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

Journal of Nematology
Volume 56 (2024): Issue 1 (March 2024)
By:
Open Access
|Aug 2024

Figures & Tables

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 analysisParameterH. carotae (PRJNA774818)xH. glycines (PRJNA381081)xH. humuli (PRJNA1048471)xH. schachtii (PRJNA767548)x
Genome statisticsTotal Number of bp95,115,141157,978,45290,806,450190,153,211
Number of Contigs17,83591,487705
Largest contig113,42523,985,585568,7464,323,191
Contigs ≥ 250006999871609
Contigs ≥ 500001039559531
Average GC%39.3936.6636.1132.36
Contig N5013,93517,907,690111,383500,954
Contig L501,836423186
Number of N’s per 100 kbp01,062.0102,253.83
Predicted number coding genes17,03722,46515,42829,851
Predicted number of transcripts17,32229,93316,84831,564
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%)
DOI: https://doi.org/10.2478/jofnem-2024-0029 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X
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Language: English
Submitted on: Apr 5, 2024
Published on: Aug 28, 2024
Published by: Society of Nematologists, Inc.
In partnership with: Paradigm Publishing Services
Publication frequency: 1 times per year
Keywords:
cyst nematodes,
hop,
long reads,
ultra-low DNA input
Related subjects:
Life sciences,
Life sciences, other

© 2024 Lester A. Núñez-Rodríguez, Catherine L. Wram, Cedar Hesse, Inga A. Zasada, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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