseler, Waltraud
, 
Kohta Yoshida

Kohta Yoshida

  • Department for Integrative Evolutionary Biology, Max Planck Institute for BiologyTübingen, Germany
  • Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata UniversityNiigata, Japan
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Yoshida, Kohta
 et 
Christian Rödelsperger

Christian Rödelsperger

Department for Integrative Evolutionary Biology, Max Planck Institute for BiologyTübingen, Germany
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Rödelsperger, Christian
  
21 juin 2025
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Catégorie d'article: Research Note
Publié en ligne: 21 juin 2025
Reçu: 09 avr. 2025
DOI: https://doi.org/10.2478/jofnem-2025-0026
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© 2025 Waltraud Röseler et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

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/scaffolds 735 404
Total genome size (Mb) 251.6 303.1
N50 (Mb) 0.8 43.6
Number of genes 22,488 22,594
BUSCO (proteins) (%) 87.6 88.4
Median protein length (amino acids) 224 [127–389] 222 [127–387]
Median exon number 7 [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]
Langue:
Anglais
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Sciences de la vie, Sciences de la vie, autres
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