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Genome Announcement: Draft Genome Assembly of Heterodera humuli Generated Using Long-Read Sequencing

Lester A. Núñez-Rodríguez

Lester A. Núñez-Rodríguez

  • Department of Botany and Plant Pathology, Oregon State UniversityCorvallis,
  • USDA-ARS Horticultural Crops Disease and Pest Management Research UnitCorvallis,
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Núñez-Rodríguez, Lester A.
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Catherine L. Wram

Catherine L. Wram

USDA-ARS Mycology and Nematology Genetic Diversity and Biology LabBeltsville,
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Wram, Catherine L.
, 
Cedar Hesse

Cedar Hesse

USDA-ARS Horticultural Crops Production and Genetic Improvement Research UnitCorvallis,
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Hesse, Cedar
 und 
Inga A. Zasada

Inga A. Zasada

USDA-ARS Horticultural Crops Disease and Pest Management Research UnitCorvallis,
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Zasada, Inga A.
  
28. Aug. 2024
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Artikel-Kategorie: Research Note
Online veröffentlicht: 28. Aug. 2024
Eingereicht: 05. Apr. 2024
DOI: https://doi.org/10.2478/jofnem-2024-0029
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© 2024 Lester A. Núñez-Rodríguez et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

Figure S1.

Visualization of the meta-assembly of Heterodera humuli genome. The Hifiasm v.0.16.1-r375 algorithm was used to assemble the reads > 3 kb from the PacBio Sequel IIe system. The Blobplot (Laetsch and Blaxter, 2017) shows assembled contigs as circles with placement of circles on the x-axis representing the proportion of GC bases and the position on the y-axis representing the coverage of the contig with the raw data.
Visualization of the meta-assembly of Heterodera humuli genome. The Hifiasm v.0.16.1-r375 algorithm was used to assemble the reads > 3 kb from the PacBio Sequel IIe system. The Blobplot (Laetsch and Blaxter, 2017) shows assembled contigs as circles with placement of circles on the x-axis representing the proportion of GC bases and the position on the y-axis representing the coverage of the contig with the raw data.

Figure S2.

Visualization of the final assembly of Heterodera humuli using reads from the PacBio Sequel IIe system. The Hifiasm v.0.16.1-r375 algorithm was used to assemble the reads. The blobplot (Laetsch and Blaxter, 2017) shows assembled contigs as circles with placement of circles on the x-axis representing the proportion of GC bases and the position on the y-axis representing the coverage of the contig with the raw data.
Visualization of the final assembly of Heterodera humuli using reads from the PacBio Sequel IIe system. The Hifiasm v.0.16.1-r375 algorithm was used to assemble the reads. The blobplot (Laetsch and Blaxter, 2017) shows assembled contigs as circles with placement of circles on the x-axis representing the proportion of GC bases and the position on the y-axis representing the coverage of the contig with the raw data.

Figure S3.

BUSCO assessment results of Heterodera species (NCBI GenBank BioProject number) using both databases, A) eukaryota_odb10 and B) nematoda_odb10.
BUSCO assessment results of Heterodera species (NCBI GenBank BioProject number) using both databases, A) eukaryota_odb10 and B) nematoda_odb10.

Figure S4.

Phylogenetic relationships between Heterodera species as inferred from Bayesian analysis of the partial cox1 gene sequences under the GTR + I + G model. Posterior probability values are given for appropriate clades. The bold name represents the H. humuli sequence derived from this study. Sequences were retrieved from GenBank, aligned, and trimmed with BioEdit v.7.0.5.3 (Hall, 1999). The best substitution model was determined using jModelTest 2.1.10 v20160303 (Darriba et al., 2012) and the Bayesian analysis was performed using MrBayes v3.2 (Ronquist et al., 2012) at the CIPRES Science Gateway. Finally, FigTree v1.4.3 (Rambaut, 2016) was used to visualize the resulting phylogenetic tree.
Phylogenetic relationships between Heterodera species as inferred from Bayesian analysis of the partial cox1 gene sequences under the GTR + I + G model. Posterior probability values are given for appropriate clades. The bold name represents the H. humuli sequence derived from this study. Sequences were retrieved from GenBank, aligned, and trimmed with BioEdit v.7.0.5.3 (Hall, 1999). The best substitution model was determined using jModelTest 2.1.10 v20160303 (Darriba et al., 2012) and the Bayesian analysis was performed using MrBayes v3.2 (Ronquist et al., 2012) at the CIPRES Science Gateway. Finally, FigTree v1.4.3 (Rambaut, 2016) was used to visualize the resulting phylogenetic tree.

Comparison of genome assembly statistics of Heterodera humuli and three other Heterodera species_

Type of analysis Parameter H. carotae (PRJNA774818)x H. glycines (PRJNA381081)x H. humuli (PRJNA1048471)x H. schachtii (PRJNA767548)x
Genome statistics Total Number of bp 95,115,141 157,978,452 90,806,450 190,153,211
Number of Contigs 17,835 9 1,487 705
Largest contig 113,425 23,985,585 568,746 4,323,191
Contigs ≥ 25000 699 9 871 609
Contigs ≥ 50000 103 9 559 531
Average GC% 39.39 36.66 36.11 32.36
Contig N50 13,935 17,907,690 111,383 500,954
Contig L50 1,836 4 231 86
Number of N’s per 100 kbp 0 1,062.01 0 2,253.83
Predicted number coding genes 17,037 22,465 15,428 29,851
Predicted number of transcripts 17,322 29,933 16,848 31,564
Predicted Protein BUSCO Analysis (Nematoda_ob10 – 3,131 genes) Complete BUSCOs (C) (%) 1,301 (41.5%) 1,884 (60.2%) 2,030 (64.9%) 2,080 (66.4%)
Complete BUSCOs and single-copy BUSCOs (S) (%) 1,237 (39.5%) 1,612 (51.5%) 1,590 (50.8%) 1,675 (53.5%)
Complete and duplicated BUSCOs (D) (%) 64 (2%) 272 (8.7%) 440 (14.1%) 405 (12.9%)
Fragmented BUSCOs (F) (%) 124 (4%) 47 (1.5%) 66 (2.1%) 69 (2.2%)
Missing BUSCOs (M) (%) 1,706 (54.5%) 1,200 (38.3%) 1,035 (33%) 982 (31.4%)
Predicted Protein BUSCO Analysis (Eukaryota_ odb10 - 255 genes) C (%) 160 (62.8%) 199 (78%) 221 (86.6%) 224 (87.8%)
S (%) 156 (61.2%) 176 (69%) 174 (68.2%) 200 (78.4%)
D (%) 4 (1.6%) 23 (9%) 47 (18.4%) 24 (9.4%)
F (%) 52 (20.4%) 20 (7.8%) 13 (5.1%) 15 (5.9%)
M (%) 43 (16.8%) 36 (14.2%) 21 (8.3%) 16 (6.3%)
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